Diff of the two buildlogs:

--
--- b1/build.log	2024-12-24 22:16:41.104887093 +0000
+++ b2/build.log	2024-12-24 22:20:30.794462276 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Tue Dec 24 10:14:08 -12 2024
-I: pbuilder-time-stamp: 1735078448
+I: Current time: Wed Dec 25 12:16:44 +14 2024
+I: pbuilder-time-stamp: 1735078604
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
 I: copying local configuration
@@ -38,52 +38,84 @@
 dpkg-source: info: applying fix_mpi.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/2349788/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/2935611/tmp/hooks/D01_modify_environment starting
+debug: Running on codethink02-arm64.
+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 Dec 24 22:16 /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/2935611/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/2935611/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='arm64'
-  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]="aarch64-unknown-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=arm64
+  DEBIAN_FRONTEND=noninteractive
   DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
-  DISTRIBUTION='trixie'
-  HOME='/root'
-  HOST_ARCH='arm64'
+  DIRSTACK=()
+  DISTRIBUTION=trixie
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=aarch64
+  HOST_ARCH=arm64
   IFS=' 	
   '
-  INVOCATION_ID='1aa28d3930974dccbde522bbe5172aa1'
-  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='2349788'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=af8ce299d69a4962bbd1d071925dec78
+  LANG=C
+  LANGUAGE=nl_BE:nl
+  LC_ALL=C
+  MACHTYPE=aarch64-unknown-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=2935611
   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.oCyOeoNK/pbuilderrc_QSzS --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oCyOeoNK/b1 --logfile b1/build.log murasaki_1.68.6-14.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'
-  http_proxy='http://192.168.101.4:3128'
+  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.oCyOeoNK/pbuilderrc_kRSy --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oCyOeoNK/b2 --logfile b2/build.log murasaki_1.68.6-14.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'
+  http_proxy=http://192.168.101.4:3128
 I: uname -a
-  Linux codethink04-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux
 I: ls -l /bin
   lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/2349788/tmp/hooks/D02_print_environment finished
+I: user script /srv/workspace/pbuilder/2935611/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -304,7 +336,7 @@
 Get: 167 http://deb.debian.org/debian trixie/main arm64 libterm-readkey-perl arm64 2.38-2+b4 [24.5 kB]
 Get: 168 http://deb.debian.org/debian trixie/main arm64 libtext-wrapper-perl all 1.05-4 [10.3 kB]
 Get: 169 http://deb.debian.org/debian trixie/main arm64 mpi-default-dev arm64 1.17 [3148 B]
-Fetched 142 MB in 1s (237 MB/s)
+Fetched 142 MB in 1s (186 MB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 Selecting previously unselected package libpython3.12-minimal:arm64.
 (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 ... 20082 files and directories currently installed.)
@@ -860,8 +892,8 @@
 Setting up tzdata (2024b-4) ...
 
 Current default time zone: 'Etc/UTC'
-Local time is now:      Tue Dec 24 22:14:49 UTC 2024.
-Universal Time is now:  Tue Dec 24 22:14:49 UTC 2024.
+Local time is now:      Tue Dec 24 22:17:48 UTC 2024.
+Universal Time is now:  Tue Dec 24 22:17:48 UTC 2024.
 Run 'dpkg-reconfigure tzdata' if you wish to change it.
 
 Setting up libboost-atomic1.83.0:arm64 (1.83.0-3.2+b2) ...
@@ -1023,7 +1055,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/murasaki-1.68.6/ && 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  > ../murasaki_1.68.6-14_source.changes
+I: user script /srv/workspace/pbuilder/2935611/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/2935611/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/murasaki-1.68.6/ && 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  > ../murasaki_1.68.6-14_source.changes
 dpkg-buildpackage: info: source package murasaki
 dpkg-buildpackage: info: source version 1.68.6-14
 dpkg-buildpackage: info: source distribution unstable
@@ -1067,21 +1103,32 @@
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c scoring.cc
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c openhash.cc
-In file included from ecolist.h:23,
-                 from ecohash.h:29,
-                 from ecohash.cc:26:
+In file included from murasaki.h:24,
+                 from dinkymath.cc:27:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
       |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from dinkymath.h:24,
+                 from dinkymath.cc:26:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from murasaki.h:24,
-                 from sequence.cc:28:
+dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)':
+dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
+   40 |   int last=0;
+      |       ^~~~
+dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)':
+dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
+   53 |   int last=0;
+      |       ^~~~
+In file included from options.h:28,
+                 from options.cc:26:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
       |                   ^~~~~~~~~~~~~~~
@@ -1092,6 +1139,7 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c genopts.cc
 In file included from ecolist.h:23,
                  from ecolist.cc:20:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -1122,43 +1170,6 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-sequence.cc: In destructor 'Sequence::~Sequence()':
-sequence.cc:377:9: warning: 'throw' will always call 'terminate' [-Wterminate]
-  377 |         throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno));
-      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-sequence.cc:377:9: note: in C++11 destructors default to 'noexcept'
-sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)':
-sequence.cc:1113:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 1113 |   memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]);
-      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_algobase.h:64,
-                 from /usr/include/c++/14/bits/stl_tree.h:63:
-/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
-  284 |     struct pair
-      |            ^~~~
-sequence.cc:1114:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 1114 |   memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]);
-      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
-  284 |     struct pair
-      |            ^~~~
-sequence.cc: In destructor 'BitSequence::~BitSequence()':
-sequence.cc:1394:9: warning: 'throw' will always call 'terminate' [-Wterminate]
- 1394 |         throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno));
-      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-sequence.cc:1394:9: note: in C++11 destructors default to 'noexcept'
-In file included from murasaki.h:24,
-                 from scoring.cc:27:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
 In file included from murasaki.h:24,
                  from murasaki.cc:37:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -1200,18 +1211,6 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from options.h:28,
-                 from options.cc:26:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
 murasaki_mpi.cc:89:29: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
    89 | struct lt_mpi_worldMemory : binary_function<int,int,bool> {
       |                             ^~~~~~~~~~~~~~~
@@ -1224,47 +1223,72 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
-sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
- 3332 |   SeqPos shortest=0,shortlen=length(spaces[0]);
-      |          ^~~~~~~~
 murasaki_mpi.cc: In function 'void mpi_hasher_client_mode(BitSequence*)':
 murasaki_mpi.cc:561:9: warning: variable 'send_done' set but not used [-Wunused-but-set-variable]
   561 |     int send_done;
       |         ^~~~~~~~~
-mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c genopts.cc
-In file included from sequence.cc:41:
-hashing.h: In instantiation of 'SBox<T>::SBox(int) [with T = short unsigned int]':
-sequence.cc:162:29:   required from here
-  162 |     sbox=new SBoxT(hash_bits);
-      |                             ^
-hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
-   56 |       random_shuffle(boxes[b],boxes[b]+boxsize);
-      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/algorithm:61,
-                 from /usr/include/boost/regex/v5/regex_workaround.hpp:23,
-                 from /usr/include/boost/regex/v5/regex.hpp:29,
-                 from /usr/include/boost/regex.hpp:34,
-                 from seqread.h:33,
-                 from binseq.hh:31,
-                 from sequence.h:32:
-/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here
- 4491 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
-      |     ^~~~~~~~~~~~~~
-In file included from sequence.h:44:
-shmvector.hh: In instantiation of 'void ShmVector<T>::shmRealloc(size_t) [with T = std::pair<long int, long int>; size_t = long unsigned int]':
-shmvector.hh:282:5:   required from 'void ShmVector<T>::resize(size_t) [with T = std::pair<long int, long int>; size_t = long unsigned int]'
-  282 |     shmRealloc(c);
-      |     ^~~~~~~~~~
-sequence.cc:1110:17:   required from here
- 1110 |   subSeqs.resize(binseq.regionSizes[0]);
-      |   ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
-shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<long int, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
-  225 |       memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity));
-      |       ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair<long int, long int>' declared here
+In file included from ecolist.h:23,
+                 from ecohash.h:29,
+                 from ecohash.cc:26:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from murasaki.h:24,
+                 from sequence.cc:28:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+sequence.cc: In destructor 'Sequence::~Sequence()':
+sequence.cc:377:9: warning: 'throw' will always call 'terminate' [-Wterminate]
+  377 |         throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno));
+      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+sequence.cc:377:9: note: in C++11 destructors default to 'noexcept'
+sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)':
+sequence.cc:1113:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
+ 1113 |   memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]);
+      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_algobase.h:64,
+                 from /usr/include/c++/14/bits/stl_tree.h:63:
+/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
   284 |     struct pair
       |            ^~~~
+sequence.cc:1114:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
+ 1114 |   memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]);
+      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
+  284 |     struct pair
+      |            ^~~~
+sequence.cc: In destructor 'BitSequence::~BitSequence()':
+sequence.cc:1394:9: warning: 'throw' will always call 'terminate' [-Wterminate]
+ 1394 |         throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno));
+      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+sequence.cc:1394:9: note: in C++11 destructors default to 'noexcept'
+In file included from murasaki.h:24,
+                 from scoring.cc:27:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)':
 seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations]
   264 |     stitchPath=stitchfile.branch_path();
@@ -1273,11 +1297,6 @@
 /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here
  1129 |     path branch_path() const { return parent_path(); }
       |          ^~~~~~~~~~~
-murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
-murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
- 1008 |   bool revZero=false;
-      |        ^~~~~~~
-mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c binseq.cc
 In file included from ecolist.h:23,
                  from openhash.h:29,
                  from openhash.cc:26:
@@ -1291,6 +1310,14 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
+sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
+ 3332 |   SeqPos shortest=0,shortlen=length(spaces[0]);
+      |          ^~~~~~~~
+murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
+murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
+ 1008 |   bool revZero=false;
+      |        ^~~~~~~
 murasaki.cc: In function 'bool convertPattern(std::string&)':
 murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<char*, __cxx11::basic_string<char> >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
  1287 |   random_shuffle(randomStr.begin(),randomStr.end());
@@ -1305,36 +1332,57 @@
 /usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here
  4491 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
       |     ^~~~~~~~~~~~~~
+In file included from sequence.cc:41:
+hashing.h: In instantiation of 'SBox<T>::SBox(int) [with T = short unsigned int]':
+sequence.cc:162:29:   required from here
+  162 |     sbox=new SBoxT(hash_bits);
+      |                             ^
+hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
+   56 |       random_shuffle(boxes[b],boxes[b]+boxsize);
+      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/algorithm:61,
+                 from /usr/include/boost/regex/v5/regex_workaround.hpp:23,
+                 from /usr/include/boost/regex/v5/regex.hpp:29,
+                 from /usr/include/boost/regex.hpp:34,
+                 from seqread.h:33,
+                 from binseq.hh:31,
+                 from sequence.h:32:
+/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here
+ 4491 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
+      |     ^~~~~~~~~~~~~~
+mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c binseq.cc
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-image.cc
-In file included from murasaki.h:24,
-                 from dinkymath.cc:27:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from dinkymath.h:24,
-                 from dinkymath.cc:26:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)':
-dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
-   40 |   int last=0;
-      |       ^~~~
-dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)':
-dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
-   53 |   int last=0;
-      |       ^~~~
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-compare.cc
+In file included from sequence.h:44:
+shmvector.hh: In instantiation of 'void ShmVector<T>::shmRealloc(size_t) [with T = std::pair<long int, long int>; size_t = long unsigned int]':
+shmvector.hh:282:5:   required from 'void ShmVector<T>::resize(size_t) [with T = std::pair<long int, long int>; size_t = long unsigned int]'
+  282 |     shmRealloc(c);
+      |     ^~~~~~~~~~
+sequence.cc:1110:17:   required from here
+ 1110 |   subSeqs.resize(binseq.regionSizes[0]);
+      |   ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
+shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<long int, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
+  225 |       memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity));
+      |       ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair<long int, long int>' declared here
+  284 |     struct pair
+      |            ^~~~
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-random.cc
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-sample.cc
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc
+cgr.cc: In member function 'void Cgr::merge(Cgr&)':
+cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable]
+  140 |   int redist=(unsigned long)(rez*rez)<=seedcount;
+      |       ^~~~~~
+cgr.cc: In member function 'bool Cgr::savePNG(std::string)':
+cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable]
+  288 |   int res;
+      |       ^~~
+cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
+cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
+  435 |   int wordwidth=1;
+      |       ^~~~~~~~~
 binseq.cc: In member function 'bool SequenceBinary::save(std::string)':
 binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
    70 |   }catch(ofstream::failure e){
@@ -1368,48 +1416,7 @@
 /usr/include/c++/14/bits/stl_pair.h:284:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<long unsigned int, long unsigned int> >, std::pair<long unsigned int, long unsigned int> >::value_type' {aka 'struct std::pair<long unsigned int, long unsigned int>'} declared here
   284 |     struct pair
       |            ^~~~
-cgr.cc: In member function 'void Cgr::merge(Cgr&)':
-cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable]
-  140 |   int redist=(unsigned long)(rez*rez)<=seedcount;
-      |       ^~~~~~
-cgr.cc: In member function 'bool Cgr::savePNG(std::string)':
-cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable]
-  288 |   int res;
-      |       ^~~
-cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
-cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
-  435 |   int wordwidth=1;
-      |       ^~~~~~~~~
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-compare.cc
-cgr-sample.cc: In function 'int main(int, char**)':
-cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
-   54 |   bool repeatmask=false,save=false;
-      |        ^~~~~~~~~~
-murasaki_mpi.cc: In function 'void mpi_types_init()':
-murasaki_mpi.cc:107:18: warning: 'msg' may be used uninitialized [-Wmaybe-uninitialized]
-  107 |   MPI_Get_address(&msg.key,disp);
-      |   ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
-In file included from murasaki_mpi.cc:29:
-/usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:1677:20: note: by argument 1 of type 'const void*' to 'int MPI_Get_address(const void*, MPI_Aint*)' declared here
- 1677 | OMPI_DECLSPEC  int MPI_Get_address(const void *location, MPI_Aint *address);
-      |                    ^~~~~~~~~~~~~~~
-murasaki_mpi.cc:102:19: note: 'msg' declared here
-  102 |   MPI_HashMessage msg;
-      |                   ^~~
-In file included from ecolist.h:23,
-                 from testeco.cc:20:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc
-mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-or.cc
 cgr.cc: In member function 'std::pair<long unsigned int, long unsigned int> Cgr::sampleHighLow(double, double)':
 cgr.cc:339:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
   339 |   delete alt;
@@ -1431,8 +1438,33 @@
 cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)'
   376 |   pix *alt=new pix[size];
       |                        ^
-mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.cc
-mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-and.cc
+cgr-sample.cc: In function 'int main(int, char**)':
+cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
+   54 |   bool repeatmask=false,save=false;
+      |        ^~~~~~~~~~
+In file included from ecolist.h:23,
+                 from testeco.cc:20:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+murasaki_mpi.cc: In function 'void mpi_types_init()':
+murasaki_mpi.cc:107:18: warning: 'msg' may be used uninitialized [-Wmaybe-uninitialized]
+  107 |   MPI_Get_address(&msg.key,disp);
+      |   ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
+In file included from murasaki_mpi.cc:29:
+/usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:1677:20: note: by argument 1 of type 'const void*' to 'int MPI_Get_address(const void*, MPI_Aint*)' declared here
+ 1677 | OMPI_DECLSPEC  int MPI_Get_address(const void *location, MPI_Aint *address);
+      |                    ^~~~~~~~~~~~~~~
+murasaki_mpi.cc:102:19: note: 'msg' declared here
+  102 |   MPI_HashMessage msg;
+      |                   ^~~
 cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)':
 cgr.cc:557:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized]
   557 |   if(data.size()<(uint)(height*width))
@@ -1446,7 +1478,7 @@
 cgr.cc:493:13: note: 'height' was declared here
   493 |   int width,height;
       |             ^~~~~~
-mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-best.cc
+mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc
 cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
 cgr.cc:485:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized]
   485 |   if(data.size()<(uint)(height*width))
@@ -1460,26 +1492,30 @@
 cgr.cc:426:13: note: 'height' was declared here
   426 |   int width,height;
       |             ^~~~~~
+mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-or.cc
+mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.cc
+mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-and.cc
+mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-best.cc
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-coverage.cc
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o   -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o   -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
-align-coverage.cc: In function 'int main(int, char**)':
-align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable]
-  148 |     bool seqStats=true;
-      |          ^~~~~~~~
-mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list<std::pair<long unsigned int, std::__cxx11::basic_string<char> > >&, std::string)':
 getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=]
   153 |     }catch(bad_lexical_cast e){
       |                             ^
+mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
+align-coverage.cc: In function 'int main(int, char**)':
+align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable]
+  148 |     bool seqStats=true;
+      |          ^~~~~~~~
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o   -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o  genopts.o   -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o   -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
-mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
+mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
@@ -1517,6 +1553,19 @@
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c scoring.cc
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c openhash.cc
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c genopts.cc
+In file included from ecolist.h:23,
+                 from ecohash.h:29,
+                 from ecohash.cc:26:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 In file included from murasaki.h:24,
                  from dinkymath.cc:27:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -1533,6 +1582,17 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+In file included from msethash.cc:25:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)':
 dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
    40 |   int last=0;
@@ -1542,20 +1602,22 @@
    53 |   int last=0;
       |       ^~~~
 In file included from murasaki.h:24,
-                 from sequence.cc:28:
+                 from murasaki.cc:37:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
       |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from murasaki.cc:29:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from ecolist.h:23,
-                 from ecohash.h:29,
-                 from ecohash.cc:26:
+In file included from options.h:28,
+                 from options.cc:26:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
       |                   ^~~~~~~~~~~~~~~
@@ -1566,22 +1628,8 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)':
-sequence.cc:1113:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 1113 |   memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]);
-      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_algobase.h:64,
-                 from /usr/include/c++/14/bits/stl_tree.h:63:
-/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
-  284 |     struct pair
-      |            ^~~~
-sequence.cc:1114:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 1114 |   memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]);
-      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
-  284 |     struct pair
-      |            ^~~~
-In file included from msethash.cc:25:
+In file included from murasaki.h:24,
+                 from arrayhash.cc:28:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
       |                   ^~~~~~~~~~~~~~~
@@ -1593,26 +1641,20 @@
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from murasaki.h:24,
-                 from murasaki.cc:37:
+                 from sequence.cc:28:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
       |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from murasaki.cc:29:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
-sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
- 3332 |   SeqPos shortest=0,shortlen=length(spaces[0]);
-      |          ^~~~~~~~
-In file included from murasaki.h:24,
-                 from scoring.cc:27:
+In file included from ecolist.h:23,
+                 from openhash.h:29,
+                 from openhash.cc:26:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
       |                   ^~~~~~~~~~~~~~~
@@ -1623,8 +1665,23 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)':
+sequence.cc:1113:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
+ 1113 |   memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]);
+      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_algobase.h:64,
+                 from /usr/include/c++/14/bits/stl_tree.h:63:
+/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
+  284 |     struct pair
+      |            ^~~~
+sequence.cc:1114:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
+ 1114 |   memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]);
+      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
+  284 |     struct pair
+      |            ^~~~
 In file included from murasaki.h:24,
-                 from arrayhash.cc:28:
+                 from scoring.cc:27:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
       |                   ^~~~~~~~~~~~~~~
@@ -1635,38 +1692,6 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from sequence.cc:41:
-hashing.h: In instantiation of 'SBox<T>::SBox(int) [with T = short unsigned int]':
-sequence.cc:162:29:   required from here
-  162 |     sbox=new SBoxT(hash_bits);
-      |                             ^
-hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
-   56 |       random_shuffle(boxes[b],boxes[b]+boxsize);
-      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/algorithm:61,
-                 from /usr/include/boost/regex/v5/regex_workaround.hpp:23,
-                 from /usr/include/boost/regex/v5/regex.hpp:29,
-                 from /usr/include/boost/regex.hpp:34,
-                 from seqread.h:33,
-                 from binseq.hh:31,
-                 from sequence.h:32:
-/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here
- 4491 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
-      |     ^~~~~~~~~~~~~~
-In file included from sequence.h:44:
-shmvector.hh: In instantiation of 'void ShmVector<T>::shmRealloc(size_t) [with T = std::pair<long int, long int>; size_t = long unsigned int]':
-shmvector.hh:282:5:   required from 'void ShmVector<T>::resize(size_t) [with T = std::pair<long int, long int>; size_t = long unsigned int]'
-  282 |     shmRealloc(c);
-      |     ^~~~~~~~~~
-sequence.cc:1110:17:   required from here
- 1110 |   subSeqs.resize(binseq.regionSizes[0]);
-      |   ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
-shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<long int, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
-  225 |       memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity));
-      |       ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair<long int, long int>' declared here
-  284 |     struct pair
-      |            ^~~~
 seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)':
 seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations]
   264 |     stitchPath=stitchfile.branch_path();
@@ -1676,19 +1701,6 @@
  1129 |     path branch_path() const { return parent_path(); }
       |          ^~~~~~~~~~~
 In file included from ecolist.h:23,
-                 from openhash.h:29,
-                 from openhash.cc:26:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from ecolist.h:23,
                  from ecolist.cc:20:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
@@ -1700,12 +1712,6 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-ecolist.cc:467:26: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  467 | struct less_map : public binary_function<const Ecolist::val_type&,const Ecolist::val_type&,bool> {
-      |                          ^~~~~~~~~~~~~~~
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
 murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
 murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
  1008 |   bool revZero=false;
@@ -1724,22 +1730,52 @@
 /usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here
  4491 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
       |     ^~~~~~~~~~~~~~
-In file included from options.h:28,
-                 from options.cc:26:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
+ecolist.cc:467:26: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  467 | struct less_map : public binary_function<const Ecolist::val_type&,const Ecolist::val_type&,bool> {
+      |                          ^~~~~~~~~~~~~~~
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c binseq.cc
+sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
+sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
+ 3332 |   SeqPos shortest=0,shortlen=length(spaces[0]);
+      |          ^~~~~~~~
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-image.cc
+In file included from sequence.cc:41:
+hashing.h: In instantiation of 'SBox<T>::SBox(int) [with T = short unsigned int]':
+sequence.cc:162:29:   required from here
+  162 |     sbox=new SBoxT(hash_bits);
+      |                             ^
+hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
+   56 |       random_shuffle(boxes[b],boxes[b]+boxsize);
+      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/algorithm:61,
+                 from /usr/include/boost/regex/v5/regex_workaround.hpp:23,
+                 from /usr/include/boost/regex/v5/regex.hpp:29,
+                 from /usr/include/boost/regex.hpp:34,
+                 from seqread.h:33,
+                 from binseq.hh:31,
+                 from sequence.h:32:
+/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here
+ 4491 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
+      |     ^~~~~~~~~~~~~~
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr.cc
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-compare.cc
+In file included from sequence.h:44:
+shmvector.hh: In instantiation of 'void ShmVector<T>::shmRealloc(size_t) [with T = std::pair<long int, long int>; size_t = long unsigned int]':
+shmvector.hh:282:5:   required from 'void ShmVector<T>::resize(size_t) [with T = std::pair<long int, long int>; size_t = long unsigned int]'
+  282 |     shmRealloc(c);
+      |     ^~~~~~~~~~
+sequence.cc:1110:17:   required from here
+ 1110 |   subSeqs.resize(binseq.regionSizes[0]);
+      |   ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
+shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<long int, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
+  225 |       memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity));
+      |       ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair<long int, long int>' declared here
+  284 |     struct pair
+      |            ^~~~
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-random.cc
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-sample.cc
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c testeco.cc
@@ -1789,6 +1825,11 @@
 /usr/include/c++/14/bits/stl_pair.h:284:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<long unsigned int, long unsigned int> >, std::pair<long unsigned int, long unsigned int> >::value_type' {aka 'struct std::pair<long unsigned int, long unsigned int>'} declared here
   284 |     struct pair
       |            ^~~~
+cgr-sample.cc: In function 'int main(int, char**)':
+cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
+   54 |   bool repeatmask=false,save=false;
+      |        ^~~~~~~~~~
+g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c alignments.cc
 In file included from ecolist.h:23,
                  from testeco.cc:20:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -1801,10 +1842,6 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-cgr-sample.cc: In function 'int main(int, char**)':
-cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
-   54 |   bool repeatmask=false,save=false;
-      |        ^~~~~~~~~~
 cgr.cc: In member function 'std::pair<long unsigned int, long unsigned int> Cgr::sampleHighLow(double, double)':
 cgr.cc:339:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
   339 |   delete alt;
@@ -1826,7 +1863,8 @@
 cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)'
   376 |   pix *alt=new pix[size];
       |                        ^
-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c alignments.cc
+g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-or.cc
+g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c geneparse.cc
 cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)':
 cgr.cc:557:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized]
   557 |   if(data.size()<(uint)(height*width))
@@ -1840,9 +1878,8 @@
 cgr.cc:493:13: note: 'height' was declared here
   493 |   int width,height;
       |             ^~~~~~
-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-or.cc
-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c geneparse.cc
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-and.cc
+g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-best.cc
 cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
 cgr.cc:485:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized]
   485 |   if(data.size()<(uint)(height*width))
@@ -1856,7 +1893,6 @@
 cgr.cc:426:13: note: 'height' was declared here
   426 |   int width,height;
       |             ^~~~~~
-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-best.cc
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-coverage.cc
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c getsegments.cc
 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c mbfa.cc
@@ -1949,17 +1985,17 @@
    dh_shlibdeps -a
    dh_installdeb
    dh_gencontrol
-dpkg-gencontrol: warning: Depends field of package murasaki-common: substitution variable ${misc:perl} used, but is not defined
 dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined
+dpkg-gencontrol: warning: Depends field of package murasaki-common: substitution variable ${misc:perl} used, but is not defined
 dpkg-gencontrol: warning: package murasaki-common: substitution variable ${perl:Depends} unused, but is defined
 dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined
    dh_md5sums
    dh_builddeb
 dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-14_arm64.deb'.
-dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-14_arm64.deb'.
-dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-14_arm64.deb'.
 dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-14_arm64.deb'.
+dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-14_arm64.deb'.
 dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-14_all.deb'.
+dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-14_arm64.deb'.
  dpkg-genbuildinfo --build=binary -O../murasaki_1.68.6-14_arm64.buildinfo
  dpkg-genchanges --build=binary -O../murasaki_1.68.6-14_arm64.changes
 dpkg-genchanges: info: binary-only upload (no source code included)
@@ -1967,12 +2003,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: not including original source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/2935611/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/2935611/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/2349788 and its subdirectories
-I: Current time: Tue Dec 24 10:16:39 -12 2024
-I: pbuilder-time-stamp: 1735078599
+I: removing directory /srv/workspace/pbuilder/2935611 and its subdirectories
+I: Current time: Wed Dec 25 12:20:29 +14 2024
+I: pbuilder-time-stamp: 1735078829