Diff of the two buildlogs:

--
--- b1/build.log	2024-12-12 05:56:36.062652047 +0000
+++ b2/build.log	2024-12-12 06:01:30.689229997 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Wed Dec 11 17:52:20 -12 2024
-I: pbuilder-time-stamp: 1733982740
+I: Current time: Thu Jan 15 02:19:38 +14 2026
+I: pbuilder-time-stamp: 1768393178
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
 I: copying local configuration
@@ -30,51 +30,83 @@
 dpkg-source: info: applying fix_BIN_OFFSETS_MAX
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/2387886/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/1512487/tmp/hooks/D01_modify_environment starting
+debug: Running on infom02-amd64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Jan 14 12:19 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/1512487/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/1512487/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build/reproducible-path'
-  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
-  BUILDUSERNAME='pbuilder1'
-  BUILD_ARCH='amd64'
-  DEBIAN_FRONTEND='noninteractive'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+  BASH_VERSION='5.2.37(1)-release'
+  BUILDDIR=/build/reproducible-path
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=amd64
+  DEBIAN_FRONTEND=noninteractive
   DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
-  DISTRIBUTION='unstable'
-  HOME='/root'
-  HOST_ARCH='amd64'
+  DIRSTACK=()
+  DISTRIBUTION=unstable
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=x86_64
+  HOST_ARCH=amd64
   IFS=' 	
   '
-  INVOCATION_ID='a606c0cb371a47f29820420797580a6a'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  MAIL='/var/mail/root'
-  OPTIND='1'
-  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
-  PBCURRENTCOMMANDLINEOPERATION='build'
-  PBUILDER_OPERATION='build'
-  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
-  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
-  PBUILDER_SYSCONFDIR='/etc'
-  PPID='2387886'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=a7405294c9b54059a880fac591eed493
+  LANG=C
+  LANGUAGE=et_EE:et
+  LC_ALL=C
+  MACHTYPE=x86_64-pc-linux-gnu
+  MAIL=/var/mail/root
+  OPTERR=1
+  OPTIND=1
+  OSTYPE=linux-gnu
+  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+  PBCURRENTCOMMANDLINEOPERATION=build
+  PBUILDER_OPERATION=build
+  PBUILDER_PKGDATADIR=/usr/share/pbuilder
+  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+  PBUILDER_SYSCONFDIR=/etc
+  PIPESTATUS=([0]="0")
+  POSIXLY_CORRECT=y
+  PPID=1512487
   PS4='+ '
-  PWD='/'
-  SHELL='/bin/bash'
-  SHLVL='2'
-  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ER4fc84a/pbuilderrc_fDKX --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ER4fc84a/b1 --logfile b1/build.log python-bx_0.13.0-1.dsc'
-  SUDO_GID='109'
-  SUDO_UID='104'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
+  PWD=/
+  SHELL=/bin/bash
+  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+  SHLVL=3
+  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ER4fc84a/pbuilderrc_CuU2 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ER4fc84a/b2 --logfile b2/build.log python-bx_0.13.0-1.dsc'
+  SUDO_GID=109
+  SUDO_UID=104
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
 I: uname -a
-  Linux infom01-amd64 6.1.0-28-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/2387886/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Nov 22  2024 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/1512487/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -233,7 +265,7 @@
 Get: 100 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB]
 Get: 101 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.4-1 [250 kB]
 Get: 102 http://deb.debian.org/debian unstable/main amd64 python3-pytest-cython all 0.3.1-1 [8032 B]
-Fetched 63.1 MB in 2s (26.4 MB/s)
+Fetched 63.1 MB in 2s (29.5 MB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 Selecting previously unselected package libpython3.12-minimal:amd64.
 (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19965 files and directories currently installed.)
@@ -574,8 +606,8 @@
 Setting up tzdata (2024b-4) ...
 
 Current default time zone: 'Etc/UTC'
-Local time is now:      Thu Dec 12 05:53:27 UTC 2024.
-Universal Time is now:  Thu Dec 12 05:53:27 UTC 2024.
+Local time is now:      Wed Jan 14 12:20:59 UTC 2026.
+Universal Time is now:  Wed Jan 14 12:20:59 UTC 2026.
 Run 'dpkg-reconfigure tzdata' if you wish to change it.
 
 Setting up libpython3.13-minimal:amd64 (3.13.1-1) ...
@@ -672,7 +704,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/python-bx-0.13.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../python-bx_0.13.0-1_source.changes
+I: user script /srv/workspace/pbuilder/1512487/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/1512487/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/python-bx-0.13.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../python-bx_0.13.0-1_source.changes
 dpkg-buildpackage: info: source package python-bx
 dpkg-buildpackage: info: source version 0.13.0-1
 dpkg-buildpackage: info: source distribution unstable
@@ -704,135 +740,135 @@
 running build_py
 creating build/lib.linux-x86_64-cpython-313/bx_extras
 copying lib/bx_extras/fpconst_tests.py -> build/lib.linux-x86_64-cpython-313/bx_extras
+copying lib/bx_extras/stats.py -> build/lib.linux-x86_64-cpython-313/bx_extras
+copying lib/bx_extras/__init__.py -> build/lib.linux-x86_64-cpython-313/bx_extras
 copying lib/bx_extras/pstat.py -> build/lib.linux-x86_64-cpython-313/bx_extras
 copying lib/bx_extras/fpconst.py -> build/lib.linux-x86_64-cpython-313/bx_extras
 copying lib/bx_extras/lrucache.py -> build/lib.linux-x86_64-cpython-313/bx_extras
-copying lib/bx_extras/__init__.py -> build/lib.linux-x86_64-cpython-313/bx_extras
-copying lib/bx_extras/stats.py -> build/lib.linux-x86_64-cpython-313/bx_extras
 creating build/lib.linux-x86_64-cpython-313/bx
-copying lib/bx/wiggle_tests.py -> build/lib.linux-x86_64-cpython-313/bx
+copying lib/bx/bitset_utils.py -> build/lib.linux-x86_64-cpython-313/bx
 copying lib/bx/filter.py -> build/lib.linux-x86_64-cpython-313/bx
-copying lib/bx/seqmapping_tests.py -> build/lib.linux-x86_64-cpython-313/bx
-copying lib/bx/interval_index_file.py -> build/lib.linux-x86_64-cpython-313/bx
+copying lib/bx/wiggle_tests.py -> build/lib.linux-x86_64-cpython-313/bx
 copying lib/bx/bitset_tests.py -> build/lib.linux-x86_64-cpython-313/bx
 copying lib/bx/wiggle.py -> build/lib.linux-x86_64-cpython-313/bx
+copying lib/bx/bitset_builders.py -> build/lib.linux-x86_64-cpython-313/bx
+copying lib/bx/seqmapping_tests.py -> build/lib.linux-x86_64-cpython-313/bx
+copying lib/bx/interval_index_file.py -> build/lib.linux-x86_64-cpython-313/bx
+copying lib/bx/__init__.py -> build/lib.linux-x86_64-cpython-313/bx
 copying lib/bx/interval_index_file_tests.py -> build/lib.linux-x86_64-cpython-313/bx
-copying lib/bx/seqmapping.py -> build/lib.linux-x86_64-cpython-313/bx
-copying lib/bx/binned_array_tests.py -> build/lib.linux-x86_64-cpython-313/bx
-copying lib/bx/gene_reader.py -> build/lib.linux-x86_64-cpython-313/bx
 copying lib/bx/binned_array.py -> build/lib.linux-x86_64-cpython-313/bx
-copying lib/bx/bitset_utils.py -> build/lib.linux-x86_64-cpython-313/bx
-copying lib/bx/__init__.py -> build/lib.linux-x86_64-cpython-313/bx
-copying lib/bx/bitset_builders.py -> build/lib.linux-x86_64-cpython-313/bx
+copying lib/bx/gene_reader.py -> build/lib.linux-x86_64-cpython-313/bx
+copying lib/bx/binned_array_tests.py -> build/lib.linux-x86_64-cpython-313/bx
+copying lib/bx/seqmapping.py -> build/lib.linux-x86_64-cpython-313/bx
 creating build/lib.linux-x86_64-cpython-313/bx/tabular
-copying lib/bx/tabular/io.py -> build/lib.linux-x86_64-cpython-313/bx/tabular
 copying lib/bx/tabular/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/tabular
-creating build/lib.linux-x86_64-cpython-313/bx/arrays
-copying lib/bx/arrays/array_tree_tests.py -> build/lib.linux-x86_64-cpython-313/bx/arrays
-copying lib/bx/arrays/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/arrays
-creating build/lib.linux-x86_64-cpython-313/bx/intseq
-copying lib/bx/intseq/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/intseq
-creating build/lib.linux-x86_64-cpython-313/bx/pwm
-copying lib/bx/pwm/pwm_score_positions.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
-copying lib/bx/pwm/position_weight_matrix.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
-copying lib/bx/pwm/pwm_score_maf.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
-copying lib/bx/pwm/bed_score_aligned_string.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
-copying lib/bx/pwm/bed_score_aligned_pwm.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
-copying lib/bx/pwm/pwm_tests.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
-copying lib/bx/pwm/pwm_score_motifs.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
-copying lib/bx/pwm/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
-copying lib/bx/pwm/maf_select_motifs.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
+copying lib/bx/tabular/io.py -> build/lib.linux-x86_64-cpython-313/bx/tabular
+creating build/lib.linux-x86_64-cpython-313/bx/cookbook
+copying lib/bx/cookbook/doc_optparse.py -> build/lib.linux-x86_64-cpython-313/bx/cookbook
+copying lib/bx/cookbook/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/cookbook
+copying lib/bx/cookbook/attribute.py -> build/lib.linux-x86_64-cpython-313/bx/cookbook
+creating build/lib.linux-x86_64-cpython-313/bx/motif
+copying lib/bx/motif/pwm_tests.py -> build/lib.linux-x86_64-cpython-313/bx/motif
+copying lib/bx/motif/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/motif
+copying lib/bx/motif/pwm.py -> build/lib.linux-x86_64-cpython-313/bx/motif
 creating build/lib.linux-x86_64-cpython-313/bx/intervals
+copying lib/bx/intervals/cluster_tests.py -> build/lib.linux-x86_64-cpython-313/bx/intervals
 copying lib/bx/intervals/intersection_tests.py -> build/lib.linux-x86_64-cpython-313/bx/intervals
 copying lib/bx/intervals/random_intervals.py -> build/lib.linux-x86_64-cpython-313/bx/intervals
-copying lib/bx/intervals/cluster_tests.py -> build/lib.linux-x86_64-cpython-313/bx/intervals
-copying lib/bx/intervals/io.py -> build/lib.linux-x86_64-cpython-313/bx/intervals
 copying lib/bx/intervals/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/intervals
-creating build/lib.linux-x86_64-cpython-313/bx/bbi
-copying lib/bx/bbi/bigwig_tests.py -> build/lib.linux-x86_64-cpython-313/bx/bbi
-copying lib/bx/bbi/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/bbi
-creating build/lib.linux-x86_64-cpython-313/bx/misc
-copying lib/bx/misc/seeklzop.py -> build/lib.linux-x86_64-cpython-313/bx/misc
-copying lib/bx/misc/seekbzip2_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc
-copying lib/bx/misc/filecache.py -> build/lib.linux-x86_64-cpython-313/bx/misc
-copying lib/bx/misc/filecache_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc
-copying lib/bx/misc/cdb_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc
-copying lib/bx/misc/cdb.py -> build/lib.linux-x86_64-cpython-313/bx/misc
-copying lib/bx/misc/seeklzop_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc
-copying lib/bx/misc/readlengths.py -> build/lib.linux-x86_64-cpython-313/bx/misc
-copying lib/bx/misc/bgzf_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc
-copying lib/bx/misc/seekbzip2.py -> build/lib.linux-x86_64-cpython-313/bx/misc
-copying lib/bx/misc/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/misc
-copying lib/bx/misc/binary_file.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/intervals/io.py -> build/lib.linux-x86_64-cpython-313/bx/intervals
+creating build/lib.linux-x86_64-cpython-313/bx/pwm
+copying lib/bx/pwm/pwm_score_motifs.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
+copying lib/bx/pwm/pwm_tests.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
+copying lib/bx/pwm/pwm_score_positions.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
+copying lib/bx/pwm/maf_select_motifs.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
+copying lib/bx/pwm/bed_score_aligned_string.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
+copying lib/bx/pwm/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
+copying lib/bx/pwm/pwm_score_maf.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
+copying lib/bx/pwm/position_weight_matrix.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
+copying lib/bx/pwm/bed_score_aligned_pwm.py -> build/lib.linux-x86_64-cpython-313/bx/pwm
 creating build/lib.linux-x86_64-cpython-313/bx/phylo
-copying lib/bx/phylo/newick_tests.py -> build/lib.linux-x86_64-cpython-313/bx/phylo
-copying lib/bx/phylo/newick.py -> build/lib.linux-x86_64-cpython-313/bx/phylo
+copying lib/bx/phylo/phast.py -> build/lib.linux-x86_64-cpython-313/bx/phylo
 copying lib/bx/phylo/phast_tests.py -> build/lib.linux-x86_64-cpython-313/bx/phylo
+copying lib/bx/phylo/newick.py -> build/lib.linux-x86_64-cpython-313/bx/phylo
+copying lib/bx/phylo/newick_tests.py -> build/lib.linux-x86_64-cpython-313/bx/phylo
 copying lib/bx/phylo/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/phylo
-copying lib/bx/phylo/phast.py -> build/lib.linux-x86_64-cpython-313/bx/phylo
-creating build/lib.linux-x86_64-cpython-313/bx/cookbook
-copying lib/bx/cookbook/attribute.py -> build/lib.linux-x86_64-cpython-313/bx/cookbook
-copying lib/bx/cookbook/doc_optparse.py -> build/lib.linux-x86_64-cpython-313/bx/cookbook
-copying lib/bx/cookbook/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/cookbook
+creating build/lib.linux-x86_64-cpython-313/bx/intseq
+copying lib/bx/intseq/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/intseq
 creating build/lib.linux-x86_64-cpython-313/bx/seq
-copying lib/bx/seq/seq.py -> build/lib.linux-x86_64-cpython-313/bx/seq
+copying lib/bx/seq/nib_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq
 copying lib/bx/seq/qdna_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq
-copying lib/bx/seq/seq_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq
 copying lib/bx/seq/nib.py -> build/lib.linux-x86_64-cpython-313/bx/seq
-copying lib/bx/seq/fasta.py -> build/lib.linux-x86_64-cpython-313/bx/seq
-copying lib/bx/seq/fasta_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq
-copying lib/bx/seq/twobit.py -> build/lib.linux-x86_64-cpython-313/bx/seq
 copying lib/bx/seq/core.py -> build/lib.linux-x86_64-cpython-313/bx/seq
-copying lib/bx/seq/nib_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq
-copying lib/bx/seq/twobit_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq
-copying lib/bx/seq/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/seq
+copying lib/bx/seq/seq_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq
 copying lib/bx/seq/qdna.py -> build/lib.linux-x86_64-cpython-313/bx/seq
-creating build/lib.linux-x86_64-cpython-313/bx/motif
-copying lib/bx/motif/pwm_tests.py -> build/lib.linux-x86_64-cpython-313/bx/motif
-copying lib/bx/motif/pwm.py -> build/lib.linux-x86_64-cpython-313/bx/motif
-copying lib/bx/motif/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/motif
+copying lib/bx/seq/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/seq
+copying lib/bx/seq/fasta_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq
+copying lib/bx/seq/twobit_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq
+copying lib/bx/seq/twobit.py -> build/lib.linux-x86_64-cpython-313/bx/seq
+copying lib/bx/seq/seq.py -> build/lib.linux-x86_64-cpython-313/bx/seq
+copying lib/bx/seq/fasta.py -> build/lib.linux-x86_64-cpython-313/bx/seq
+creating build/lib.linux-x86_64-cpython-313/bx/bbi
+copying lib/bx/bbi/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/bbi
+copying lib/bx/bbi/bigwig_tests.py -> build/lib.linux-x86_64-cpython-313/bx/bbi
 creating build/lib.linux-x86_64-cpython-313/bx/align
-copying lib/bx/align/score_tests.py -> build/lib.linux-x86_64-cpython-313/bx/align
-copying lib/bx/align/epo.py -> build/lib.linux-x86_64-cpython-313/bx/align
 copying lib/bx/align/lav_tests.py -> build/lib.linux-x86_64-cpython-313/bx/align
-copying lib/bx/align/axt.py -> build/lib.linux-x86_64-cpython-313/bx/align
-copying lib/bx/align/score.py -> build/lib.linux-x86_64-cpython-313/bx/align
+copying lib/bx/align/lav.py -> build/lib.linux-x86_64-cpython-313/bx/align
+copying lib/bx/align/epo.py -> build/lib.linux-x86_64-cpython-313/bx/align
 copying lib/bx/align/core.py -> build/lib.linux-x86_64-cpython-313/bx/align
+copying lib/bx/align/score.py -> build/lib.linux-x86_64-cpython-313/bx/align
+copying lib/bx/align/maf.py -> build/lib.linux-x86_64-cpython-313/bx/align
 copying lib/bx/align/maf_tests.py -> build/lib.linux-x86_64-cpython-313/bx/align
 copying lib/bx/align/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/align
-copying lib/bx/align/lav.py -> build/lib.linux-x86_64-cpython-313/bx/align
+copying lib/bx/align/axt.py -> build/lib.linux-x86_64-cpython-313/bx/align
+copying lib/bx/align/score_tests.py -> build/lib.linux-x86_64-cpython-313/bx/align
 copying lib/bx/align/epo_tests.py -> build/lib.linux-x86_64-cpython-313/bx/align
-copying lib/bx/align/maf.py -> build/lib.linux-x86_64-cpython-313/bx/align
+creating build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/misc/cdb_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/misc/seekbzip2_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/misc/cdb.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/misc/seeklzop_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/misc/bgzf_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/misc/filecache.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/misc/binary_file.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/misc/seekbzip2.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/misc/filecache_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/misc/readlengths.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/misc/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+copying lib/bx/misc/seeklzop.py -> build/lib.linux-x86_64-cpython-313/bx/misc
+creating build/lib.linux-x86_64-cpython-313/bx/arrays
+copying lib/bx/arrays/array_tree_tests.py -> build/lib.linux-x86_64-cpython-313/bx/arrays
+copying lib/bx/arrays/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/arrays
+creating build/lib.linux-x86_64-cpython-313/bx/motif/logo
+copying lib/bx/motif/logo/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/motif/logo
+creating build/lib.linux-x86_64-cpython-313/bx/motif/io
+copying lib/bx/motif/io/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/motif/io
+copying lib/bx/motif/io/transfac.py -> build/lib.linux-x86_64-cpython-313/bx/motif/io
+copying lib/bx/motif/io/transfac_tests.py -> build/lib.linux-x86_64-cpython-313/bx/motif/io
 creating build/lib.linux-x86_64-cpython-313/bx/intervals/operations
 copying lib/bx/intervals/operations/base_coverage.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
-copying lib/bx/intervals/operations/intersect.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
-copying lib/bx/intervals/operations/join.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
 copying lib/bx/intervals/operations/complement.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
-copying lib/bx/intervals/operations/coverage.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
 copying lib/bx/intervals/operations/find_clusters.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
-copying lib/bx/intervals/operations/quicksect.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
-copying lib/bx/intervals/operations/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
+copying lib/bx/intervals/operations/concat.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
+copying lib/bx/intervals/operations/intersect.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
 copying lib/bx/intervals/operations/subtract.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
 copying lib/bx/intervals/operations/merge.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
-copying lib/bx/intervals/operations/concat.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
-creating build/lib.linux-x86_64-cpython-313/bx/motif/io
-copying lib/bx/motif/io/transfac.py -> build/lib.linux-x86_64-cpython-313/bx/motif/io
-copying lib/bx/motif/io/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/motif/io
-copying lib/bx/motif/io/transfac_tests.py -> build/lib.linux-x86_64-cpython-313/bx/motif/io
-creating build/lib.linux-x86_64-cpython-313/bx/motif/logo
-copying lib/bx/motif/logo/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/motif/logo
-creating build/lib.linux-x86_64-cpython-313/bx/align/sitemask
-copying lib/bx/align/sitemask/cpg.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask
-copying lib/bx/align/sitemask/core.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask
-copying lib/bx/align/sitemask/quality.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask
-copying lib/bx/align/sitemask/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask
-copying lib/bx/align/sitemask/sitemask_tests.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask
+copying lib/bx/intervals/operations/coverage.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
+copying lib/bx/intervals/operations/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
+copying lib/bx/intervals/operations/quicksect.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
+copying lib/bx/intervals/operations/join.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations
 creating build/lib.linux-x86_64-cpython-313/bx/align/tools
-copying lib/bx/align/tools/tile.py -> build/lib.linux-x86_64-cpython-313/bx/align/tools
 copying lib/bx/align/tools/fuse.py -> build/lib.linux-x86_64-cpython-313/bx/align/tools
 copying lib/bx/align/tools/thread.py -> build/lib.linux-x86_64-cpython-313/bx/align/tools
 copying lib/bx/align/tools/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/align/tools
 copying lib/bx/align/tools/chop.py -> build/lib.linux-x86_64-cpython-313/bx/align/tools
+copying lib/bx/align/tools/tile.py -> build/lib.linux-x86_64-cpython-313/bx/align/tools
+creating build/lib.linux-x86_64-cpython-313/bx/align/sitemask
+copying lib/bx/align/sitemask/sitemask_tests.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask
+copying lib/bx/align/sitemask/quality.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask
+copying lib/bx/align/sitemask/core.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask
+copying lib/bx/align/sitemask/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask
+copying lib/bx/align/sitemask/cpg.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask
 copying lib/bx/motif/logo/template.ps -> build/lib.linux-x86_64-cpython-313/bx/motif/logo
 running build_ext
 /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/python-bx-0.13.0/lib/bx/bitset.pyx
@@ -1148,352 +1184,352 @@
 x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/lib/bx/misc/_seekbzip2.o build/temp.linux-x86_64-cpython-313/src/bunzip/micro-bunzip.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/misc/_seekbzip2.cpython-313-x86_64-linux-gnu.so
 running build_scripts
 creating build/scripts-3.13
-copying and adjusting scripts/maf_extract_ranges_indexed.py -> build/scripts-3.13
-copying and adjusting scripts/maf_drop_overlapping.py -> build/scripts-3.13
-copying and adjusting scripts/maf_col_counts_all.py -> build/scripts-3.13
-copying and adjusting scripts/maf_truncate.py -> build/scripts-3.13
-copying and adjusting scripts/lav_to_maf.py -> build/scripts-3.13
-copying and adjusting scripts/interval_count_intersections.py -> build/scripts-3.13
-copying and adjusting scripts/maf_to_axt.py -> build/scripts-3.13
-copying and adjusting scripts/maf_limit_to_species.py -> build/scripts-3.13
-copying and adjusting scripts/bed_coverage_by_interval.py -> build/scripts-3.13
-copying and adjusting scripts/maf_to_concat_fasta.py -> build/scripts-3.13
+copying and adjusting scripts/wiggle_to_binned_array.py -> build/scripts-3.13
+copying and adjusting scripts/maf_thread_for_species.py -> build/scripts-3.13
+copying and adjusting scripts/lzop_build_offset_table.py -> build/scripts-3.13
+copying and adjusting scripts/axt_to_fasta.py -> build/scripts-3.13
+copying and adjusting scripts/maf_split_by_src.py -> build/scripts-3.13
+copying and adjusting scripts/find_in_sorted_file.py -> build/scripts-3.13
+copying and adjusting scripts/pretty_table.py -> build/scripts-3.13
+copying and adjusting scripts/aggregate_scores_in_intervals.py -> build/scripts-3.13
+copying and adjusting scripts/gene_fourfold_sites.py -> build/scripts-3.13
+copying and adjusting scripts/maf_filter_max_wc.py -> build/scripts-3.13
+copying and adjusting scripts/bed_rand_intersect.py -> build/scripts-3.13
+copying and adjusting scripts/nib_length.py -> build/scripts-3.13
+copying and adjusting scripts/maf_chunk.py -> build/scripts-3.13
+copying and adjusting scripts/bed_bigwig_profile.py -> build/scripts-3.13
+copying and adjusting scripts/bed_coverage.py -> build/scripts-3.13
+copying and adjusting scripts/maf_print_scores.py -> build/scripts-3.13
+copying and adjusting scripts/maf_div_sites.py -> build/scripts-3.13
+copying and adjusting scripts/maf_to_fasta.py -> build/scripts-3.13
+copying and adjusting scripts/bed_subtract_basewise.py -> build/scripts-3.13
 copying and adjusting scripts/bed_count_by_interval.py -> build/scripts-3.13
-copying and adjusting scripts/maf_to_int_seqs.py -> build/scripts-3.13
+copying and adjusting scripts/maf_gap_frequency.py -> build/scripts-3.13
+copying and adjusting scripts/axt_to_maf.py -> build/scripts-3.13
+copying and adjusting scripts/div_snp_table_chr.py -> build/scripts-3.13
+copying and adjusting scripts/mMK_bitset.py -> build/scripts-3.13
+copying and adjusting scripts/maf_word_frequency.py -> build/scripts-3.13
+copying and adjusting scripts/random_lines.py -> build/scripts-3.13
+copying and adjusting scripts/bed_count_overlapping.py -> build/scripts-3.13
+copying and adjusting scripts/maf_to_concat_fasta.py -> build/scripts-3.13
+copying and adjusting scripts/get_scores_in_intervals.py -> build/scripts-3.13
 copying and adjusting scripts/maf_shuffle_columns.py -> build/scripts-3.13
-copying and adjusting scripts/maf_covered_ranges.py -> build/scripts-3.13
-copying and adjusting scripts/maf_filter.py -> build/scripts-3.13
+copying and adjusting scripts/maf_limit_to_species.py -> build/scripts-3.13
+copying and adjusting scripts/qv_to_bqv.py -> build/scripts-3.13
 copying and adjusting scripts/bed_merge_overlapping.py -> build/scripts-3.13
-copying and adjusting scripts/table_filter.py -> build/scripts-3.13
+copying and adjusting scripts/interval_count_intersections.py -> build/scripts-3.13
+copying and adjusting scripts/maf_col_counts_all.py -> build/scripts-3.13
+copying and adjusting scripts/bed_intersect.py -> build/scripts-3.13
+copying and adjusting scripts/prefix_lines.py -> build/scripts-3.13
+copying and adjusting scripts/maf_col_counts.py -> build/scripts-3.13
+copying and adjusting scripts/bed_diff_basewise_summary.py -> build/scripts-3.13
+copying and adjusting scripts/ucsc_gene_table_to_intervals.py -> build/scripts-3.13
+copying and adjusting scripts/maf_count.py -> build/scripts-3.13
+copying and adjusting scripts/maf_extract_chrom_ranges.py -> build/scripts-3.13
+copying and adjusting scripts/bed_coverage_by_interval.py -> build/scripts-3.13
 copying and adjusting scripts/axt_extract_ranges.py -> build/scripts-3.13
-copying and adjusting scripts/maf_tile_2bit.py -> build/scripts-3.13
-copying and adjusting scripts/gene_fourfold_sites.py -> build/scripts-3.13
-copying and adjusting scripts/maf_chop.py -> build/scripts-3.13
-copying and adjusting scripts/qv_to_bqv.py -> build/scripts-3.13
+copying and adjusting scripts/maf_extract_ranges.py -> build/scripts-3.13
+copying and adjusting scripts/bed_complement.py -> build/scripts-3.13
+copying and adjusting scripts/maf_drop_overlapping.py -> build/scripts-3.13
 copying and adjusting scripts/maf_percent_columns_matching.py -> build/scripts-3.13
-copying and adjusting scripts/maf_select.py -> build/scripts-3.13
-copying and adjusting scripts/div_snp_table_chr.py -> build/scripts-3.13
-copying and adjusting scripts/maf_split_by_src.py -> build/scripts-3.13
-copying and adjusting scripts/bed_extend_to.py -> build/scripts-3.13
-copying and adjusting scripts/maf_gc_content.py -> build/scripts-3.13
-copying and adjusting scripts/maf_extract_chrom_ranges.py -> build/scripts-3.13
-copying and adjusting scripts/maf_col_counts.py -> build/scripts-3.13
+copying and adjusting scripts/maf_to_int_seqs.py -> build/scripts-3.13
+copying and adjusting scripts/one_field_per_line.py -> build/scripts-3.13
+copying and adjusting scripts/align_print_template.py -> build/scripts-3.13
+copying and adjusting scripts/maf_species_in_all_files.py -> build/scripts-3.13
 copying and adjusting scripts/wiggle_to_array_tree.py -> build/scripts-3.13
-copying and adjusting scripts/aggregate_scores_in_intervals.py -> build/scripts-3.13
-copying and adjusting scripts/maf_word_frequency.py -> build/scripts-3.13
-copying and adjusting scripts/mMK_bitset.py -> build/scripts-3.13
-copying and adjusting scripts/mask_quality.py -> build/scripts-3.13
+copying and adjusting scripts/maf_gc_content.py -> build/scripts-3.13
 copying and adjusting scripts/bed_intersect_basewise.py -> build/scripts-3.13
-copying and adjusting scripts/maf_interval_alignibility.py -> build/scripts-3.13
-copying and adjusting scripts/maf_chunk.py -> build/scripts-3.13
-copying and adjusting scripts/align_print_template.py -> build/scripts-3.13
-copying and adjusting scripts/maf_covered_regions.py -> build/scripts-3.13
-copying and adjusting scripts/one_field_per_line.py -> build/scripts-3.13
-copying and adjusting scripts/nib_length.py -> build/scripts-3.13
-copying and adjusting scripts/line_select.py -> build/scripts-3.13
-copying and adjusting scripts/maf_region_coverage_by_src.py -> build/scripts-3.13
-copying and adjusting scripts/bed_bigwig_profile.py -> build/scripts-3.13
-copying and adjusting scripts/maf_mapping_word_frequency.py -> build/scripts-3.13
+copying and adjusting scripts/maf_chop.py -> build/scripts-3.13
+copying and adjusting scripts/out_to_chain.py -> build/scripts-3.13
+copying and adjusting scripts/maf_mask_cpg.py -> build/scripts-3.13
 copying and adjusting scripts/maf_print_chroms.py -> build/scripts-3.13
-copying and adjusting scripts/maf_tile.py -> build/scripts-3.13
-copying and adjusting scripts/bed_diff_basewise_summary.py -> build/scripts-3.13
-copying and adjusting scripts/maf_extract_ranges.py -> build/scripts-3.13
-copying and adjusting scripts/maf_print_scores.py -> build/scripts-3.13
-copying and adjusting scripts/int_seqs_to_char_strings.py -> build/scripts-3.13
-copying and adjusting scripts/bed_rand_intersect.py -> build/scripts-3.13
-copying and adjusting scripts/tfloc_summary.py -> build/scripts-3.13
-copying and adjusting scripts/maf_percent_identity.py -> build/scripts-3.13
-copying and adjusting scripts/bed_subtract_basewise.py -> build/scripts-3.13
+copying and adjusting scripts/table_filter.py -> build/scripts-3.13
+copying and adjusting scripts/maf_filter.py -> build/scripts-3.13
+copying and adjusting scripts/maf_region_coverage_by_src.py -> build/scripts-3.13
+copying and adjusting scripts/maf_extract_ranges_indexed.py -> build/scripts-3.13
 copying and adjusting scripts/bed_build_windows.py -> build/scripts-3.13
-copying and adjusting scripts/axt_to_fasta.py -> build/scripts-3.13
-copying and adjusting scripts/maf_mask_cpg.py -> build/scripts-3.13
-copying and adjusting scripts/pretty_table.py -> build/scripts-3.13
-copying and adjusting scripts/maf_to_fasta.py -> build/scripts-3.13
-copying and adjusting scripts/maf_randomize.py -> build/scripts-3.13
-copying and adjusting scripts/interval_join.py -> build/scripts-3.13
-copying and adjusting scripts/maf_filter_max_wc.py -> build/scripts-3.13
-copying and adjusting scripts/out_to_chain.py -> build/scripts-3.13
+copying and adjusting scripts/int_seqs_to_char_strings.py -> build/scripts-3.13
+copying and adjusting scripts/maf_truncate.py -> build/scripts-3.13
 copying and adjusting scripts/wiggle_to_simple.py -> build/scripts-3.13
-copying and adjusting scripts/lav_to_axt.py -> build/scripts-3.13
-copying and adjusting scripts/bed_complement.py -> build/scripts-3.13
-copying and adjusting scripts/wiggle_to_chr_binned_array.py -> build/scripts-3.13
+copying and adjusting scripts/interval_join.py -> build/scripts-3.13
 copying and adjusting scripts/table_add_column.py -> build/scripts-3.13
-copying and adjusting scripts/axt_to_maf.py -> build/scripts-3.13
-copying and adjusting scripts/bed_count_overlapping.py -> build/scripts-3.13
-copying and adjusting scripts/bnMapper.py -> build/scripts-3.13
-copying and adjusting scripts/maf_species_in_all_files.py -> build/scripts-3.13
-copying and adjusting scripts/nib_intervals_to_fasta.py -> build/scripts-3.13
-copying and adjusting scripts/wiggle_to_binned_array.py -> build/scripts-3.13
-copying and adjusting scripts/maf_count.py -> build/scripts-3.13
-copying and adjusting scripts/bed_coverage.py -> build/scripts-3.13
-copying and adjusting scripts/random_lines.py -> build/scripts-3.13
-copying and adjusting scripts/maf_gap_frequency.py -> build/scripts-3.13
-copying and adjusting scripts/get_scores_in_intervals.py -> build/scripts-3.13
+copying and adjusting scripts/line_select.py -> build/scripts-3.13
 copying and adjusting scripts/maf_mean_length_ungapped_piece.py -> build/scripts-3.13
+copying and adjusting scripts/maf_translate_chars.py -> build/scripts-3.13
+copying and adjusting scripts/maf_to_axt.py -> build/scripts-3.13
+copying and adjusting scripts/lav_to_maf.py -> build/scripts-3.13
+copying and adjusting scripts/maf_tile_2.py -> build/scripts-3.13
 copying and adjusting scripts/maf_build_index.py -> build/scripts-3.13
+copying and adjusting scripts/bnMapper.py -> build/scripts-3.13
+copying and adjusting scripts/maf_interval_alignibility.py -> build/scripts-3.13
+copying and adjusting scripts/nib_intervals_to_fasta.py -> build/scripts-3.13
+copying and adjusting scripts/tfloc_summary.py -> build/scripts-3.13
+copying and adjusting scripts/mask_quality.py -> build/scripts-3.13
+copying and adjusting scripts/maf_select.py -> build/scripts-3.13
+copying and adjusting scripts/maf_mapping_word_frequency.py -> build/scripts-3.13
+copying and adjusting scripts/maf_randomize.py -> build/scripts-3.13
 copying and adjusting scripts/axt_to_lav.py -> build/scripts-3.13
-copying and adjusting scripts/lzop_build_offset_table.py -> build/scripts-3.13
-copying and adjusting scripts/bed_intersect.py -> build/scripts-3.13
-copying and adjusting scripts/find_in_sorted_file.py -> build/scripts-3.13
-copying and adjusting scripts/ucsc_gene_table_to_intervals.py -> build/scripts-3.13
-copying and adjusting scripts/maf_tile_2.py -> build/scripts-3.13
-copying and adjusting scripts/maf_thread_for_species.py -> build/scripts-3.13
-copying and adjusting scripts/maf_translate_chars.py -> build/scripts-3.13
+copying and adjusting scripts/bed_extend_to.py -> build/scripts-3.13
+copying and adjusting scripts/maf_tile.py -> build/scripts-3.13
+copying and adjusting scripts/maf_tile_2bit.py -> build/scripts-3.13
+copying and adjusting scripts/maf_percent_identity.py -> build/scripts-3.13
+copying and adjusting scripts/lav_to_axt.py -> build/scripts-3.13
+copying and adjusting scripts/wiggle_to_chr_binned_array.py -> build/scripts-3.13
+copying and adjusting scripts/maf_covered_ranges.py -> build/scripts-3.13
 copying and adjusting scripts/nib_chrom_intervals_to_fasta.py -> build/scripts-3.13
-copying and adjusting scripts/prefix_lines.py -> build/scripts-3.13
-copying and adjusting scripts/maf_div_sites.py -> build/scripts-3.13
-changing mode of build/scripts-3.13/maf_extract_ranges_indexed.py from 644 to 755
-changing mode of build/scripts-3.13/maf_drop_overlapping.py from 644 to 755
-changing mode of build/scripts-3.13/maf_col_counts_all.py from 644 to 755
-changing mode of build/scripts-3.13/maf_truncate.py from 644 to 755
-changing mode of build/scripts-3.13/lav_to_maf.py from 644 to 755
-changing mode of build/scripts-3.13/interval_count_intersections.py from 644 to 755
-changing mode of build/scripts-3.13/maf_to_axt.py from 644 to 755
-changing mode of build/scripts-3.13/maf_limit_to_species.py from 644 to 755
-changing mode of build/scripts-3.13/bed_coverage_by_interval.py from 644 to 755
-changing mode of build/scripts-3.13/maf_to_concat_fasta.py from 644 to 755
+copying and adjusting scripts/maf_covered_regions.py -> build/scripts-3.13
+changing mode of build/scripts-3.13/wiggle_to_binned_array.py from 644 to 755
+changing mode of build/scripts-3.13/maf_thread_for_species.py from 644 to 755
+changing mode of build/scripts-3.13/lzop_build_offset_table.py from 644 to 755
+changing mode of build/scripts-3.13/axt_to_fasta.py from 644 to 755
+changing mode of build/scripts-3.13/maf_split_by_src.py from 644 to 755
+changing mode of build/scripts-3.13/find_in_sorted_file.py from 644 to 755
+changing mode of build/scripts-3.13/pretty_table.py from 644 to 755
+changing mode of build/scripts-3.13/aggregate_scores_in_intervals.py from 644 to 755
+changing mode of build/scripts-3.13/gene_fourfold_sites.py from 644 to 755
+changing mode of build/scripts-3.13/maf_filter_max_wc.py from 644 to 755
+changing mode of build/scripts-3.13/bed_rand_intersect.py from 644 to 755
+changing mode of build/scripts-3.13/nib_length.py from 644 to 755
+changing mode of build/scripts-3.13/maf_chunk.py from 644 to 755
+changing mode of build/scripts-3.13/bed_bigwig_profile.py from 644 to 755
+changing mode of build/scripts-3.13/bed_coverage.py from 644 to 755
+changing mode of build/scripts-3.13/maf_print_scores.py from 644 to 755
+changing mode of build/scripts-3.13/maf_div_sites.py from 644 to 755
+changing mode of build/scripts-3.13/maf_to_fasta.py from 644 to 755
+changing mode of build/scripts-3.13/bed_subtract_basewise.py from 644 to 755
 changing mode of build/scripts-3.13/bed_count_by_interval.py from 644 to 755
-changing mode of build/scripts-3.13/maf_to_int_seqs.py from 644 to 755
+changing mode of build/scripts-3.13/maf_gap_frequency.py from 644 to 755
+changing mode of build/scripts-3.13/axt_to_maf.py from 644 to 755
+changing mode of build/scripts-3.13/div_snp_table_chr.py from 644 to 755
+changing mode of build/scripts-3.13/mMK_bitset.py from 644 to 755
+changing mode of build/scripts-3.13/maf_word_frequency.py from 644 to 755
+changing mode of build/scripts-3.13/random_lines.py from 644 to 755
+changing mode of build/scripts-3.13/bed_count_overlapping.py from 644 to 755
+changing mode of build/scripts-3.13/maf_to_concat_fasta.py from 644 to 755
+changing mode of build/scripts-3.13/get_scores_in_intervals.py from 644 to 755
 changing mode of build/scripts-3.13/maf_shuffle_columns.py from 644 to 755
-changing mode of build/scripts-3.13/maf_covered_ranges.py from 644 to 755
-changing mode of build/scripts-3.13/maf_filter.py from 644 to 755
+changing mode of build/scripts-3.13/maf_limit_to_species.py from 644 to 755
+changing mode of build/scripts-3.13/qv_to_bqv.py from 644 to 755
 changing mode of build/scripts-3.13/bed_merge_overlapping.py from 644 to 755
-changing mode of build/scripts-3.13/table_filter.py from 644 to 755
+changing mode of build/scripts-3.13/interval_count_intersections.py from 644 to 755
+changing mode of build/scripts-3.13/maf_col_counts_all.py from 644 to 755
+changing mode of build/scripts-3.13/bed_intersect.py from 644 to 755
+changing mode of build/scripts-3.13/prefix_lines.py from 644 to 755
+changing mode of build/scripts-3.13/maf_col_counts.py from 644 to 755
+changing mode of build/scripts-3.13/bed_diff_basewise_summary.py from 644 to 755
+changing mode of build/scripts-3.13/ucsc_gene_table_to_intervals.py from 644 to 755
+changing mode of build/scripts-3.13/maf_count.py from 644 to 755
+changing mode of build/scripts-3.13/maf_extract_chrom_ranges.py from 644 to 755
+changing mode of build/scripts-3.13/bed_coverage_by_interval.py from 644 to 755
 changing mode of build/scripts-3.13/axt_extract_ranges.py from 644 to 755
-changing mode of build/scripts-3.13/maf_tile_2bit.py from 644 to 755
-changing mode of build/scripts-3.13/gene_fourfold_sites.py from 644 to 755
-changing mode of build/scripts-3.13/maf_chop.py from 644 to 755
-changing mode of build/scripts-3.13/qv_to_bqv.py from 644 to 755
+changing mode of build/scripts-3.13/maf_extract_ranges.py from 644 to 755
+changing mode of build/scripts-3.13/bed_complement.py from 644 to 755
+changing mode of build/scripts-3.13/maf_drop_overlapping.py from 644 to 755
 changing mode of build/scripts-3.13/maf_percent_columns_matching.py from 644 to 755
-changing mode of build/scripts-3.13/maf_select.py from 644 to 755
-changing mode of build/scripts-3.13/div_snp_table_chr.py from 644 to 755
-changing mode of build/scripts-3.13/maf_split_by_src.py from 644 to 755
-changing mode of build/scripts-3.13/bed_extend_to.py from 644 to 755
-changing mode of build/scripts-3.13/maf_gc_content.py from 644 to 755
-changing mode of build/scripts-3.13/maf_extract_chrom_ranges.py from 644 to 755
-changing mode of build/scripts-3.13/maf_col_counts.py from 644 to 755
+changing mode of build/scripts-3.13/maf_to_int_seqs.py from 644 to 755
+changing mode of build/scripts-3.13/one_field_per_line.py from 644 to 755
+changing mode of build/scripts-3.13/align_print_template.py from 644 to 755
+changing mode of build/scripts-3.13/maf_species_in_all_files.py from 644 to 755
 changing mode of build/scripts-3.13/wiggle_to_array_tree.py from 644 to 755
-changing mode of build/scripts-3.13/aggregate_scores_in_intervals.py from 644 to 755
-changing mode of build/scripts-3.13/maf_word_frequency.py from 644 to 755
-changing mode of build/scripts-3.13/mMK_bitset.py from 644 to 755
-changing mode of build/scripts-3.13/mask_quality.py from 644 to 755
+changing mode of build/scripts-3.13/maf_gc_content.py from 644 to 755
 changing mode of build/scripts-3.13/bed_intersect_basewise.py from 644 to 755
-changing mode of build/scripts-3.13/maf_interval_alignibility.py from 644 to 755
-changing mode of build/scripts-3.13/maf_chunk.py from 644 to 755
-changing mode of build/scripts-3.13/align_print_template.py from 644 to 755
-changing mode of build/scripts-3.13/maf_covered_regions.py from 644 to 755
-changing mode of build/scripts-3.13/one_field_per_line.py from 644 to 755
-changing mode of build/scripts-3.13/nib_length.py from 644 to 755
-changing mode of build/scripts-3.13/line_select.py from 644 to 755
-changing mode of build/scripts-3.13/maf_region_coverage_by_src.py from 644 to 755
-changing mode of build/scripts-3.13/bed_bigwig_profile.py from 644 to 755
-changing mode of build/scripts-3.13/maf_mapping_word_frequency.py from 644 to 755
+changing mode of build/scripts-3.13/maf_chop.py from 644 to 755
+changing mode of build/scripts-3.13/out_to_chain.py from 644 to 755
+changing mode of build/scripts-3.13/maf_mask_cpg.py from 644 to 755
 changing mode of build/scripts-3.13/maf_print_chroms.py from 644 to 755
-changing mode of build/scripts-3.13/maf_tile.py from 644 to 755
-changing mode of build/scripts-3.13/bed_diff_basewise_summary.py from 644 to 755
-changing mode of build/scripts-3.13/maf_extract_ranges.py from 644 to 755
-changing mode of build/scripts-3.13/maf_print_scores.py from 644 to 755
-changing mode of build/scripts-3.13/int_seqs_to_char_strings.py from 644 to 755
-changing mode of build/scripts-3.13/bed_rand_intersect.py from 644 to 755
-changing mode of build/scripts-3.13/tfloc_summary.py from 644 to 755
-changing mode of build/scripts-3.13/maf_percent_identity.py from 644 to 755
-changing mode of build/scripts-3.13/bed_subtract_basewise.py from 644 to 755
+changing mode of build/scripts-3.13/table_filter.py from 644 to 755
+changing mode of build/scripts-3.13/maf_filter.py from 644 to 755
+changing mode of build/scripts-3.13/maf_region_coverage_by_src.py from 644 to 755
+changing mode of build/scripts-3.13/maf_extract_ranges_indexed.py from 644 to 755
 changing mode of build/scripts-3.13/bed_build_windows.py from 644 to 755
-changing mode of build/scripts-3.13/axt_to_fasta.py from 644 to 755
-changing mode of build/scripts-3.13/maf_mask_cpg.py from 644 to 755
-changing mode of build/scripts-3.13/pretty_table.py from 644 to 755
-changing mode of build/scripts-3.13/maf_to_fasta.py from 644 to 755
-changing mode of build/scripts-3.13/maf_randomize.py from 644 to 755
-changing mode of build/scripts-3.13/interval_join.py from 644 to 755
-changing mode of build/scripts-3.13/maf_filter_max_wc.py from 644 to 755
-changing mode of build/scripts-3.13/out_to_chain.py from 644 to 755
+changing mode of build/scripts-3.13/int_seqs_to_char_strings.py from 644 to 755
+changing mode of build/scripts-3.13/maf_truncate.py from 644 to 755
 changing mode of build/scripts-3.13/wiggle_to_simple.py from 644 to 755
-changing mode of build/scripts-3.13/lav_to_axt.py from 644 to 755
-changing mode of build/scripts-3.13/bed_complement.py from 644 to 755
-changing mode of build/scripts-3.13/wiggle_to_chr_binned_array.py from 644 to 755
+changing mode of build/scripts-3.13/interval_join.py from 644 to 755
 changing mode of build/scripts-3.13/table_add_column.py from 644 to 755
-changing mode of build/scripts-3.13/axt_to_maf.py from 644 to 755
-changing mode of build/scripts-3.13/bed_count_overlapping.py from 644 to 755
-changing mode of build/scripts-3.13/bnMapper.py from 644 to 755
-changing mode of build/scripts-3.13/maf_species_in_all_files.py from 644 to 755
-changing mode of build/scripts-3.13/nib_intervals_to_fasta.py from 644 to 755
-changing mode of build/scripts-3.13/wiggle_to_binned_array.py from 644 to 755
-changing mode of build/scripts-3.13/maf_count.py from 644 to 755
-changing mode of build/scripts-3.13/bed_coverage.py from 644 to 755
-changing mode of build/scripts-3.13/random_lines.py from 644 to 755
-changing mode of build/scripts-3.13/maf_gap_frequency.py from 644 to 755
-changing mode of build/scripts-3.13/get_scores_in_intervals.py from 644 to 755
+changing mode of build/scripts-3.13/line_select.py from 644 to 755
 changing mode of build/scripts-3.13/maf_mean_length_ungapped_piece.py from 644 to 755
+changing mode of build/scripts-3.13/maf_translate_chars.py from 644 to 755
+changing mode of build/scripts-3.13/maf_to_axt.py from 644 to 755
+changing mode of build/scripts-3.13/lav_to_maf.py from 644 to 755
+changing mode of build/scripts-3.13/maf_tile_2.py from 644 to 755
 changing mode of build/scripts-3.13/maf_build_index.py from 644 to 755
+changing mode of build/scripts-3.13/bnMapper.py from 644 to 755
+changing mode of build/scripts-3.13/maf_interval_alignibility.py from 644 to 755
+changing mode of build/scripts-3.13/nib_intervals_to_fasta.py from 644 to 755
+changing mode of build/scripts-3.13/tfloc_summary.py from 644 to 755
+changing mode of build/scripts-3.13/mask_quality.py from 644 to 755
+changing mode of build/scripts-3.13/maf_select.py from 644 to 755
+changing mode of build/scripts-3.13/maf_mapping_word_frequency.py from 644 to 755
+changing mode of build/scripts-3.13/maf_randomize.py from 644 to 755
 changing mode of build/scripts-3.13/axt_to_lav.py from 644 to 755
-changing mode of build/scripts-3.13/lzop_build_offset_table.py from 644 to 755
-changing mode of build/scripts-3.13/bed_intersect.py from 644 to 755
-changing mode of build/scripts-3.13/find_in_sorted_file.py from 644 to 755
-changing mode of build/scripts-3.13/ucsc_gene_table_to_intervals.py from 644 to 755
-changing mode of build/scripts-3.13/maf_tile_2.py from 644 to 755
-changing mode of build/scripts-3.13/maf_thread_for_species.py from 644 to 755
-changing mode of build/scripts-3.13/maf_translate_chars.py from 644 to 755
+changing mode of build/scripts-3.13/bed_extend_to.py from 644 to 755
+changing mode of build/scripts-3.13/maf_tile.py from 644 to 755
+changing mode of build/scripts-3.13/maf_tile_2bit.py from 644 to 755
+changing mode of build/scripts-3.13/maf_percent_identity.py from 644 to 755
+changing mode of build/scripts-3.13/lav_to_axt.py from 644 to 755
+changing mode of build/scripts-3.13/wiggle_to_chr_binned_array.py from 644 to 755
+changing mode of build/scripts-3.13/maf_covered_ranges.py from 644 to 755
 changing mode of build/scripts-3.13/nib_chrom_intervals_to_fasta.py from 644 to 755
-changing mode of build/scripts-3.13/prefix_lines.py from 644 to 755
-changing mode of build/scripts-3.13/maf_div_sites.py from 644 to 755
+changing mode of build/scripts-3.13/maf_covered_regions.py from 644 to 755
 installing to build/bdist.linux-x86_64/wheel
 running install
 running install_lib
 creating build/bdist.linux-x86_64/wheel
 creating build/bdist.linux-x86_64/wheel/bx_extras
 copying build/lib.linux-x86_64-cpython-313/bx_extras/fpconst_tests.py -> build/bdist.linux-x86_64/wheel/./bx_extras
+copying build/lib.linux-x86_64-cpython-313/bx_extras/stats.py -> build/bdist.linux-x86_64/wheel/./bx_extras
+copying build/lib.linux-x86_64-cpython-313/bx_extras/__init__.py -> build/bdist.linux-x86_64/wheel/./bx_extras
 copying build/lib.linux-x86_64-cpython-313/bx_extras/pstat.py -> build/bdist.linux-x86_64/wheel/./bx_extras
 copying build/lib.linux-x86_64-cpython-313/bx_extras/fpconst.py -> build/bdist.linux-x86_64/wheel/./bx_extras
 copying build/lib.linux-x86_64-cpython-313/bx_extras/lrucache.py -> build/bdist.linux-x86_64/wheel/./bx_extras
-copying build/lib.linux-x86_64-cpython-313/bx_extras/__init__.py -> build/bdist.linux-x86_64/wheel/./bx_extras
-copying build/lib.linux-x86_64-cpython-313/bx_extras/stats.py -> build/bdist.linux-x86_64/wheel/./bx_extras
 creating build/bdist.linux-x86_64/wheel/bx
-copying build/lib.linux-x86_64-cpython-313/bx/wiggle_tests.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-313/bx/bitset_utils.py -> build/bdist.linux-x86_64/wheel/./bx
 copying build/lib.linux-x86_64-cpython-313/bx/filter.py -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-313/bx/seqmapping_tests.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-313/bx/wiggle_tests.py -> build/bdist.linux-x86_64/wheel/./bx
 creating build/bdist.linux-x86_64/wheel/bx/tabular
-copying build/lib.linux-x86_64-cpython-313/bx/tabular/io.py -> build/bdist.linux-x86_64/wheel/./bx/tabular
 copying build/lib.linux-x86_64-cpython-313/bx/tabular/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/tabular
-creating build/bdist.linux-x86_64/wheel/bx/arrays
-copying build/lib.linux-x86_64-cpython-313/bx/arrays/array_tree.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays
-copying build/lib.linux-x86_64-cpython-313/bx/arrays/bed.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays
-copying build/lib.linux-x86_64-cpython-313/bx/arrays/array_tree_tests.py -> build/bdist.linux-x86_64/wheel/./bx/arrays
-copying build/lib.linux-x86_64-cpython-313/bx/arrays/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/arrays
-copying build/lib.linux-x86_64-cpython-313/bx/arrays/wiggle.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays
-copying build/lib.linux-x86_64-cpython-313/bx/_seqmapping.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-313/bx/interval_index_file.py -> build/bdist.linux-x86_64/wheel/./bx
-creating build/bdist.linux-x86_64/wheel/bx/intseq
-copying build/lib.linux-x86_64-cpython-313/bx/intseq/ngramcount.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intseq
-copying build/lib.linux-x86_64-cpython-313/bx/intseq/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intseq
-creating build/bdist.linux-x86_64/wheel/bx/pwm
-copying build/lib.linux-x86_64-cpython-313/bx/pwm/pwm_score_positions.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-313/bx/pwm/position_weight_matrix.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-313/bx/pwm/pwm_score_maf.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-313/bx/pwm/bed_score_aligned_string.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-313/bx/pwm/bed_score_aligned_pwm.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-313/bx/pwm/_position_weight_matrix.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-313/bx/pwm/pwm_tests.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-313/bx/pwm/pwm_score_motifs.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-313/bx/pwm/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-313/bx/pwm/maf_select_motifs.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-313/bx/tabular/io.py -> build/bdist.linux-x86_64/wheel/./bx/tabular
+copying build/lib.linux-x86_64-cpython-313/bx/bitset.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx
+creating build/bdist.linux-x86_64/wheel/bx/cookbook
+copying build/lib.linux-x86_64-cpython-313/bx/cookbook/doc_optparse.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook
+copying build/lib.linux-x86_64-cpython-313/bx/cookbook/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook
+copying build/lib.linux-x86_64-cpython-313/bx/cookbook/attribute.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook
+creating build/bdist.linux-x86_64/wheel/bx/motif
+copying build/lib.linux-x86_64-cpython-313/bx/motif/pwm_tests.py -> build/bdist.linux-x86_64/wheel/./bx/motif
+creating build/bdist.linux-x86_64/wheel/bx/motif/logo
+copying build/lib.linux-x86_64-cpython-313/bx/motif/logo/template.ps -> build/bdist.linux-x86_64/wheel/./bx/motif/logo
+copying build/lib.linux-x86_64-cpython-313/bx/motif/logo/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif/logo
+creating build/bdist.linux-x86_64/wheel/bx/motif/io
+copying build/lib.linux-x86_64-cpython-313/bx/motif/io/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io
+copying build/lib.linux-x86_64-cpython-313/bx/motif/io/transfac.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io
+copying build/lib.linux-x86_64-cpython-313/bx/motif/io/transfac_tests.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io
+copying build/lib.linux-x86_64-cpython-313/bx/motif/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif
+copying build/lib.linux-x86_64-cpython-313/bx/motif/_pwm.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/motif
+copying build/lib.linux-x86_64-cpython-313/bx/motif/pwm.py -> build/bdist.linux-x86_64/wheel/./bx/motif
 creating build/bdist.linux-x86_64/wheel/bx/intervals
+copying build/lib.linux-x86_64-cpython-313/bx/intervals/cluster_tests.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
 copying build/lib.linux-x86_64-cpython-313/bx/intervals/intersection_tests.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
 copying build/lib.linux-x86_64-cpython-313/bx/intervals/random_intervals.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
-copying build/lib.linux-x86_64-cpython-313/bx/intervals/cluster_tests.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
 copying build/lib.linux-x86_64-cpython-313/bx/intervals/intersection.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intervals
-copying build/lib.linux-x86_64-cpython-313/bx/intervals/io.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
 copying build/lib.linux-x86_64-cpython-313/bx/intervals/cluster.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intervals
 copying build/lib.linux-x86_64-cpython-313/bx/intervals/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
+copying build/lib.linux-x86_64-cpython-313/bx/intervals/io.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
 creating build/bdist.linux-x86_64/wheel/bx/intervals/operations
 copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/base_coverage.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/intersect.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/join.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
 copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/complement.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/coverage.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
 copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/find_clusters.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/quicksect.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
+copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/concat.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
+copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/intersect.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
 copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/subtract.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
 copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/merge.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/concat.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
+copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/coverage.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
+copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
+copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/quicksect.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
+copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/join.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
 copying build/lib.linux-x86_64-cpython-313/bx/bitset_tests.py -> build/bdist.linux-x86_64/wheel/./bx
 copying build/lib.linux-x86_64-cpython-313/bx/wiggle.py -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-313/bx/interval_index_file_tests.py -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-313/bx/seqmapping.py -> build/bdist.linux-x86_64/wheel/./bx
-creating build/bdist.linux-x86_64/wheel/bx/bbi
-copying build/lib.linux-x86_64-cpython-313/bx/bbi/bigwig_tests.py -> build/bdist.linux-x86_64/wheel/./bx/bbi
-copying build/lib.linux-x86_64-cpython-313/bx/bbi/cirtree_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
-copying build/lib.linux-x86_64-cpython-313/bx/bbi/bbi_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
-copying build/lib.linux-x86_64-cpython-313/bx/bbi/bigwig_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
-copying build/lib.linux-x86_64-cpython-313/bx/bbi/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/bbi
-copying build/lib.linux-x86_64-cpython-313/bx/bbi/bigbed_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
-copying build/lib.linux-x86_64-cpython-313/bx/bbi/bpt_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
-creating build/bdist.linux-x86_64/wheel/bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/seeklzop.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/seekbzip2_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/filecache.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/filecache_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/cdb_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/cdb.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/seeklzop_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/_seekbzip2.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/readlengths.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/bgzf_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/seekbzip2.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/bgzf.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/misc/binary_file.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-313/bx/binned_array_tests.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-313/bx/bitset_builders.py -> build/bdist.linux-x86_64/wheel/./bx
+creating build/bdist.linux-x86_64/wheel/bx/pwm
+copying build/lib.linux-x86_64-cpython-313/bx/pwm/pwm_score_motifs.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-313/bx/pwm/pwm_tests.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-313/bx/pwm/pwm_score_positions.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-313/bx/pwm/maf_select_motifs.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-313/bx/pwm/_position_weight_matrix.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-313/bx/pwm/bed_score_aligned_string.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-313/bx/pwm/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-313/bx/pwm/pwm_score_maf.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-313/bx/pwm/position_weight_matrix.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-313/bx/pwm/bed_score_aligned_pwm.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
 creating build/bdist.linux-x86_64/wheel/bx/phylo
-copying build/lib.linux-x86_64-cpython-313/bx/phylo/newick_tests.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
-copying build/lib.linux-x86_64-cpython-313/bx/phylo/newick.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
+copying build/lib.linux-x86_64-cpython-313/bx/phylo/phast.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
 copying build/lib.linux-x86_64-cpython-313/bx/phylo/phast_tests.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
+copying build/lib.linux-x86_64-cpython-313/bx/phylo/newick.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
+copying build/lib.linux-x86_64-cpython-313/bx/phylo/newick_tests.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
 copying build/lib.linux-x86_64-cpython-313/bx/phylo/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
-copying build/lib.linux-x86_64-cpython-313/bx/phylo/phast.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
-creating build/bdist.linux-x86_64/wheel/bx/cookbook
-copying build/lib.linux-x86_64-cpython-313/bx/cookbook/attribute.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook
-copying build/lib.linux-x86_64-cpython-313/bx/cookbook/doc_optparse.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook
-copying build/lib.linux-x86_64-cpython-313/bx/cookbook/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook
-copying build/lib.linux-x86_64-cpython-313/bx/gene_reader.py -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-313/bx/binned_array.py -> build/bdist.linux-x86_64/wheel/./bx
+creating build/bdist.linux-x86_64/wheel/bx/intseq
+copying build/lib.linux-x86_64-cpython-313/bx/intseq/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intseq
+copying build/lib.linux-x86_64-cpython-313/bx/intseq/ngramcount.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intseq
 creating build/bdist.linux-x86_64/wheel/bx/seq
-copying build/lib.linux-x86_64-cpython-313/bx/seq/_twobit.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-313/bx/seq/seq.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-313/bx/seq/nib_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
 copying build/lib.linux-x86_64-cpython-313/bx/seq/qdna_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-313/bx/seq/seq_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-313/bx/seq/nib.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-313/bx/seq/fasta.py -> build/bdist.linux-x86_64/wheel/./bx/seq
 copying build/lib.linux-x86_64-cpython-313/bx/seq/_nib.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-313/bx/seq/fasta_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-313/bx/seq/twobit.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-313/bx/seq/nib.py -> build/bdist.linux-x86_64/wheel/./bx/seq
 copying build/lib.linux-x86_64-cpython-313/bx/seq/core.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-313/bx/seq/nib_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-313/bx/seq/twobit_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-313/bx/seq/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-313/bx/seq/seq_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
 copying build/lib.linux-x86_64-cpython-313/bx/seq/qdna.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-creating build/bdist.linux-x86_64/wheel/bx/motif
-creating build/bdist.linux-x86_64/wheel/bx/motif/io
-copying build/lib.linux-x86_64-cpython-313/bx/motif/io/transfac.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io
-copying build/lib.linux-x86_64-cpython-313/bx/motif/io/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io
-copying build/lib.linux-x86_64-cpython-313/bx/motif/io/transfac_tests.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io
-copying build/lib.linux-x86_64-cpython-313/bx/motif/_pwm.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/motif
-creating build/bdist.linux-x86_64/wheel/bx/motif/logo
-copying build/lib.linux-x86_64-cpython-313/bx/motif/logo/template.ps -> build/bdist.linux-x86_64/wheel/./bx/motif/logo
-copying build/lib.linux-x86_64-cpython-313/bx/motif/logo/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif/logo
-copying build/lib.linux-x86_64-cpython-313/bx/motif/pwm_tests.py -> build/bdist.linux-x86_64/wheel/./bx/motif
-copying build/lib.linux-x86_64-cpython-313/bx/motif/pwm.py -> build/bdist.linux-x86_64/wheel/./bx/motif
-copying build/lib.linux-x86_64-cpython-313/bx/motif/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif
-copying build/lib.linux-x86_64-cpython-313/bx/bitset_utils.py -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-313/bx/__init__.py -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-313/bx/bitset.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-313/bx/seq/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-313/bx/seq/fasta_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-313/bx/seq/twobit_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-313/bx/seq/_twobit.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-313/bx/seq/twobit.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-313/bx/seq/seq.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-313/bx/seq/fasta.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+creating build/bdist.linux-x86_64/wheel/bx/bbi
+copying build/lib.linux-x86_64-cpython-313/bx/bbi/bpt_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-313/bx/bbi/bigbed_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-313/bx/bbi/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-313/bx/bbi/bigwig_tests.py -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-313/bx/bbi/bigwig_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-313/bx/bbi/bbi_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-313/bx/bbi/cirtree_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-313/bx/seqmapping_tests.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-313/bx/interval_index_file.py -> build/bdist.linux-x86_64/wheel/./bx
 creating build/bdist.linux-x86_64/wheel/bx/align
-creating build/bdist.linux-x86_64/wheel/bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/_cpg.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/cpg.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/core.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/quality.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/sitemask_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-313/bx/align/score_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-313/bx/align/epo.py -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-313/bx/align/lav_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-313/bx/align/axt.py -> build/bdist.linux-x86_64/wheel/./bx/align
 creating build/bdist.linux-x86_64/wheel/bx/align/tools
-copying build/lib.linux-x86_64-cpython-313/bx/align/tools/tile.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools
 copying build/lib.linux-x86_64-cpython-313/bx/align/tools/fuse.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools
 copying build/lib.linux-x86_64-cpython-313/bx/align/tools/thread.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools
 copying build/lib.linux-x86_64-cpython-313/bx/align/tools/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools
 copying build/lib.linux-x86_64-cpython-313/bx/align/tools/chop.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools
-copying build/lib.linux-x86_64-cpython-313/bx/align/_epo.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-313/bx/align/score.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-313/bx/align/tools/tile.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools
+copying build/lib.linux-x86_64-cpython-313/bx/align/lav_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-313/bx/align/lav.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-313/bx/align/epo.py -> build/bdist.linux-x86_64/wheel/./bx/align
+creating build/bdist.linux-x86_64/wheel/bx/align/sitemask
+copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/sitemask_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
+copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/quality.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
+copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/core.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
+copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
+copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/_cpg.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
+copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/cpg.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
 copying build/lib.linux-x86_64-cpython-313/bx/align/core.py -> build/bdist.linux-x86_64/wheel/./bx/align
 copying build/lib.linux-x86_64-cpython-313/bx/align/_core.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-313/bx/align/score.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-313/bx/align/_epo.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-313/bx/align/maf.py -> build/bdist.linux-x86_64/wheel/./bx/align
 copying build/lib.linux-x86_64-cpython-313/bx/align/maf_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align
 copying build/lib.linux-x86_64-cpython-313/bx/align/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-313/bx/align/lav.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-313/bx/align/axt.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-313/bx/align/score_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align
 copying build/lib.linux-x86_64-cpython-313/bx/align/epo_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-313/bx/align/maf.py -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-313/bx/bitset_builders.py -> build/bdist.linux-x86_64/wheel/./bx
+creating build/bdist.linux-x86_64/wheel/bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/cdb_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/seekbzip2_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/cdb.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/seeklzop_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/bgzf_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/filecache.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/binary_file.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/seekbzip2.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/filecache_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/readlengths.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/_seekbzip2.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/seeklzop.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/misc/bgzf.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-313/bx/__init__.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-313/bx/interval_index_file_tests.py -> build/bdist.linux-x86_64/wheel/./bx
+creating build/bdist.linux-x86_64/wheel/bx/arrays
+copying build/lib.linux-x86_64-cpython-313/bx/arrays/bed.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays
+copying build/lib.linux-x86_64-cpython-313/bx/arrays/array_tree.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays
+copying build/lib.linux-x86_64-cpython-313/bx/arrays/array_tree_tests.py -> build/bdist.linux-x86_64/wheel/./bx/arrays
+copying build/lib.linux-x86_64-cpython-313/bx/arrays/wiggle.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays
+copying build/lib.linux-x86_64-cpython-313/bx/arrays/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/arrays
+copying build/lib.linux-x86_64-cpython-313/bx/binned_array.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-313/bx/gene_reader.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-313/bx/_seqmapping.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-313/bx/binned_array_tests.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-313/bx/seqmapping.py -> build/bdist.linux-x86_64/wheel/./bx
 running install_egg_info
 running egg_info
 creating lib/bx_python.egg-info
@@ -1509,196 +1545,196 @@
 Copying lib/bx_python.egg-info to build/bdist.linux-x86_64/wheel/./bx_python-0.13.0.egg-info
 running install_scripts
 creating build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_extract_ranges_indexed.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_drop_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_col_counts_all.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_truncate.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/lav_to_maf.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/interval_count_intersections.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_to_axt.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_limit_to_species.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/bed_coverage_by_interval.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_to_concat_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/wiggle_to_binned_array.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_thread_for_species.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/lzop_build_offset_table.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/axt_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_split_by_src.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/find_in_sorted_file.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/pretty_table.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/aggregate_scores_in_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/gene_fourfold_sites.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_filter_max_wc.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/bed_rand_intersect.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/nib_length.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_chunk.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/bed_bigwig_profile.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/bed_coverage.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_print_scores.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_div_sites.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/bed_subtract_basewise.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/bed_count_by_interval.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_to_int_seqs.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_gap_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/axt_to_maf.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/div_snp_table_chr.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/mMK_bitset.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_word_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/random_lines.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/bed_count_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_to_concat_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/get_scores_in_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/maf_shuffle_columns.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_covered_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_filter.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_limit_to_species.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/qv_to_bqv.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/bed_merge_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/table_filter.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/interval_count_intersections.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_col_counts_all.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/bed_intersect.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/prefix_lines.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_col_counts.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/bed_diff_basewise_summary.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/ucsc_gene_table_to_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_count.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_extract_chrom_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/bed_coverage_by_interval.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/axt_extract_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_tile_2bit.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/gene_fourfold_sites.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_chop.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/qv_to_bqv.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_extract_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/bed_complement.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_drop_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/maf_percent_columns_matching.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_select.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/div_snp_table_chr.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_split_by_src.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/bed_extend_to.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_gc_content.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_extract_chrom_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_col_counts.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_to_int_seqs.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/one_field_per_line.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/align_print_template.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_species_in_all_files.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/wiggle_to_array_tree.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/aggregate_scores_in_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_word_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/mMK_bitset.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/mask_quality.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_gc_content.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/bed_intersect_basewise.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_interval_alignibility.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_chunk.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/align_print_template.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_covered_regions.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/one_field_per_line.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/nib_length.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/line_select.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_region_coverage_by_src.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/bed_bigwig_profile.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_mapping_word_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_chop.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/out_to_chain.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_mask_cpg.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/maf_print_chroms.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_tile.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/bed_diff_basewise_summary.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_extract_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_print_scores.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/int_seqs_to_char_strings.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/bed_rand_intersect.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/tfloc_summary.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_percent_identity.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/bed_subtract_basewise.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/table_filter.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_filter.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_region_coverage_by_src.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_extract_ranges_indexed.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/bed_build_windows.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/axt_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_mask_cpg.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/pretty_table.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_randomize.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/interval_join.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_filter_max_wc.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/out_to_chain.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/int_seqs_to_char_strings.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_truncate.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/wiggle_to_simple.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/lav_to_axt.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/bed_complement.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/wiggle_to_chr_binned_array.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/interval_join.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/table_add_column.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/axt_to_maf.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/bed_count_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/bnMapper.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_species_in_all_files.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/nib_intervals_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/wiggle_to_binned_array.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_count.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/bed_coverage.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/random_lines.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_gap_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/get_scores_in_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/line_select.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/maf_mean_length_ungapped_piece.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_translate_chars.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_to_axt.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/lav_to_maf.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_tile_2.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/maf_build_index.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/bnMapper.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_interval_alignibility.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/nib_intervals_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/tfloc_summary.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/mask_quality.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_select.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_mapping_word_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_randomize.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/axt_to_lav.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/lzop_build_offset_table.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/bed_intersect.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/find_in_sorted_file.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/ucsc_gene_table_to_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_tile_2.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_thread_for_species.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_translate_chars.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/bed_extend_to.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_tile.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_tile_2bit.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_percent_identity.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/lav_to_axt.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/wiggle_to_chr_binned_array.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.13/maf_covered_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.13/nib_chrom_intervals_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/prefix_lines.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.13/maf_div_sites.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_ranges_indexed.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_drop_overlapping.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_col_counts_all.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_truncate.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lav_to_maf.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/interval_count_intersections.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_axt.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_limit_to_species.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_coverage_by_interval.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_concat_fasta.py to 755
+copying build/scripts-3.13/maf_covered_regions.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_binned_array.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_thread_for_species.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lzop_build_offset_table.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_fasta.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_split_by_src.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/find_in_sorted_file.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/pretty_table.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/aggregate_scores_in_intervals.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/gene_fourfold_sites.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_filter_max_wc.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_rand_intersect.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_length.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_chunk.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_bigwig_profile.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_coverage.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_print_scores.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_div_sites.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_fasta.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_subtract_basewise.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_count_by_interval.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_int_seqs.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_gap_frequency.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_maf.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/div_snp_table_chr.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/mMK_bitset.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_word_frequency.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/random_lines.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_count_overlapping.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_concat_fasta.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/get_scores_in_intervals.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_shuffle_columns.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_covered_ranges.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_filter.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_limit_to_species.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/qv_to_bqv.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_merge_overlapping.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/table_filter.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/interval_count_intersections.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_col_counts_all.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_intersect.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/prefix_lines.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_col_counts.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_diff_basewise_summary.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/ucsc_gene_table_to_intervals.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_count.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_chrom_ranges.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_coverage_by_interval.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_extract_ranges.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile_2bit.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/gene_fourfold_sites.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_chop.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/qv_to_bqv.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_ranges.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_complement.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_drop_overlapping.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_percent_columns_matching.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_select.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/div_snp_table_chr.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_split_by_src.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_extend_to.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_gc_content.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_chrom_ranges.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_col_counts.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_int_seqs.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/one_field_per_line.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/align_print_template.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_species_in_all_files.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_array_tree.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/aggregate_scores_in_intervals.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_word_frequency.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/mMK_bitset.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/mask_quality.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_gc_content.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_intersect_basewise.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_interval_alignibility.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_chunk.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/align_print_template.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_covered_regions.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/one_field_per_line.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_length.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/line_select.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_region_coverage_by_src.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_bigwig_profile.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mapping_word_frequency.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_chop.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/out_to_chain.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mask_cpg.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_print_chroms.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_diff_basewise_summary.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_ranges.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_print_scores.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/int_seqs_to_char_strings.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_rand_intersect.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/tfloc_summary.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_percent_identity.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_subtract_basewise.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/table_filter.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_filter.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_region_coverage_by_src.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_ranges_indexed.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_build_windows.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_fasta.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mask_cpg.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/pretty_table.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_fasta.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_randomize.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/interval_join.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_filter_max_wc.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/out_to_chain.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/int_seqs_to_char_strings.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_truncate.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_simple.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lav_to_axt.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_complement.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_chr_binned_array.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/interval_join.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/table_add_column.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_maf.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_count_overlapping.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bnMapper.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_species_in_all_files.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_intervals_to_fasta.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_binned_array.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_count.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_coverage.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/random_lines.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_gap_frequency.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/get_scores_in_intervals.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/line_select.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mean_length_ungapped_piece.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_translate_chars.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_axt.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lav_to_maf.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile_2.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_build_index.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bnMapper.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_interval_alignibility.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_intervals_to_fasta.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/tfloc_summary.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/mask_quality.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_select.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mapping_word_frequency.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_randomize.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_lav.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lzop_build_offset_table.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_intersect.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/find_in_sorted_file.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/ucsc_gene_table_to_intervals.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile_2.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_thread_for_species.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_translate_chars.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_extend_to.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile_2bit.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_percent_identity.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lav_to_axt.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_chr_binned_array.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_covered_ranges.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_chrom_intervals_to_fasta.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/prefix_lines.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_div_sites.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_covered_regions.py to 755
 creating build/bdist.linux-x86_64/wheel/bx_python-0.13.0.dist-info/WHEEL
-creating '/build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.13_bx-python/.tmp-_5xmyymy/bx_python-0.13.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
+creating '/build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.13_bx-python/.tmp-n95abucg/bx_python-0.13.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
 adding 'bx/__init__.py'
 adding 'bx/_seqmapping.cpython-313-x86_64-linux-gnu.so'
 adding 'bx/binned_array.py'
@@ -1944,135 +1980,135 @@
 running build_py
 creating build/lib.linux-x86_64-cpython-312/bx_extras
 copying lib/bx_extras/fpconst_tests.py -> build/lib.linux-x86_64-cpython-312/bx_extras
+copying lib/bx_extras/stats.py -> build/lib.linux-x86_64-cpython-312/bx_extras
+copying lib/bx_extras/__init__.py -> build/lib.linux-x86_64-cpython-312/bx_extras
 copying lib/bx_extras/pstat.py -> build/lib.linux-x86_64-cpython-312/bx_extras
 copying lib/bx_extras/fpconst.py -> build/lib.linux-x86_64-cpython-312/bx_extras
 copying lib/bx_extras/lrucache.py -> build/lib.linux-x86_64-cpython-312/bx_extras
-copying lib/bx_extras/__init__.py -> build/lib.linux-x86_64-cpython-312/bx_extras
-copying lib/bx_extras/stats.py -> build/lib.linux-x86_64-cpython-312/bx_extras
 creating build/lib.linux-x86_64-cpython-312/bx
-copying lib/bx/wiggle_tests.py -> build/lib.linux-x86_64-cpython-312/bx
+copying lib/bx/bitset_utils.py -> build/lib.linux-x86_64-cpython-312/bx
 copying lib/bx/filter.py -> build/lib.linux-x86_64-cpython-312/bx
-copying lib/bx/seqmapping_tests.py -> build/lib.linux-x86_64-cpython-312/bx
-copying lib/bx/interval_index_file.py -> build/lib.linux-x86_64-cpython-312/bx
+copying lib/bx/wiggle_tests.py -> build/lib.linux-x86_64-cpython-312/bx
 copying lib/bx/bitset_tests.py -> build/lib.linux-x86_64-cpython-312/bx
 copying lib/bx/wiggle.py -> build/lib.linux-x86_64-cpython-312/bx
+copying lib/bx/bitset_builders.py -> build/lib.linux-x86_64-cpython-312/bx
+copying lib/bx/seqmapping_tests.py -> build/lib.linux-x86_64-cpython-312/bx
+copying lib/bx/interval_index_file.py -> build/lib.linux-x86_64-cpython-312/bx
+copying lib/bx/__init__.py -> build/lib.linux-x86_64-cpython-312/bx
 copying lib/bx/interval_index_file_tests.py -> build/lib.linux-x86_64-cpython-312/bx
-copying lib/bx/seqmapping.py -> build/lib.linux-x86_64-cpython-312/bx
-copying lib/bx/binned_array_tests.py -> build/lib.linux-x86_64-cpython-312/bx
-copying lib/bx/gene_reader.py -> build/lib.linux-x86_64-cpython-312/bx
 copying lib/bx/binned_array.py -> build/lib.linux-x86_64-cpython-312/bx
-copying lib/bx/bitset_utils.py -> build/lib.linux-x86_64-cpython-312/bx
-copying lib/bx/__init__.py -> build/lib.linux-x86_64-cpython-312/bx
-copying lib/bx/bitset_builders.py -> build/lib.linux-x86_64-cpython-312/bx
+copying lib/bx/gene_reader.py -> build/lib.linux-x86_64-cpython-312/bx
+copying lib/bx/binned_array_tests.py -> build/lib.linux-x86_64-cpython-312/bx
+copying lib/bx/seqmapping.py -> build/lib.linux-x86_64-cpython-312/bx
 creating build/lib.linux-x86_64-cpython-312/bx/tabular
-copying lib/bx/tabular/io.py -> build/lib.linux-x86_64-cpython-312/bx/tabular
 copying lib/bx/tabular/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/tabular
-creating build/lib.linux-x86_64-cpython-312/bx/arrays
-copying lib/bx/arrays/array_tree_tests.py -> build/lib.linux-x86_64-cpython-312/bx/arrays
-copying lib/bx/arrays/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/arrays
-creating build/lib.linux-x86_64-cpython-312/bx/intseq
-copying lib/bx/intseq/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/intseq
-creating build/lib.linux-x86_64-cpython-312/bx/pwm
-copying lib/bx/pwm/pwm_score_positions.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
-copying lib/bx/pwm/position_weight_matrix.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
-copying lib/bx/pwm/pwm_score_maf.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
-copying lib/bx/pwm/bed_score_aligned_string.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
-copying lib/bx/pwm/bed_score_aligned_pwm.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
-copying lib/bx/pwm/pwm_tests.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
-copying lib/bx/pwm/pwm_score_motifs.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
-copying lib/bx/pwm/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
-copying lib/bx/pwm/maf_select_motifs.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
+copying lib/bx/tabular/io.py -> build/lib.linux-x86_64-cpython-312/bx/tabular
+creating build/lib.linux-x86_64-cpython-312/bx/cookbook
+copying lib/bx/cookbook/doc_optparse.py -> build/lib.linux-x86_64-cpython-312/bx/cookbook
+copying lib/bx/cookbook/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/cookbook
+copying lib/bx/cookbook/attribute.py -> build/lib.linux-x86_64-cpython-312/bx/cookbook
+creating build/lib.linux-x86_64-cpython-312/bx/motif
+copying lib/bx/motif/pwm_tests.py -> build/lib.linux-x86_64-cpython-312/bx/motif
+copying lib/bx/motif/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/motif
+copying lib/bx/motif/pwm.py -> build/lib.linux-x86_64-cpython-312/bx/motif
 creating build/lib.linux-x86_64-cpython-312/bx/intervals
+copying lib/bx/intervals/cluster_tests.py -> build/lib.linux-x86_64-cpython-312/bx/intervals
 copying lib/bx/intervals/intersection_tests.py -> build/lib.linux-x86_64-cpython-312/bx/intervals
 copying lib/bx/intervals/random_intervals.py -> build/lib.linux-x86_64-cpython-312/bx/intervals
-copying lib/bx/intervals/cluster_tests.py -> build/lib.linux-x86_64-cpython-312/bx/intervals
-copying lib/bx/intervals/io.py -> build/lib.linux-x86_64-cpython-312/bx/intervals
 copying lib/bx/intervals/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/intervals
-creating build/lib.linux-x86_64-cpython-312/bx/bbi
-copying lib/bx/bbi/bigwig_tests.py -> build/lib.linux-x86_64-cpython-312/bx/bbi
-copying lib/bx/bbi/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/bbi
-creating build/lib.linux-x86_64-cpython-312/bx/misc
-copying lib/bx/misc/seeklzop.py -> build/lib.linux-x86_64-cpython-312/bx/misc
-copying lib/bx/misc/seekbzip2_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc
-copying lib/bx/misc/filecache.py -> build/lib.linux-x86_64-cpython-312/bx/misc
-copying lib/bx/misc/filecache_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc
-copying lib/bx/misc/cdb_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc
-copying lib/bx/misc/cdb.py -> build/lib.linux-x86_64-cpython-312/bx/misc
-copying lib/bx/misc/seeklzop_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc
-copying lib/bx/misc/readlengths.py -> build/lib.linux-x86_64-cpython-312/bx/misc
-copying lib/bx/misc/bgzf_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc
-copying lib/bx/misc/seekbzip2.py -> build/lib.linux-x86_64-cpython-312/bx/misc
-copying lib/bx/misc/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/misc
-copying lib/bx/misc/binary_file.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/intervals/io.py -> build/lib.linux-x86_64-cpython-312/bx/intervals
+creating build/lib.linux-x86_64-cpython-312/bx/pwm
+copying lib/bx/pwm/pwm_score_motifs.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
+copying lib/bx/pwm/pwm_tests.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
+copying lib/bx/pwm/pwm_score_positions.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
+copying lib/bx/pwm/maf_select_motifs.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
+copying lib/bx/pwm/bed_score_aligned_string.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
+copying lib/bx/pwm/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
+copying lib/bx/pwm/pwm_score_maf.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
+copying lib/bx/pwm/position_weight_matrix.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
+copying lib/bx/pwm/bed_score_aligned_pwm.py -> build/lib.linux-x86_64-cpython-312/bx/pwm
 creating build/lib.linux-x86_64-cpython-312/bx/phylo
-copying lib/bx/phylo/newick_tests.py -> build/lib.linux-x86_64-cpython-312/bx/phylo
-copying lib/bx/phylo/newick.py -> build/lib.linux-x86_64-cpython-312/bx/phylo
+copying lib/bx/phylo/phast.py -> build/lib.linux-x86_64-cpython-312/bx/phylo
 copying lib/bx/phylo/phast_tests.py -> build/lib.linux-x86_64-cpython-312/bx/phylo
+copying lib/bx/phylo/newick.py -> build/lib.linux-x86_64-cpython-312/bx/phylo
+copying lib/bx/phylo/newick_tests.py -> build/lib.linux-x86_64-cpython-312/bx/phylo
 copying lib/bx/phylo/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/phylo
-copying lib/bx/phylo/phast.py -> build/lib.linux-x86_64-cpython-312/bx/phylo
-creating build/lib.linux-x86_64-cpython-312/bx/cookbook
-copying lib/bx/cookbook/attribute.py -> build/lib.linux-x86_64-cpython-312/bx/cookbook
-copying lib/bx/cookbook/doc_optparse.py -> build/lib.linux-x86_64-cpython-312/bx/cookbook
-copying lib/bx/cookbook/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/cookbook
+creating build/lib.linux-x86_64-cpython-312/bx/intseq
+copying lib/bx/intseq/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/intseq
 creating build/lib.linux-x86_64-cpython-312/bx/seq
-copying lib/bx/seq/seq.py -> build/lib.linux-x86_64-cpython-312/bx/seq
+copying lib/bx/seq/nib_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq
 copying lib/bx/seq/qdna_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq
-copying lib/bx/seq/seq_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq
 copying lib/bx/seq/nib.py -> build/lib.linux-x86_64-cpython-312/bx/seq
-copying lib/bx/seq/fasta.py -> build/lib.linux-x86_64-cpython-312/bx/seq
-copying lib/bx/seq/fasta_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq
-copying lib/bx/seq/twobit.py -> build/lib.linux-x86_64-cpython-312/bx/seq
 copying lib/bx/seq/core.py -> build/lib.linux-x86_64-cpython-312/bx/seq
-copying lib/bx/seq/nib_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq
-copying lib/bx/seq/twobit_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq
-copying lib/bx/seq/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/seq
+copying lib/bx/seq/seq_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq
 copying lib/bx/seq/qdna.py -> build/lib.linux-x86_64-cpython-312/bx/seq
-creating build/lib.linux-x86_64-cpython-312/bx/motif
-copying lib/bx/motif/pwm_tests.py -> build/lib.linux-x86_64-cpython-312/bx/motif
-copying lib/bx/motif/pwm.py -> build/lib.linux-x86_64-cpython-312/bx/motif
-copying lib/bx/motif/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/motif
+copying lib/bx/seq/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/seq
+copying lib/bx/seq/fasta_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq
+copying lib/bx/seq/twobit_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq
+copying lib/bx/seq/twobit.py -> build/lib.linux-x86_64-cpython-312/bx/seq
+copying lib/bx/seq/seq.py -> build/lib.linux-x86_64-cpython-312/bx/seq
+copying lib/bx/seq/fasta.py -> build/lib.linux-x86_64-cpython-312/bx/seq
+creating build/lib.linux-x86_64-cpython-312/bx/bbi
+copying lib/bx/bbi/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/bbi
+copying lib/bx/bbi/bigwig_tests.py -> build/lib.linux-x86_64-cpython-312/bx/bbi
 creating build/lib.linux-x86_64-cpython-312/bx/align
-copying lib/bx/align/score_tests.py -> build/lib.linux-x86_64-cpython-312/bx/align
-copying lib/bx/align/epo.py -> build/lib.linux-x86_64-cpython-312/bx/align
 copying lib/bx/align/lav_tests.py -> build/lib.linux-x86_64-cpython-312/bx/align
-copying lib/bx/align/axt.py -> build/lib.linux-x86_64-cpython-312/bx/align
-copying lib/bx/align/score.py -> build/lib.linux-x86_64-cpython-312/bx/align
+copying lib/bx/align/lav.py -> build/lib.linux-x86_64-cpython-312/bx/align
+copying lib/bx/align/epo.py -> build/lib.linux-x86_64-cpython-312/bx/align
 copying lib/bx/align/core.py -> build/lib.linux-x86_64-cpython-312/bx/align
+copying lib/bx/align/score.py -> build/lib.linux-x86_64-cpython-312/bx/align
+copying lib/bx/align/maf.py -> build/lib.linux-x86_64-cpython-312/bx/align
 copying lib/bx/align/maf_tests.py -> build/lib.linux-x86_64-cpython-312/bx/align
 copying lib/bx/align/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/align
-copying lib/bx/align/lav.py -> build/lib.linux-x86_64-cpython-312/bx/align
+copying lib/bx/align/axt.py -> build/lib.linux-x86_64-cpython-312/bx/align
+copying lib/bx/align/score_tests.py -> build/lib.linux-x86_64-cpython-312/bx/align
 copying lib/bx/align/epo_tests.py -> build/lib.linux-x86_64-cpython-312/bx/align
-copying lib/bx/align/maf.py -> build/lib.linux-x86_64-cpython-312/bx/align
+creating build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/misc/cdb_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/misc/seekbzip2_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/misc/cdb.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/misc/seeklzop_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/misc/bgzf_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/misc/filecache.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/misc/binary_file.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/misc/seekbzip2.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/misc/filecache_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/misc/readlengths.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/misc/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+copying lib/bx/misc/seeklzop.py -> build/lib.linux-x86_64-cpython-312/bx/misc
+creating build/lib.linux-x86_64-cpython-312/bx/arrays
+copying lib/bx/arrays/array_tree_tests.py -> build/lib.linux-x86_64-cpython-312/bx/arrays
+copying lib/bx/arrays/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/arrays
+creating build/lib.linux-x86_64-cpython-312/bx/motif/logo
+copying lib/bx/motif/logo/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/motif/logo
+creating build/lib.linux-x86_64-cpython-312/bx/motif/io
+copying lib/bx/motif/io/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/motif/io
+copying lib/bx/motif/io/transfac.py -> build/lib.linux-x86_64-cpython-312/bx/motif/io
+copying lib/bx/motif/io/transfac_tests.py -> build/lib.linux-x86_64-cpython-312/bx/motif/io
 creating build/lib.linux-x86_64-cpython-312/bx/intervals/operations
 copying lib/bx/intervals/operations/base_coverage.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
-copying lib/bx/intervals/operations/intersect.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
-copying lib/bx/intervals/operations/join.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
 copying lib/bx/intervals/operations/complement.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
-copying lib/bx/intervals/operations/coverage.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
 copying lib/bx/intervals/operations/find_clusters.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
-copying lib/bx/intervals/operations/quicksect.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
-copying lib/bx/intervals/operations/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
+copying lib/bx/intervals/operations/concat.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
+copying lib/bx/intervals/operations/intersect.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
 copying lib/bx/intervals/operations/subtract.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
 copying lib/bx/intervals/operations/merge.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
-copying lib/bx/intervals/operations/concat.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
-creating build/lib.linux-x86_64-cpython-312/bx/motif/io
-copying lib/bx/motif/io/transfac.py -> build/lib.linux-x86_64-cpython-312/bx/motif/io
-copying lib/bx/motif/io/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/motif/io
-copying lib/bx/motif/io/transfac_tests.py -> build/lib.linux-x86_64-cpython-312/bx/motif/io
-creating build/lib.linux-x86_64-cpython-312/bx/motif/logo
-copying lib/bx/motif/logo/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/motif/logo
-creating build/lib.linux-x86_64-cpython-312/bx/align/sitemask
-copying lib/bx/align/sitemask/cpg.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask
-copying lib/bx/align/sitemask/core.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask
-copying lib/bx/align/sitemask/quality.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask
-copying lib/bx/align/sitemask/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask
-copying lib/bx/align/sitemask/sitemask_tests.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask
+copying lib/bx/intervals/operations/coverage.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
+copying lib/bx/intervals/operations/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
+copying lib/bx/intervals/operations/quicksect.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
+copying lib/bx/intervals/operations/join.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations
 creating build/lib.linux-x86_64-cpython-312/bx/align/tools
-copying lib/bx/align/tools/tile.py -> build/lib.linux-x86_64-cpython-312/bx/align/tools
 copying lib/bx/align/tools/fuse.py -> build/lib.linux-x86_64-cpython-312/bx/align/tools
 copying lib/bx/align/tools/thread.py -> build/lib.linux-x86_64-cpython-312/bx/align/tools
 copying lib/bx/align/tools/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/align/tools
 copying lib/bx/align/tools/chop.py -> build/lib.linux-x86_64-cpython-312/bx/align/tools
+copying lib/bx/align/tools/tile.py -> build/lib.linux-x86_64-cpython-312/bx/align/tools
+creating build/lib.linux-x86_64-cpython-312/bx/align/sitemask
+copying lib/bx/align/sitemask/sitemask_tests.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask
+copying lib/bx/align/sitemask/quality.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask
+copying lib/bx/align/sitemask/core.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask
+copying lib/bx/align/sitemask/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask
+copying lib/bx/align/sitemask/cpg.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask
 copying lib/bx/motif/logo/template.ps -> build/lib.linux-x86_64-cpython-312/bx/motif/logo
 running build_ext
 building 'bx.bitset' extension
@@ -2299,352 +2335,352 @@
 x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/lib/bx/misc/_seekbzip2.o build/temp.linux-x86_64-cpython-312/src/bunzip/micro-bunzip.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/misc/_seekbzip2.cpython-312-x86_64-linux-gnu.so
 running build_scripts
 creating build/scripts-3.12
-copying and adjusting scripts/maf_extract_ranges_indexed.py -> build/scripts-3.12
-copying and adjusting scripts/maf_drop_overlapping.py -> build/scripts-3.12
-copying and adjusting scripts/maf_col_counts_all.py -> build/scripts-3.12
-copying and adjusting scripts/maf_truncate.py -> build/scripts-3.12
-copying and adjusting scripts/lav_to_maf.py -> build/scripts-3.12
-copying and adjusting scripts/interval_count_intersections.py -> build/scripts-3.12
-copying and adjusting scripts/maf_to_axt.py -> build/scripts-3.12
-copying and adjusting scripts/maf_limit_to_species.py -> build/scripts-3.12
-copying and adjusting scripts/bed_coverage_by_interval.py -> build/scripts-3.12
-copying and adjusting scripts/maf_to_concat_fasta.py -> build/scripts-3.12
+copying and adjusting scripts/wiggle_to_binned_array.py -> build/scripts-3.12
+copying and adjusting scripts/maf_thread_for_species.py -> build/scripts-3.12
+copying and adjusting scripts/lzop_build_offset_table.py -> build/scripts-3.12
+copying and adjusting scripts/axt_to_fasta.py -> build/scripts-3.12
+copying and adjusting scripts/maf_split_by_src.py -> build/scripts-3.12
+copying and adjusting scripts/find_in_sorted_file.py -> build/scripts-3.12
+copying and adjusting scripts/pretty_table.py -> build/scripts-3.12
+copying and adjusting scripts/aggregate_scores_in_intervals.py -> build/scripts-3.12
+copying and adjusting scripts/gene_fourfold_sites.py -> build/scripts-3.12
+copying and adjusting scripts/maf_filter_max_wc.py -> build/scripts-3.12
+copying and adjusting scripts/bed_rand_intersect.py -> build/scripts-3.12
+copying and adjusting scripts/nib_length.py -> build/scripts-3.12
+copying and adjusting scripts/maf_chunk.py -> build/scripts-3.12
+copying and adjusting scripts/bed_bigwig_profile.py -> build/scripts-3.12
+copying and adjusting scripts/bed_coverage.py -> build/scripts-3.12
+copying and adjusting scripts/maf_print_scores.py -> build/scripts-3.12
+copying and adjusting scripts/maf_div_sites.py -> build/scripts-3.12
+copying and adjusting scripts/maf_to_fasta.py -> build/scripts-3.12
+copying and adjusting scripts/bed_subtract_basewise.py -> build/scripts-3.12
 copying and adjusting scripts/bed_count_by_interval.py -> build/scripts-3.12
-copying and adjusting scripts/maf_to_int_seqs.py -> build/scripts-3.12
+copying and adjusting scripts/maf_gap_frequency.py -> build/scripts-3.12
+copying and adjusting scripts/axt_to_maf.py -> build/scripts-3.12
+copying and adjusting scripts/div_snp_table_chr.py -> build/scripts-3.12
+copying and adjusting scripts/mMK_bitset.py -> build/scripts-3.12
+copying and adjusting scripts/maf_word_frequency.py -> build/scripts-3.12
+copying and adjusting scripts/random_lines.py -> build/scripts-3.12
+copying and adjusting scripts/bed_count_overlapping.py -> build/scripts-3.12
+copying and adjusting scripts/maf_to_concat_fasta.py -> build/scripts-3.12
+copying and adjusting scripts/get_scores_in_intervals.py -> build/scripts-3.12
 copying and adjusting scripts/maf_shuffle_columns.py -> build/scripts-3.12
-copying and adjusting scripts/maf_covered_ranges.py -> build/scripts-3.12
-copying and adjusting scripts/maf_filter.py -> build/scripts-3.12
+copying and adjusting scripts/maf_limit_to_species.py -> build/scripts-3.12
+copying and adjusting scripts/qv_to_bqv.py -> build/scripts-3.12
 copying and adjusting scripts/bed_merge_overlapping.py -> build/scripts-3.12
-copying and adjusting scripts/table_filter.py -> build/scripts-3.12
+copying and adjusting scripts/interval_count_intersections.py -> build/scripts-3.12
+copying and adjusting scripts/maf_col_counts_all.py -> build/scripts-3.12
+copying and adjusting scripts/bed_intersect.py -> build/scripts-3.12
+copying and adjusting scripts/prefix_lines.py -> build/scripts-3.12
+copying and adjusting scripts/maf_col_counts.py -> build/scripts-3.12
+copying and adjusting scripts/bed_diff_basewise_summary.py -> build/scripts-3.12
+copying and adjusting scripts/ucsc_gene_table_to_intervals.py -> build/scripts-3.12
+copying and adjusting scripts/maf_count.py -> build/scripts-3.12
+copying and adjusting scripts/maf_extract_chrom_ranges.py -> build/scripts-3.12
+copying and adjusting scripts/bed_coverage_by_interval.py -> build/scripts-3.12
 copying and adjusting scripts/axt_extract_ranges.py -> build/scripts-3.12
-copying and adjusting scripts/maf_tile_2bit.py -> build/scripts-3.12
-copying and adjusting scripts/gene_fourfold_sites.py -> build/scripts-3.12
-copying and adjusting scripts/maf_chop.py -> build/scripts-3.12
-copying and adjusting scripts/qv_to_bqv.py -> build/scripts-3.12
+copying and adjusting scripts/maf_extract_ranges.py -> build/scripts-3.12
+copying and adjusting scripts/bed_complement.py -> build/scripts-3.12
+copying and adjusting scripts/maf_drop_overlapping.py -> build/scripts-3.12
 copying and adjusting scripts/maf_percent_columns_matching.py -> build/scripts-3.12
-copying and adjusting scripts/maf_select.py -> build/scripts-3.12
-copying and adjusting scripts/div_snp_table_chr.py -> build/scripts-3.12
-copying and adjusting scripts/maf_split_by_src.py -> build/scripts-3.12
-copying and adjusting scripts/bed_extend_to.py -> build/scripts-3.12
-copying and adjusting scripts/maf_gc_content.py -> build/scripts-3.12
-copying and adjusting scripts/maf_extract_chrom_ranges.py -> build/scripts-3.12
-copying and adjusting scripts/maf_col_counts.py -> build/scripts-3.12
+copying and adjusting scripts/maf_to_int_seqs.py -> build/scripts-3.12
+copying and adjusting scripts/one_field_per_line.py -> build/scripts-3.12
+copying and adjusting scripts/align_print_template.py -> build/scripts-3.12
+copying and adjusting scripts/maf_species_in_all_files.py -> build/scripts-3.12
 copying and adjusting scripts/wiggle_to_array_tree.py -> build/scripts-3.12
-copying and adjusting scripts/aggregate_scores_in_intervals.py -> build/scripts-3.12
-copying and adjusting scripts/maf_word_frequency.py -> build/scripts-3.12
-copying and adjusting scripts/mMK_bitset.py -> build/scripts-3.12
-copying and adjusting scripts/mask_quality.py -> build/scripts-3.12
+copying and adjusting scripts/maf_gc_content.py -> build/scripts-3.12
 copying and adjusting scripts/bed_intersect_basewise.py -> build/scripts-3.12
-copying and adjusting scripts/maf_interval_alignibility.py -> build/scripts-3.12
-copying and adjusting scripts/maf_chunk.py -> build/scripts-3.12
-copying and adjusting scripts/align_print_template.py -> build/scripts-3.12
-copying and adjusting scripts/maf_covered_regions.py -> build/scripts-3.12
-copying and adjusting scripts/one_field_per_line.py -> build/scripts-3.12
-copying and adjusting scripts/nib_length.py -> build/scripts-3.12
-copying and adjusting scripts/line_select.py -> build/scripts-3.12
-copying and adjusting scripts/maf_region_coverage_by_src.py -> build/scripts-3.12
-copying and adjusting scripts/bed_bigwig_profile.py -> build/scripts-3.12
-copying and adjusting scripts/maf_mapping_word_frequency.py -> build/scripts-3.12
+copying and adjusting scripts/maf_chop.py -> build/scripts-3.12
+copying and adjusting scripts/out_to_chain.py -> build/scripts-3.12
+copying and adjusting scripts/maf_mask_cpg.py -> build/scripts-3.12
 copying and adjusting scripts/maf_print_chroms.py -> build/scripts-3.12
-copying and adjusting scripts/maf_tile.py -> build/scripts-3.12
-copying and adjusting scripts/bed_diff_basewise_summary.py -> build/scripts-3.12
-copying and adjusting scripts/maf_extract_ranges.py -> build/scripts-3.12
-copying and adjusting scripts/maf_print_scores.py -> build/scripts-3.12
-copying and adjusting scripts/int_seqs_to_char_strings.py -> build/scripts-3.12
-copying and adjusting scripts/bed_rand_intersect.py -> build/scripts-3.12
-copying and adjusting scripts/tfloc_summary.py -> build/scripts-3.12
-copying and adjusting scripts/maf_percent_identity.py -> build/scripts-3.12
-copying and adjusting scripts/bed_subtract_basewise.py -> build/scripts-3.12
+copying and adjusting scripts/table_filter.py -> build/scripts-3.12
+copying and adjusting scripts/maf_filter.py -> build/scripts-3.12
+copying and adjusting scripts/maf_region_coverage_by_src.py -> build/scripts-3.12
+copying and adjusting scripts/maf_extract_ranges_indexed.py -> build/scripts-3.12
 copying and adjusting scripts/bed_build_windows.py -> build/scripts-3.12
-copying and adjusting scripts/axt_to_fasta.py -> build/scripts-3.12
-copying and adjusting scripts/maf_mask_cpg.py -> build/scripts-3.12
-copying and adjusting scripts/pretty_table.py -> build/scripts-3.12
-copying and adjusting scripts/maf_to_fasta.py -> build/scripts-3.12
-copying and adjusting scripts/maf_randomize.py -> build/scripts-3.12
-copying and adjusting scripts/interval_join.py -> build/scripts-3.12
-copying and adjusting scripts/maf_filter_max_wc.py -> build/scripts-3.12
-copying and adjusting scripts/out_to_chain.py -> build/scripts-3.12
+copying and adjusting scripts/int_seqs_to_char_strings.py -> build/scripts-3.12
+copying and adjusting scripts/maf_truncate.py -> build/scripts-3.12
 copying and adjusting scripts/wiggle_to_simple.py -> build/scripts-3.12
-copying and adjusting scripts/lav_to_axt.py -> build/scripts-3.12
-copying and adjusting scripts/bed_complement.py -> build/scripts-3.12
-copying and adjusting scripts/wiggle_to_chr_binned_array.py -> build/scripts-3.12
+copying and adjusting scripts/interval_join.py -> build/scripts-3.12
 copying and adjusting scripts/table_add_column.py -> build/scripts-3.12
-copying and adjusting scripts/axt_to_maf.py -> build/scripts-3.12
-copying and adjusting scripts/bed_count_overlapping.py -> build/scripts-3.12
-copying and adjusting scripts/bnMapper.py -> build/scripts-3.12
-copying and adjusting scripts/maf_species_in_all_files.py -> build/scripts-3.12
-copying and adjusting scripts/nib_intervals_to_fasta.py -> build/scripts-3.12
-copying and adjusting scripts/wiggle_to_binned_array.py -> build/scripts-3.12
-copying and adjusting scripts/maf_count.py -> build/scripts-3.12
-copying and adjusting scripts/bed_coverage.py -> build/scripts-3.12
-copying and adjusting scripts/random_lines.py -> build/scripts-3.12
-copying and adjusting scripts/maf_gap_frequency.py -> build/scripts-3.12
-copying and adjusting scripts/get_scores_in_intervals.py -> build/scripts-3.12
+copying and adjusting scripts/line_select.py -> build/scripts-3.12
 copying and adjusting scripts/maf_mean_length_ungapped_piece.py -> build/scripts-3.12
+copying and adjusting scripts/maf_translate_chars.py -> build/scripts-3.12
+copying and adjusting scripts/maf_to_axt.py -> build/scripts-3.12
+copying and adjusting scripts/lav_to_maf.py -> build/scripts-3.12
+copying and adjusting scripts/maf_tile_2.py -> build/scripts-3.12
 copying and adjusting scripts/maf_build_index.py -> build/scripts-3.12
+copying and adjusting scripts/bnMapper.py -> build/scripts-3.12
+copying and adjusting scripts/maf_interval_alignibility.py -> build/scripts-3.12
+copying and adjusting scripts/nib_intervals_to_fasta.py -> build/scripts-3.12
+copying and adjusting scripts/tfloc_summary.py -> build/scripts-3.12
+copying and adjusting scripts/mask_quality.py -> build/scripts-3.12
+copying and adjusting scripts/maf_select.py -> build/scripts-3.12
+copying and adjusting scripts/maf_mapping_word_frequency.py -> build/scripts-3.12
+copying and adjusting scripts/maf_randomize.py -> build/scripts-3.12
 copying and adjusting scripts/axt_to_lav.py -> build/scripts-3.12
-copying and adjusting scripts/lzop_build_offset_table.py -> build/scripts-3.12
-copying and adjusting scripts/bed_intersect.py -> build/scripts-3.12
-copying and adjusting scripts/find_in_sorted_file.py -> build/scripts-3.12
-copying and adjusting scripts/ucsc_gene_table_to_intervals.py -> build/scripts-3.12
-copying and adjusting scripts/maf_tile_2.py -> build/scripts-3.12
-copying and adjusting scripts/maf_thread_for_species.py -> build/scripts-3.12
-copying and adjusting scripts/maf_translate_chars.py -> build/scripts-3.12
+copying and adjusting scripts/bed_extend_to.py -> build/scripts-3.12
+copying and adjusting scripts/maf_tile.py -> build/scripts-3.12
+copying and adjusting scripts/maf_tile_2bit.py -> build/scripts-3.12
+copying and adjusting scripts/maf_percent_identity.py -> build/scripts-3.12
+copying and adjusting scripts/lav_to_axt.py -> build/scripts-3.12
+copying and adjusting scripts/wiggle_to_chr_binned_array.py -> build/scripts-3.12
+copying and adjusting scripts/maf_covered_ranges.py -> build/scripts-3.12
 copying and adjusting scripts/nib_chrom_intervals_to_fasta.py -> build/scripts-3.12
-copying and adjusting scripts/prefix_lines.py -> build/scripts-3.12
-copying and adjusting scripts/maf_div_sites.py -> build/scripts-3.12
-changing mode of build/scripts-3.12/maf_extract_ranges_indexed.py from 644 to 755
-changing mode of build/scripts-3.12/maf_drop_overlapping.py from 644 to 755
-changing mode of build/scripts-3.12/maf_col_counts_all.py from 644 to 755
-changing mode of build/scripts-3.12/maf_truncate.py from 644 to 755
-changing mode of build/scripts-3.12/lav_to_maf.py from 644 to 755
-changing mode of build/scripts-3.12/interval_count_intersections.py from 644 to 755
-changing mode of build/scripts-3.12/maf_to_axt.py from 644 to 755
-changing mode of build/scripts-3.12/maf_limit_to_species.py from 644 to 755
-changing mode of build/scripts-3.12/bed_coverage_by_interval.py from 644 to 755
-changing mode of build/scripts-3.12/maf_to_concat_fasta.py from 644 to 755
+copying and adjusting scripts/maf_covered_regions.py -> build/scripts-3.12
+changing mode of build/scripts-3.12/wiggle_to_binned_array.py from 644 to 755
+changing mode of build/scripts-3.12/maf_thread_for_species.py from 644 to 755
+changing mode of build/scripts-3.12/lzop_build_offset_table.py from 644 to 755
+changing mode of build/scripts-3.12/axt_to_fasta.py from 644 to 755
+changing mode of build/scripts-3.12/maf_split_by_src.py from 644 to 755
+changing mode of build/scripts-3.12/find_in_sorted_file.py from 644 to 755
+changing mode of build/scripts-3.12/pretty_table.py from 644 to 755
+changing mode of build/scripts-3.12/aggregate_scores_in_intervals.py from 644 to 755
+changing mode of build/scripts-3.12/gene_fourfold_sites.py from 644 to 755
+changing mode of build/scripts-3.12/maf_filter_max_wc.py from 644 to 755
+changing mode of build/scripts-3.12/bed_rand_intersect.py from 644 to 755
+changing mode of build/scripts-3.12/nib_length.py from 644 to 755
+changing mode of build/scripts-3.12/maf_chunk.py from 644 to 755
+changing mode of build/scripts-3.12/bed_bigwig_profile.py from 644 to 755
+changing mode of build/scripts-3.12/bed_coverage.py from 644 to 755
+changing mode of build/scripts-3.12/maf_print_scores.py from 644 to 755
+changing mode of build/scripts-3.12/maf_div_sites.py from 644 to 755
+changing mode of build/scripts-3.12/maf_to_fasta.py from 644 to 755
+changing mode of build/scripts-3.12/bed_subtract_basewise.py from 644 to 755
 changing mode of build/scripts-3.12/bed_count_by_interval.py from 644 to 755
-changing mode of build/scripts-3.12/maf_to_int_seqs.py from 644 to 755
+changing mode of build/scripts-3.12/maf_gap_frequency.py from 644 to 755
+changing mode of build/scripts-3.12/axt_to_maf.py from 644 to 755
+changing mode of build/scripts-3.12/div_snp_table_chr.py from 644 to 755
+changing mode of build/scripts-3.12/mMK_bitset.py from 644 to 755
+changing mode of build/scripts-3.12/maf_word_frequency.py from 644 to 755
+changing mode of build/scripts-3.12/random_lines.py from 644 to 755
+changing mode of build/scripts-3.12/bed_count_overlapping.py from 644 to 755
+changing mode of build/scripts-3.12/maf_to_concat_fasta.py from 644 to 755
+changing mode of build/scripts-3.12/get_scores_in_intervals.py from 644 to 755
 changing mode of build/scripts-3.12/maf_shuffle_columns.py from 644 to 755
-changing mode of build/scripts-3.12/maf_covered_ranges.py from 644 to 755
-changing mode of build/scripts-3.12/maf_filter.py from 644 to 755
+changing mode of build/scripts-3.12/maf_limit_to_species.py from 644 to 755
+changing mode of build/scripts-3.12/qv_to_bqv.py from 644 to 755
 changing mode of build/scripts-3.12/bed_merge_overlapping.py from 644 to 755
-changing mode of build/scripts-3.12/table_filter.py from 644 to 755
+changing mode of build/scripts-3.12/interval_count_intersections.py from 644 to 755
+changing mode of build/scripts-3.12/maf_col_counts_all.py from 644 to 755
+changing mode of build/scripts-3.12/bed_intersect.py from 644 to 755
+changing mode of build/scripts-3.12/prefix_lines.py from 644 to 755
+changing mode of build/scripts-3.12/maf_col_counts.py from 644 to 755
+changing mode of build/scripts-3.12/bed_diff_basewise_summary.py from 644 to 755
+changing mode of build/scripts-3.12/ucsc_gene_table_to_intervals.py from 644 to 755
+changing mode of build/scripts-3.12/maf_count.py from 644 to 755
+changing mode of build/scripts-3.12/maf_extract_chrom_ranges.py from 644 to 755
+changing mode of build/scripts-3.12/bed_coverage_by_interval.py from 644 to 755
 changing mode of build/scripts-3.12/axt_extract_ranges.py from 644 to 755
-changing mode of build/scripts-3.12/maf_tile_2bit.py from 644 to 755
-changing mode of build/scripts-3.12/gene_fourfold_sites.py from 644 to 755
-changing mode of build/scripts-3.12/maf_chop.py from 644 to 755
-changing mode of build/scripts-3.12/qv_to_bqv.py from 644 to 755
+changing mode of build/scripts-3.12/maf_extract_ranges.py from 644 to 755
+changing mode of build/scripts-3.12/bed_complement.py from 644 to 755
+changing mode of build/scripts-3.12/maf_drop_overlapping.py from 644 to 755
 changing mode of build/scripts-3.12/maf_percent_columns_matching.py from 644 to 755
-changing mode of build/scripts-3.12/maf_select.py from 644 to 755
-changing mode of build/scripts-3.12/div_snp_table_chr.py from 644 to 755
-changing mode of build/scripts-3.12/maf_split_by_src.py from 644 to 755
-changing mode of build/scripts-3.12/bed_extend_to.py from 644 to 755
-changing mode of build/scripts-3.12/maf_gc_content.py from 644 to 755
-changing mode of build/scripts-3.12/maf_extract_chrom_ranges.py from 644 to 755
-changing mode of build/scripts-3.12/maf_col_counts.py from 644 to 755
+changing mode of build/scripts-3.12/maf_to_int_seqs.py from 644 to 755
+changing mode of build/scripts-3.12/one_field_per_line.py from 644 to 755
+changing mode of build/scripts-3.12/align_print_template.py from 644 to 755
+changing mode of build/scripts-3.12/maf_species_in_all_files.py from 644 to 755
 changing mode of build/scripts-3.12/wiggle_to_array_tree.py from 644 to 755
-changing mode of build/scripts-3.12/aggregate_scores_in_intervals.py from 644 to 755
-changing mode of build/scripts-3.12/maf_word_frequency.py from 644 to 755
-changing mode of build/scripts-3.12/mMK_bitset.py from 644 to 755
-changing mode of build/scripts-3.12/mask_quality.py from 644 to 755
+changing mode of build/scripts-3.12/maf_gc_content.py from 644 to 755
 changing mode of build/scripts-3.12/bed_intersect_basewise.py from 644 to 755
-changing mode of build/scripts-3.12/maf_interval_alignibility.py from 644 to 755
-changing mode of build/scripts-3.12/maf_chunk.py from 644 to 755
-changing mode of build/scripts-3.12/align_print_template.py from 644 to 755
-changing mode of build/scripts-3.12/maf_covered_regions.py from 644 to 755
-changing mode of build/scripts-3.12/one_field_per_line.py from 644 to 755
-changing mode of build/scripts-3.12/nib_length.py from 644 to 755
-changing mode of build/scripts-3.12/line_select.py from 644 to 755
-changing mode of build/scripts-3.12/maf_region_coverage_by_src.py from 644 to 755
-changing mode of build/scripts-3.12/bed_bigwig_profile.py from 644 to 755
-changing mode of build/scripts-3.12/maf_mapping_word_frequency.py from 644 to 755
+changing mode of build/scripts-3.12/maf_chop.py from 644 to 755
+changing mode of build/scripts-3.12/out_to_chain.py from 644 to 755
+changing mode of build/scripts-3.12/maf_mask_cpg.py from 644 to 755
 changing mode of build/scripts-3.12/maf_print_chroms.py from 644 to 755
-changing mode of build/scripts-3.12/maf_tile.py from 644 to 755
-changing mode of build/scripts-3.12/bed_diff_basewise_summary.py from 644 to 755
-changing mode of build/scripts-3.12/maf_extract_ranges.py from 644 to 755
-changing mode of build/scripts-3.12/maf_print_scores.py from 644 to 755
-changing mode of build/scripts-3.12/int_seqs_to_char_strings.py from 644 to 755
-changing mode of build/scripts-3.12/bed_rand_intersect.py from 644 to 755
-changing mode of build/scripts-3.12/tfloc_summary.py from 644 to 755
-changing mode of build/scripts-3.12/maf_percent_identity.py from 644 to 755
-changing mode of build/scripts-3.12/bed_subtract_basewise.py from 644 to 755
+changing mode of build/scripts-3.12/table_filter.py from 644 to 755
+changing mode of build/scripts-3.12/maf_filter.py from 644 to 755
+changing mode of build/scripts-3.12/maf_region_coverage_by_src.py from 644 to 755
+changing mode of build/scripts-3.12/maf_extract_ranges_indexed.py from 644 to 755
 changing mode of build/scripts-3.12/bed_build_windows.py from 644 to 755
-changing mode of build/scripts-3.12/axt_to_fasta.py from 644 to 755
-changing mode of build/scripts-3.12/maf_mask_cpg.py from 644 to 755
-changing mode of build/scripts-3.12/pretty_table.py from 644 to 755
-changing mode of build/scripts-3.12/maf_to_fasta.py from 644 to 755
-changing mode of build/scripts-3.12/maf_randomize.py from 644 to 755
-changing mode of build/scripts-3.12/interval_join.py from 644 to 755
-changing mode of build/scripts-3.12/maf_filter_max_wc.py from 644 to 755
-changing mode of build/scripts-3.12/out_to_chain.py from 644 to 755
+changing mode of build/scripts-3.12/int_seqs_to_char_strings.py from 644 to 755
+changing mode of build/scripts-3.12/maf_truncate.py from 644 to 755
 changing mode of build/scripts-3.12/wiggle_to_simple.py from 644 to 755
-changing mode of build/scripts-3.12/lav_to_axt.py from 644 to 755
-changing mode of build/scripts-3.12/bed_complement.py from 644 to 755
-changing mode of build/scripts-3.12/wiggle_to_chr_binned_array.py from 644 to 755
+changing mode of build/scripts-3.12/interval_join.py from 644 to 755
 changing mode of build/scripts-3.12/table_add_column.py from 644 to 755
-changing mode of build/scripts-3.12/axt_to_maf.py from 644 to 755
-changing mode of build/scripts-3.12/bed_count_overlapping.py from 644 to 755
-changing mode of build/scripts-3.12/bnMapper.py from 644 to 755
-changing mode of build/scripts-3.12/maf_species_in_all_files.py from 644 to 755
-changing mode of build/scripts-3.12/nib_intervals_to_fasta.py from 644 to 755
-changing mode of build/scripts-3.12/wiggle_to_binned_array.py from 644 to 755
-changing mode of build/scripts-3.12/maf_count.py from 644 to 755
-changing mode of build/scripts-3.12/bed_coverage.py from 644 to 755
-changing mode of build/scripts-3.12/random_lines.py from 644 to 755
-changing mode of build/scripts-3.12/maf_gap_frequency.py from 644 to 755
-changing mode of build/scripts-3.12/get_scores_in_intervals.py from 644 to 755
+changing mode of build/scripts-3.12/line_select.py from 644 to 755
 changing mode of build/scripts-3.12/maf_mean_length_ungapped_piece.py from 644 to 755
+changing mode of build/scripts-3.12/maf_translate_chars.py from 644 to 755
+changing mode of build/scripts-3.12/maf_to_axt.py from 644 to 755
+changing mode of build/scripts-3.12/lav_to_maf.py from 644 to 755
+changing mode of build/scripts-3.12/maf_tile_2.py from 644 to 755
 changing mode of build/scripts-3.12/maf_build_index.py from 644 to 755
+changing mode of build/scripts-3.12/bnMapper.py from 644 to 755
+changing mode of build/scripts-3.12/maf_interval_alignibility.py from 644 to 755
+changing mode of build/scripts-3.12/nib_intervals_to_fasta.py from 644 to 755
+changing mode of build/scripts-3.12/tfloc_summary.py from 644 to 755
+changing mode of build/scripts-3.12/mask_quality.py from 644 to 755
+changing mode of build/scripts-3.12/maf_select.py from 644 to 755
+changing mode of build/scripts-3.12/maf_mapping_word_frequency.py from 644 to 755
+changing mode of build/scripts-3.12/maf_randomize.py from 644 to 755
 changing mode of build/scripts-3.12/axt_to_lav.py from 644 to 755
-changing mode of build/scripts-3.12/lzop_build_offset_table.py from 644 to 755
-changing mode of build/scripts-3.12/bed_intersect.py from 644 to 755
-changing mode of build/scripts-3.12/find_in_sorted_file.py from 644 to 755
-changing mode of build/scripts-3.12/ucsc_gene_table_to_intervals.py from 644 to 755
-changing mode of build/scripts-3.12/maf_tile_2.py from 644 to 755
-changing mode of build/scripts-3.12/maf_thread_for_species.py from 644 to 755
-changing mode of build/scripts-3.12/maf_translate_chars.py from 644 to 755
+changing mode of build/scripts-3.12/bed_extend_to.py from 644 to 755
+changing mode of build/scripts-3.12/maf_tile.py from 644 to 755
+changing mode of build/scripts-3.12/maf_tile_2bit.py from 644 to 755
+changing mode of build/scripts-3.12/maf_percent_identity.py from 644 to 755
+changing mode of build/scripts-3.12/lav_to_axt.py from 644 to 755
+changing mode of build/scripts-3.12/wiggle_to_chr_binned_array.py from 644 to 755
+changing mode of build/scripts-3.12/maf_covered_ranges.py from 644 to 755
 changing mode of build/scripts-3.12/nib_chrom_intervals_to_fasta.py from 644 to 755
-changing mode of build/scripts-3.12/prefix_lines.py from 644 to 755
-changing mode of build/scripts-3.12/maf_div_sites.py from 644 to 755
+changing mode of build/scripts-3.12/maf_covered_regions.py from 644 to 755
 installing to build/bdist.linux-x86_64/wheel
 running install
 running install_lib
 creating build/bdist.linux-x86_64/wheel
 creating build/bdist.linux-x86_64/wheel/bx_extras
 copying build/lib.linux-x86_64-cpython-312/bx_extras/fpconst_tests.py -> build/bdist.linux-x86_64/wheel/./bx_extras
+copying build/lib.linux-x86_64-cpython-312/bx_extras/stats.py -> build/bdist.linux-x86_64/wheel/./bx_extras
+copying build/lib.linux-x86_64-cpython-312/bx_extras/__init__.py -> build/bdist.linux-x86_64/wheel/./bx_extras
 copying build/lib.linux-x86_64-cpython-312/bx_extras/pstat.py -> build/bdist.linux-x86_64/wheel/./bx_extras
 copying build/lib.linux-x86_64-cpython-312/bx_extras/fpconst.py -> build/bdist.linux-x86_64/wheel/./bx_extras
 copying build/lib.linux-x86_64-cpython-312/bx_extras/lrucache.py -> build/bdist.linux-x86_64/wheel/./bx_extras
-copying build/lib.linux-x86_64-cpython-312/bx_extras/__init__.py -> build/bdist.linux-x86_64/wheel/./bx_extras
-copying build/lib.linux-x86_64-cpython-312/bx_extras/stats.py -> build/bdist.linux-x86_64/wheel/./bx_extras
 creating build/bdist.linux-x86_64/wheel/bx
-copying build/lib.linux-x86_64-cpython-312/bx/wiggle_tests.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-312/bx/bitset_utils.py -> build/bdist.linux-x86_64/wheel/./bx
 copying build/lib.linux-x86_64-cpython-312/bx/filter.py -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-312/bx/seqmapping_tests.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-312/bx/wiggle_tests.py -> build/bdist.linux-x86_64/wheel/./bx
 creating build/bdist.linux-x86_64/wheel/bx/tabular
-copying build/lib.linux-x86_64-cpython-312/bx/tabular/io.py -> build/bdist.linux-x86_64/wheel/./bx/tabular
 copying build/lib.linux-x86_64-cpython-312/bx/tabular/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/tabular
-creating build/bdist.linux-x86_64/wheel/bx/arrays
-copying build/lib.linux-x86_64-cpython-312/bx/arrays/wiggle.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays
-copying build/lib.linux-x86_64-cpython-312/bx/arrays/array_tree_tests.py -> build/bdist.linux-x86_64/wheel/./bx/arrays
-copying build/lib.linux-x86_64-cpython-312/bx/arrays/array_tree.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays
-copying build/lib.linux-x86_64-cpython-312/bx/arrays/bed.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays
-copying build/lib.linux-x86_64-cpython-312/bx/arrays/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/arrays
-copying build/lib.linux-x86_64-cpython-312/bx/interval_index_file.py -> build/bdist.linux-x86_64/wheel/./bx
-creating build/bdist.linux-x86_64/wheel/bx/intseq
-copying build/lib.linux-x86_64-cpython-312/bx/intseq/ngramcount.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intseq
-copying build/lib.linux-x86_64-cpython-312/bx/intseq/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intseq
-creating build/bdist.linux-x86_64/wheel/bx/pwm
-copying build/lib.linux-x86_64-cpython-312/bx/pwm/pwm_score_positions.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-312/bx/pwm/position_weight_matrix.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-312/bx/pwm/pwm_score_maf.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-312/bx/pwm/bed_score_aligned_string.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-312/bx/pwm/bed_score_aligned_pwm.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-312/bx/pwm/pwm_tests.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-312/bx/pwm/pwm_score_motifs.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-312/bx/pwm/_position_weight_matrix.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-312/bx/pwm/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
-copying build/lib.linux-x86_64-cpython-312/bx/pwm/maf_select_motifs.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-312/bx/tabular/io.py -> build/bdist.linux-x86_64/wheel/./bx/tabular
+creating build/bdist.linux-x86_64/wheel/bx/cookbook
+copying build/lib.linux-x86_64-cpython-312/bx/cookbook/doc_optparse.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook
+copying build/lib.linux-x86_64-cpython-312/bx/cookbook/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook
+copying build/lib.linux-x86_64-cpython-312/bx/cookbook/attribute.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook
+copying build/lib.linux-x86_64-cpython-312/bx/bitset.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx
+creating build/bdist.linux-x86_64/wheel/bx/motif
+copying build/lib.linux-x86_64-cpython-312/bx/motif/pwm_tests.py -> build/bdist.linux-x86_64/wheel/./bx/motif
+creating build/bdist.linux-x86_64/wheel/bx/motif/logo
+copying build/lib.linux-x86_64-cpython-312/bx/motif/logo/template.ps -> build/bdist.linux-x86_64/wheel/./bx/motif/logo
+copying build/lib.linux-x86_64-cpython-312/bx/motif/logo/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif/logo
+creating build/bdist.linux-x86_64/wheel/bx/motif/io
+copying build/lib.linux-x86_64-cpython-312/bx/motif/io/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io
+copying build/lib.linux-x86_64-cpython-312/bx/motif/io/transfac.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io
+copying build/lib.linux-x86_64-cpython-312/bx/motif/io/transfac_tests.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io
+copying build/lib.linux-x86_64-cpython-312/bx/motif/_pwm.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/motif
+copying build/lib.linux-x86_64-cpython-312/bx/motif/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif
+copying build/lib.linux-x86_64-cpython-312/bx/motif/pwm.py -> build/bdist.linux-x86_64/wheel/./bx/motif
 creating build/bdist.linux-x86_64/wheel/bx/intervals
+copying build/lib.linux-x86_64-cpython-312/bx/intervals/cluster_tests.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
 copying build/lib.linux-x86_64-cpython-312/bx/intervals/intersection_tests.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
 copying build/lib.linux-x86_64-cpython-312/bx/intervals/random_intervals.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
 copying build/lib.linux-x86_64-cpython-312/bx/intervals/cluster.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intervals
-copying build/lib.linux-x86_64-cpython-312/bx/intervals/cluster_tests.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
-copying build/lib.linux-x86_64-cpython-312/bx/intervals/io.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
-copying build/lib.linux-x86_64-cpython-312/bx/intervals/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
 copying build/lib.linux-x86_64-cpython-312/bx/intervals/intersection.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intervals
+copying build/lib.linux-x86_64-cpython-312/bx/intervals/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
+copying build/lib.linux-x86_64-cpython-312/bx/intervals/io.py -> build/bdist.linux-x86_64/wheel/./bx/intervals
 creating build/bdist.linux-x86_64/wheel/bx/intervals/operations
 copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/base_coverage.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/intersect.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/join.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
 copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/complement.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/coverage.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
 copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/find_clusters.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/quicksect.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
+copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/concat.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
+copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/intersect.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
 copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/subtract.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
 copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/merge.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/concat.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
-copying build/lib.linux-x86_64-cpython-312/bx/bitset.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/coverage.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
+copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
+copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/quicksect.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
+copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/join.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations
 copying build/lib.linux-x86_64-cpython-312/bx/bitset_tests.py -> build/bdist.linux-x86_64/wheel/./bx
 copying build/lib.linux-x86_64-cpython-312/bx/wiggle.py -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-312/bx/interval_index_file_tests.py -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-312/bx/seqmapping.py -> build/bdist.linux-x86_64/wheel/./bx
-creating build/bdist.linux-x86_64/wheel/bx/bbi
-copying build/lib.linux-x86_64-cpython-312/bx/bbi/bigwig_tests.py -> build/bdist.linux-x86_64/wheel/./bx/bbi
-copying build/lib.linux-x86_64-cpython-312/bx/bbi/bbi_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
-copying build/lib.linux-x86_64-cpython-312/bx/bbi/bpt_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
-copying build/lib.linux-x86_64-cpython-312/bx/bbi/bigbed_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
-copying build/lib.linux-x86_64-cpython-312/bx/bbi/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/bbi
-copying build/lib.linux-x86_64-cpython-312/bx/bbi/cirtree_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
-copying build/lib.linux-x86_64-cpython-312/bx/bbi/bigwig_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
-creating build/bdist.linux-x86_64/wheel/bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/seeklzop.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/seekbzip2_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/filecache.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/filecache_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/cdb_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/cdb.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/seeklzop_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/_seekbzip2.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/readlengths.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/bgzf_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/bgzf.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/seekbzip2.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/misc/binary_file.py -> build/bdist.linux-x86_64/wheel/./bx/misc
-copying build/lib.linux-x86_64-cpython-312/bx/binned_array_tests.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-312/bx/bitset_builders.py -> build/bdist.linux-x86_64/wheel/./bx
+creating build/bdist.linux-x86_64/wheel/bx/pwm
+copying build/lib.linux-x86_64-cpython-312/bx/pwm/pwm_score_motifs.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-312/bx/pwm/pwm_tests.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-312/bx/pwm/pwm_score_positions.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-312/bx/pwm/maf_select_motifs.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-312/bx/pwm/bed_score_aligned_string.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-312/bx/pwm/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-312/bx/pwm/pwm_score_maf.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-312/bx/pwm/position_weight_matrix.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-312/bx/pwm/bed_score_aligned_pwm.py -> build/bdist.linux-x86_64/wheel/./bx/pwm
+copying build/lib.linux-x86_64-cpython-312/bx/pwm/_position_weight_matrix.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/pwm
 creating build/bdist.linux-x86_64/wheel/bx/phylo
-copying build/lib.linux-x86_64-cpython-312/bx/phylo/newick_tests.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
-copying build/lib.linux-x86_64-cpython-312/bx/phylo/newick.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
+copying build/lib.linux-x86_64-cpython-312/bx/phylo/phast.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
 copying build/lib.linux-x86_64-cpython-312/bx/phylo/phast_tests.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
+copying build/lib.linux-x86_64-cpython-312/bx/phylo/newick.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
+copying build/lib.linux-x86_64-cpython-312/bx/phylo/newick_tests.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
 copying build/lib.linux-x86_64-cpython-312/bx/phylo/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
-copying build/lib.linux-x86_64-cpython-312/bx/phylo/phast.py -> build/bdist.linux-x86_64/wheel/./bx/phylo
-creating build/bdist.linux-x86_64/wheel/bx/cookbook
-copying build/lib.linux-x86_64-cpython-312/bx/cookbook/attribute.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook
-copying build/lib.linux-x86_64-cpython-312/bx/cookbook/doc_optparse.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook
-copying build/lib.linux-x86_64-cpython-312/bx/cookbook/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook
-copying build/lib.linux-x86_64-cpython-312/bx/gene_reader.py -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-312/bx/binned_array.py -> build/bdist.linux-x86_64/wheel/./bx
+creating build/bdist.linux-x86_64/wheel/bx/intseq
+copying build/lib.linux-x86_64-cpython-312/bx/intseq/ngramcount.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intseq
+copying build/lib.linux-x86_64-cpython-312/bx/intseq/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intseq
 creating build/bdist.linux-x86_64/wheel/bx/seq
-copying build/lib.linux-x86_64-cpython-312/bx/seq/seq.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-312/bx/seq/nib_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
 copying build/lib.linux-x86_64-cpython-312/bx/seq/qdna_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-312/bx/seq/seq_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
 copying build/lib.linux-x86_64-cpython-312/bx/seq/nib.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-312/bx/seq/fasta.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-312/bx/seq/fasta_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-312/bx/seq/twobit.py -> build/bdist.linux-x86_64/wheel/./bx/seq
 copying build/lib.linux-x86_64-cpython-312/bx/seq/core.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-312/bx/seq/nib_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-312/bx/seq/twobit_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
-copying build/lib.linux-x86_64-cpython-312/bx/seq/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-312/bx/seq/seq_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
 copying build/lib.linux-x86_64-cpython-312/bx/seq/qdna.py -> build/bdist.linux-x86_64/wheel/./bx/seq
 copying build/lib.linux-x86_64-cpython-312/bx/seq/_nib.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-312/bx/seq/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-312/bx/seq/fasta_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-312/bx/seq/twobit_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq
 copying build/lib.linux-x86_64-cpython-312/bx/seq/_twobit.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/seq
-creating build/bdist.linux-x86_64/wheel/bx/motif
-copying build/lib.linux-x86_64-cpython-312/bx/motif/_pwm.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/motif
-creating build/bdist.linux-x86_64/wheel/bx/motif/io
-copying build/lib.linux-x86_64-cpython-312/bx/motif/io/transfac.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io
-copying build/lib.linux-x86_64-cpython-312/bx/motif/io/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io
-copying build/lib.linux-x86_64-cpython-312/bx/motif/io/transfac_tests.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io
-creating build/bdist.linux-x86_64/wheel/bx/motif/logo
-copying build/lib.linux-x86_64-cpython-312/bx/motif/logo/template.ps -> build/bdist.linux-x86_64/wheel/./bx/motif/logo
-copying build/lib.linux-x86_64-cpython-312/bx/motif/logo/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif/logo
-copying build/lib.linux-x86_64-cpython-312/bx/motif/pwm_tests.py -> build/bdist.linux-x86_64/wheel/./bx/motif
-copying build/lib.linux-x86_64-cpython-312/bx/motif/pwm.py -> build/bdist.linux-x86_64/wheel/./bx/motif
-copying build/lib.linux-x86_64-cpython-312/bx/motif/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif
-copying build/lib.linux-x86_64-cpython-312/bx/bitset_utils.py -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-312/bx/__init__.py -> build/bdist.linux-x86_64/wheel/./bx
-copying build/lib.linux-x86_64-cpython-312/bx/_seqmapping.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-312/bx/seq/twobit.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-312/bx/seq/seq.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+copying build/lib.linux-x86_64-cpython-312/bx/seq/fasta.py -> build/bdist.linux-x86_64/wheel/./bx/seq
+creating build/bdist.linux-x86_64/wheel/bx/bbi
+copying build/lib.linux-x86_64-cpython-312/bx/bbi/bpt_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-312/bx/bbi/bigwig_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-312/bx/bbi/bigbed_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-312/bx/bbi/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-312/bx/bbi/bigwig_tests.py -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-312/bx/bbi/bbi_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-312/bx/bbi/cirtree_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi
+copying build/lib.linux-x86_64-cpython-312/bx/seqmapping_tests.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-312/bx/interval_index_file.py -> build/bdist.linux-x86_64/wheel/./bx
 creating build/bdist.linux-x86_64/wheel/bx/align
-creating build/bdist.linux-x86_64/wheel/bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/cpg.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/core.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/_cpg.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/quality.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/sitemask_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
-copying build/lib.linux-x86_64-cpython-312/bx/align/score_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-312/bx/align/epo.py -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-312/bx/align/lav_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align
 copying build/lib.linux-x86_64-cpython-312/bx/align/_epo.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-312/bx/align/axt.py -> build/bdist.linux-x86_64/wheel/./bx/align
 creating build/bdist.linux-x86_64/wheel/bx/align/tools
-copying build/lib.linux-x86_64-cpython-312/bx/align/tools/tile.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools
 copying build/lib.linux-x86_64-cpython-312/bx/align/tools/fuse.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools
 copying build/lib.linux-x86_64-cpython-312/bx/align/tools/thread.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools
 copying build/lib.linux-x86_64-cpython-312/bx/align/tools/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools
 copying build/lib.linux-x86_64-cpython-312/bx/align/tools/chop.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools
-copying build/lib.linux-x86_64-cpython-312/bx/align/_core.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-312/bx/align/score.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-312/bx/align/tools/tile.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools
+copying build/lib.linux-x86_64-cpython-312/bx/align/lav_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-312/bx/align/lav.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-312/bx/align/epo.py -> build/bdist.linux-x86_64/wheel/./bx/align
+creating build/bdist.linux-x86_64/wheel/bx/align/sitemask
+copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/sitemask_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
+copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/quality.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
+copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/core.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
+copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
+copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/_cpg.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
+copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/cpg.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask
 copying build/lib.linux-x86_64-cpython-312/bx/align/core.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-312/bx/align/score.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-312/bx/align/maf.py -> build/bdist.linux-x86_64/wheel/./bx/align
 copying build/lib.linux-x86_64-cpython-312/bx/align/maf_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align
 copying build/lib.linux-x86_64-cpython-312/bx/align/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-312/bx/align/lav.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-312/bx/align/_core.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-312/bx/align/axt.py -> build/bdist.linux-x86_64/wheel/./bx/align
+copying build/lib.linux-x86_64-cpython-312/bx/align/score_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align
 copying build/lib.linux-x86_64-cpython-312/bx/align/epo_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-312/bx/align/maf.py -> build/bdist.linux-x86_64/wheel/./bx/align
-copying build/lib.linux-x86_64-cpython-312/bx/bitset_builders.py -> build/bdist.linux-x86_64/wheel/./bx
+creating build/bdist.linux-x86_64/wheel/bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/cdb_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/_seekbzip2.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/seekbzip2_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/cdb.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/seeklzop_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/bgzf_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/filecache.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/binary_file.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/seekbzip2.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/filecache_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/readlengths.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/bgzf.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/misc/seeklzop.py -> build/bdist.linux-x86_64/wheel/./bx/misc
+copying build/lib.linux-x86_64-cpython-312/bx/__init__.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-312/bx/interval_index_file_tests.py -> build/bdist.linux-x86_64/wheel/./bx
+creating build/bdist.linux-x86_64/wheel/bx/arrays
+copying build/lib.linux-x86_64-cpython-312/bx/arrays/bed.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays
+copying build/lib.linux-x86_64-cpython-312/bx/arrays/array_tree_tests.py -> build/bdist.linux-x86_64/wheel/./bx/arrays
+copying build/lib.linux-x86_64-cpython-312/bx/arrays/array_tree.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays
+copying build/lib.linux-x86_64-cpython-312/bx/arrays/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/arrays
+copying build/lib.linux-x86_64-cpython-312/bx/arrays/wiggle.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays
+copying build/lib.linux-x86_64-cpython-312/bx/binned_array.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-312/bx/gene_reader.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-312/bx/binned_array_tests.py -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-312/bx/_seqmapping.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx
+copying build/lib.linux-x86_64-cpython-312/bx/seqmapping.py -> build/bdist.linux-x86_64/wheel/./bx
 running install_egg_info
 running egg_info
 writing lib/bx_python.egg-info/PKG-INFO
@@ -2658,196 +2694,196 @@
 Copying lib/bx_python.egg-info to build/bdist.linux-x86_64/wheel/./bx_python-0.13.0.egg-info
 running install_scripts
 creating build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_extract_ranges_indexed.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_drop_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_col_counts_all.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_truncate.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/lav_to_maf.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/interval_count_intersections.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_to_axt.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_limit_to_species.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/bed_coverage_by_interval.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_to_concat_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/wiggle_to_binned_array.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_thread_for_species.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/lzop_build_offset_table.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/axt_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_split_by_src.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/find_in_sorted_file.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/pretty_table.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/aggregate_scores_in_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/gene_fourfold_sites.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_filter_max_wc.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/bed_rand_intersect.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/nib_length.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_chunk.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/bed_bigwig_profile.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/bed_coverage.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_print_scores.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_div_sites.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/bed_subtract_basewise.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/bed_count_by_interval.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_to_int_seqs.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_gap_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/axt_to_maf.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/div_snp_table_chr.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/mMK_bitset.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_word_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/random_lines.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/bed_count_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_to_concat_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/get_scores_in_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/maf_shuffle_columns.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_covered_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_filter.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_limit_to_species.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/qv_to_bqv.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/bed_merge_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/table_filter.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/interval_count_intersections.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_col_counts_all.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/bed_intersect.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/prefix_lines.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_col_counts.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/bed_diff_basewise_summary.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/ucsc_gene_table_to_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_count.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_extract_chrom_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/bed_coverage_by_interval.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/axt_extract_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_tile_2bit.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/gene_fourfold_sites.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_chop.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/qv_to_bqv.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_extract_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/bed_complement.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_drop_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/maf_percent_columns_matching.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_select.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/div_snp_table_chr.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_split_by_src.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/bed_extend_to.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_gc_content.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_extract_chrom_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_col_counts.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_to_int_seqs.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/one_field_per_line.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/align_print_template.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_species_in_all_files.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/wiggle_to_array_tree.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/aggregate_scores_in_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_word_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/mMK_bitset.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/mask_quality.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_gc_content.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/bed_intersect_basewise.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_interval_alignibility.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_chunk.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/align_print_template.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_covered_regions.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/one_field_per_line.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/nib_length.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/line_select.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_region_coverage_by_src.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/bed_bigwig_profile.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_mapping_word_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_chop.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/out_to_chain.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_mask_cpg.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/maf_print_chroms.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_tile.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/bed_diff_basewise_summary.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_extract_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_print_scores.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/int_seqs_to_char_strings.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/bed_rand_intersect.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/tfloc_summary.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_percent_identity.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/bed_subtract_basewise.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/table_filter.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_filter.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_region_coverage_by_src.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_extract_ranges_indexed.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/bed_build_windows.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/axt_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_mask_cpg.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/pretty_table.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_randomize.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/interval_join.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_filter_max_wc.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/out_to_chain.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/int_seqs_to_char_strings.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_truncate.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/wiggle_to_simple.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/lav_to_axt.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/bed_complement.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/wiggle_to_chr_binned_array.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/interval_join.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/table_add_column.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/axt_to_maf.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/bed_count_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/bnMapper.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_species_in_all_files.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/nib_intervals_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/wiggle_to_binned_array.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_count.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/bed_coverage.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/random_lines.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_gap_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/get_scores_in_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/line_select.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/maf_mean_length_ungapped_piece.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_translate_chars.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_to_axt.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/lav_to_maf.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_tile_2.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/maf_build_index.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/bnMapper.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_interval_alignibility.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/nib_intervals_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/tfloc_summary.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/mask_quality.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_select.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_mapping_word_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_randomize.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/axt_to_lav.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/lzop_build_offset_table.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/bed_intersect.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/find_in_sorted_file.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/ucsc_gene_table_to_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_tile_2.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_thread_for_species.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_translate_chars.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/bed_extend_to.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_tile.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_tile_2bit.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_percent_identity.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/lav_to_axt.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/wiggle_to_chr_binned_array.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+copying build/scripts-3.12/maf_covered_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
 copying build/scripts-3.12/nib_chrom_intervals_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/prefix_lines.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-copying build/scripts-3.12/maf_div_sites.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_ranges_indexed.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_drop_overlapping.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_col_counts_all.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_truncate.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lav_to_maf.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/interval_count_intersections.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_axt.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_limit_to_species.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_coverage_by_interval.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_concat_fasta.py to 755
+copying build/scripts-3.12/maf_covered_regions.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_binned_array.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_thread_for_species.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lzop_build_offset_table.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_fasta.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_split_by_src.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/find_in_sorted_file.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/pretty_table.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/aggregate_scores_in_intervals.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/gene_fourfold_sites.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_filter_max_wc.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_rand_intersect.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_length.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_chunk.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_bigwig_profile.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_coverage.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_print_scores.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_div_sites.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_fasta.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_subtract_basewise.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_count_by_interval.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_int_seqs.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_gap_frequency.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_maf.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/div_snp_table_chr.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/mMK_bitset.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_word_frequency.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/random_lines.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_count_overlapping.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_concat_fasta.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/get_scores_in_intervals.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_shuffle_columns.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_covered_ranges.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_filter.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_limit_to_species.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/qv_to_bqv.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_merge_overlapping.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/table_filter.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/interval_count_intersections.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_col_counts_all.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_intersect.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/prefix_lines.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_col_counts.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_diff_basewise_summary.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/ucsc_gene_table_to_intervals.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_count.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_chrom_ranges.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_coverage_by_interval.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_extract_ranges.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile_2bit.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/gene_fourfold_sites.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_chop.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/qv_to_bqv.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_ranges.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_complement.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_drop_overlapping.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_percent_columns_matching.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_select.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/div_snp_table_chr.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_split_by_src.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_extend_to.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_gc_content.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_chrom_ranges.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_col_counts.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_int_seqs.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/one_field_per_line.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/align_print_template.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_species_in_all_files.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_array_tree.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/aggregate_scores_in_intervals.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_word_frequency.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/mMK_bitset.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/mask_quality.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_gc_content.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_intersect_basewise.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_interval_alignibility.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_chunk.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/align_print_template.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_covered_regions.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/one_field_per_line.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_length.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/line_select.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_region_coverage_by_src.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_bigwig_profile.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mapping_word_frequency.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_chop.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/out_to_chain.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mask_cpg.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_print_chroms.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_diff_basewise_summary.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_ranges.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_print_scores.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/int_seqs_to_char_strings.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_rand_intersect.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/tfloc_summary.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_percent_identity.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_subtract_basewise.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/table_filter.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_filter.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_region_coverage_by_src.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_ranges_indexed.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_build_windows.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_fasta.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mask_cpg.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/pretty_table.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_fasta.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_randomize.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/interval_join.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_filter_max_wc.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/out_to_chain.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/int_seqs_to_char_strings.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_truncate.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_simple.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lav_to_axt.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_complement.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_chr_binned_array.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/interval_join.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/table_add_column.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_maf.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_count_overlapping.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bnMapper.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_species_in_all_files.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_intervals_to_fasta.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_binned_array.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_count.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_coverage.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/random_lines.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_gap_frequency.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/get_scores_in_intervals.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/line_select.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mean_length_ungapped_piece.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_translate_chars.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_axt.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lav_to_maf.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile_2.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_build_index.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bnMapper.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_interval_alignibility.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_intervals_to_fasta.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/tfloc_summary.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/mask_quality.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_select.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mapping_word_frequency.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_randomize.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_lav.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lzop_build_offset_table.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_intersect.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/find_in_sorted_file.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/ucsc_gene_table_to_intervals.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile_2.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_thread_for_species.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_translate_chars.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_extend_to.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile_2bit.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_percent_identity.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lav_to_axt.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_chr_binned_array.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_covered_ranges.py to 755
 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_chrom_intervals_to_fasta.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/prefix_lines.py to 755
-changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_div_sites.py to 755
+changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_covered_regions.py to 755
 creating build/bdist.linux-x86_64/wheel/bx_python-0.13.0.dist-info/WHEEL
-creating '/build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.12_bx-python/.tmp-ksds_piv/bx_python-0.13.0-cp312-cp312-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
+creating '/build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.12_bx-python/.tmp-dh8dzl0o/bx_python-0.13.0-cp312-cp312-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
 adding 'bx/__init__.py'
 adding 'bx/_seqmapping.cpython-312-x86_64-linux-gnu.so'
 adding 'bx/binned_array.py'
@@ -3091,7 +3127,7 @@
 platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0
 rootdir: /build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.13_bx-python/build
 configfile: pytest.ini
-plugins: cython-0.3.1, typeguard-4.4.1
+plugins: typeguard-4.4.1, cython-0.3.1
 collected 139 items
 
 bx/align/epo_tests.py .....                                              [  3%]
@@ -3138,13 +3174,13 @@
     assert allclose(sd.sum_data / sd.valid_count, values)
 
 -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
-======================= 139 passed, 6 warnings in 3.08s ========================
+======================= 139 passed, 6 warnings in 3.66s ========================
 I: pybuild base:311: cd /build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.12_bx-python/build; python3.12 -m pytest 
 ============================= test session starts ==============================
 platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0
 rootdir: /build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.12_bx-python/build
 configfile: pytest.ini
-plugins: cython-0.3.1, typeguard-4.4.1
+plugins: typeguard-4.4.1, cython-0.3.1
 collected 139 items
 
 bx/align/epo_tests.py .....                                              [  3%]
@@ -3191,7 +3227,7 @@
     assert allclose(sd.sum_data / sd.valid_count, values)
 
 -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
-======================= 139 passed, 6 warnings in 3.84s ========================
+======================= 139 passed, 6 warnings in 5.05s ========================
    create-stamp debian/debhelper-build-stamp
    dh_testroot -O--buildsystem=pybuild
    dh_prep -O--buildsystem=pybuild
@@ -3203,100 +3239,100 @@
    debian/rules override_dh_python3
 make[1]: Entering directory '/build/reproducible-path/python-bx-0.13.0'
 dh_python3 --shebang=/usr/bin/python3
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_extract_ranges_indexed.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_drop_overlapping.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_col_counts_all.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_truncate.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/lav_to_maf.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/interval_count_intersections.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_to_axt.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_limit_to_species.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_coverage_by_interval.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_to_concat_fasta.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/wiggle_to_binned_array.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_thread_for_species.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/lzop_build_offset_table.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/axt_to_fasta.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_split_by_src.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/find_in_sorted_file.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/pretty_table.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/aggregate_scores_in_intervals.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/gene_fourfold_sites.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_filter_max_wc.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_rand_intersect.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/nib_length.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_chunk.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_bigwig_profile.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_coverage.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_print_scores.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_div_sites.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_to_fasta.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_subtract_basewise.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_count_by_interval.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_to_int_seqs.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_gap_frequency.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/axt_to_maf.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/div_snp_table_chr.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/mMK_bitset.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_word_frequency.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/random_lines.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_count_overlapping.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_to_concat_fasta.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/get_scores_in_intervals.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_shuffle_columns.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_covered_ranges.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_filter.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_limit_to_species.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/qv_to_bqv.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_merge_overlapping.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/table_filter.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/interval_count_intersections.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_col_counts_all.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_intersect.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/prefix_lines.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_col_counts.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_diff_basewise_summary.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/ucsc_gene_table_to_intervals.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_count.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_extract_chrom_ranges.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_coverage_by_interval.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/axt_extract_ranges.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_tile_2bit.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/gene_fourfold_sites.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_chop.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/qv_to_bqv.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_extract_ranges.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_complement.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_drop_overlapping.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_percent_columns_matching.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_select.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/div_snp_table_chr.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_split_by_src.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_extend_to.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_gc_content.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_extract_chrom_ranges.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_col_counts.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_to_int_seqs.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/one_field_per_line.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/align_print_template.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_species_in_all_files.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/wiggle_to_array_tree.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/aggregate_scores_in_intervals.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_word_frequency.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/mMK_bitset.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/mask_quality.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_gc_content.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_intersect_basewise.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_interval_alignibility.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_chunk.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/align_print_template.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_covered_regions.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/one_field_per_line.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/nib_length.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/line_select.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_region_coverage_by_src.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_bigwig_profile.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_mapping_word_frequency.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_chop.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/out_to_chain.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_mask_cpg.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_print_chroms.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_tile.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_diff_basewise_summary.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_extract_ranges.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_print_scores.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/int_seqs_to_char_strings.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_rand_intersect.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/tfloc_summary.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_percent_identity.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_subtract_basewise.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/table_filter.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_filter.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_region_coverage_by_src.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_extract_ranges_indexed.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_build_windows.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/axt_to_fasta.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_mask_cpg.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/pretty_table.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_to_fasta.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_randomize.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/interval_join.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_filter_max_wc.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/out_to_chain.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/int_seqs_to_char_strings.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_truncate.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/wiggle_to_simple.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/lav_to_axt.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_complement.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/wiggle_to_chr_binned_array.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/interval_join.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/table_add_column.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/axt_to_maf.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_count_overlapping.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bnMapper.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_species_in_all_files.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/nib_intervals_to_fasta.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/wiggle_to_binned_array.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_count.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_coverage.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/random_lines.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_gap_frequency.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/get_scores_in_intervals.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/line_select.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_mean_length_ungapped_piece.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_translate_chars.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_to_axt.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/lav_to_maf.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_tile_2.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_build_index.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bnMapper.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_interval_alignibility.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/nib_intervals_to_fasta.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/tfloc_summary.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/mask_quality.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_select.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_mapping_word_frequency.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_randomize.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/axt_to_lav.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/lzop_build_offset_table.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_intersect.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/find_in_sorted_file.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/ucsc_gene_table_to_intervals.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_tile_2.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_thread_for_species.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_translate_chars.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/bed_extend_to.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_tile.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_tile_2bit.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_percent_identity.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/lav_to_axt.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/wiggle_to_chr_binned_array.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_covered_ranges.py
 I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/nib_chrom_intervals_to_fasta.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/prefix_lines.py
-I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_div_sites.py
+I: dh_python3 tools:113: replacing shebang in debian/python3-bx/usr/bin/maf_covered_regions.py
 dh_numpy3
 make[1]: Leaving directory '/build/reproducible-path/python-bx-0.13.0'
    dh_installsystemduser -O--buildsystem=pybuild
@@ -3324,12 +3360,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: including full source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/1512487/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/1512487/tmp/hooks/B01_cleanup finished
 I: unmounting dev/ptmx filesystem
 I: unmounting dev/pts filesystem
 I: unmounting dev/shm filesystem
 I: unmounting proc filesystem
 I: unmounting sys filesystem
 I: cleaning the build env 
-I: removing directory /srv/workspace/pbuilder/2387886 and its subdirectories
-I: Current time: Wed Dec 11 17:56:35 -12 2024
-I: pbuilder-time-stamp: 1733982995
+I: removing directory /srv/workspace/pbuilder/1512487 and its subdirectories
+I: Current time: Thu Jan 15 02:24:29 +14 2026
+I: pbuilder-time-stamp: 1768393469