--- /srv/reproducible-results/rbuild-debian/r-b-build.vNBeAiMR/b1/htsjdk_3.0.4+dfsg-2_amd64.changes
+++ /srv/reproducible-results/rbuild-debian/r-b-build.vNBeAiMR/b2/htsjdk_3.0.4+dfsg-2_amd64.changes
├── Files
│ @@ -1,3 +1,3 @@
│  
│ - ade76d3e47ac7c87ff978658c9a13b8a 1039096 doc optional libhtsjdk-java-doc_3.0.4+dfsg-2_all.deb
│ + 96b25c388cdab2d1f1d20ddaf510edab 1039072 doc optional libhtsjdk-java-doc_3.0.4+dfsg-2_all.deb
│   3375151baf60e103b9d2d83d44ecd7ab 1813244 java optional libhtsjdk-java_3.0.4+dfsg-2_all.deb
├── libhtsjdk-java-doc_3.0.4+dfsg-2_all.deb
│ ├── file list
│ │ @@ -1,3 +1,3 @@
│ │  -rw-r--r--   0        0        0        4 2023-01-24 03:16:14.000000 debian-binary
│ │  -rw-r--r--   0        0        0    26364 2023-01-24 03:16:14.000000 control.tar.xz
│ │ --rw-r--r--   0        0        0  1012540 2023-01-24 03:16:14.000000 data.tar.xz
│ │ +-rw-r--r--   0        0        0  1012516 2023-01-24 03:16:14.000000 data.tar.xz
│ ├── control.tar.xz
│ │ ├── control.tar
│ │ │ ├── ./control
│ │ │ │ @@ -1,13 +1,13 @@
│ │ │ │  Package: libhtsjdk-java-doc
│ │ │ │  Source: htsjdk
│ │ │ │  Version: 3.0.4+dfsg-2
│ │ │ │  Architecture: all
│ │ │ │  Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
│ │ │ │ -Installed-Size: 25095
│ │ │ │ +Installed-Size: 25093
│ │ │ │  Section: doc
│ │ │ │  Priority: optional
│ │ │ │  Multi-Arch: foreign
│ │ │ │  Homepage: https://samtools.github.io/htsjdk/
│ │ │ │  Description: Documentation for the java HTSJDK library
│ │ │ │   HTSJDK is an implementation of a unified Java library for accessing common
│ │ │ │   file formats, such as SAM (Sequence Alignment/Map) and VCF, used for
│ │ │ ├── ./md5sums
│ │ │ │ ├── ./md5sums
│ │ │ │ │┄ Files differ
│ ├── data.tar.xz
│ │ ├── data.tar
│ │ │ ├── file list
│ │ │ │ @@ -1079,22 +1079,22 @@
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    10867 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    32388 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    29765 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     9958 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFTextTransformer.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    28441 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFUtils.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    14736 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-summary.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    13991 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-tree.html
│ │ │ │ --rw-r--r--   0 root         (0) root         (0)  3125889 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/index-all.html
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)  3125124 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/index-all.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    25187 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/index.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1498 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/jquery-ui.overrides.css
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/legal/
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1522 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/legal/ASSEMBLY_EXCEPTION
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     2936 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/legal/jquery.md
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1870 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/legal/jqueryUI.md
│ │ │ │ --rw-r--r--   0 root         (0) root         (0)   801891 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/member-search-index.js
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)   801636 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/member-search-index.js
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)       45 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/module-search-index.js
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      826 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/overview-summary.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)   237418 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/overview-tree.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     3152 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/package-search-index.js
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/resources/
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      499 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/resources/glass.png
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      394 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/resources/x.png
│ │ │ ├── ./usr/share/doc/libhtsjdk-java/api/index-all.html
│ │ │ │ @@ -6640,25 +6640,25 @@
│ │ │ │  <div class="block">Scans the classpath for classes within the specified package and sub-packages that
│ │ │ │   extend the parentType.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/cram/CRAIIndex.html#find(java.util.List,int,int,int)" class="member-name-link">find(List&lt;CRAIEntry&gt;, int, int, int)</a> - Static method in class htsjdk.samtools.cram.<a href="htsjdk/samtools/cram/CRAIIndex.html" title="class in htsjdk.samtools.cram">CRAIIndex</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Currently unused, but retained for the native rai query implementation</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#findAndLoadSequenceDictionary(java.nio.file.Path)" class="member-name-link">findAndLoadSequenceDictionary(Path)</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#findAndLoadSequenceDictionary(java.nio.file.Path)" class="member-name-link">findAndLoadSequenceDictionary(Path)</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Attempts to find and load the sequence dictionary if present.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/util/IntervalTree.html#findByIndex(int)" class="member-name-link">findByIndex(int)</a> - Method in class htsjdk.samtools.util.<a href="htsjdk/samtools/util/IntervalTree.html" title="class in htsjdk.samtools.util">IntervalTree</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Find the nth interval in the tree.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SAMFlag.html#findByName(java.lang.String)" class="member-name-link">findByName(String)</a> - Static method in enum class htsjdk.samtools.<a href="htsjdk/samtools/SAMFlag.html" title="enum class in htsjdk.samtools">SAMFlag</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#findFastaIndex(java.nio.file.Path)" class="member-name-link">findFastaIndex(Path)</a> - Static method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#findFastaIndex(java.nio.file.Path)" class="member-name-link">findFastaIndex(Path)</a> - Static method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SamFiles.html#findIndex(java.io.File)" class="member-name-link">findIndex(File)</a> - Static method in class htsjdk.samtools.<a href="htsjdk/samtools/SamFiles.html" title="class in htsjdk.samtools">SamFiles</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Finds the index file associated with the provided SAM file.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SamFiles.html#findIndex(java.nio.file.Path)" class="member-name-link">findIndex(Path)</a> - Static method in class htsjdk.samtools.<a href="htsjdk/samtools/SamFiles.html" title="class in htsjdk.samtools">SamFiles</a></dt>
│ │ │ │  <dd>
│ │ │ │ @@ -6670,23 +6670,23 @@
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/tribble/index/interval/IntervalTree.html#findOverlapping(htsjdk.tribble.index.interval.Interval)" class="member-name-link">findOverlapping(Interval)</a> - Method in class htsjdk.tribble.index.interval.<a href="htsjdk/tribble/index/interval/IntervalTree.html" title="class in htsjdk.tribble.index.interval">IntervalTree</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/util/TrimmingUtil.html#findQualityTrimPoint(byte%5B%5D,int)" class="member-name-link">findQualityTrimPoint(byte[], int)</a> - Static method in class htsjdk.samtools.util.<a href="htsjdk/samtools/util/TrimmingUtil.html" title="class in htsjdk.samtools.util">TrimmingUtil</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Implements phred-style quality trimming.</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#findRequiredFastaIndexFile(java.nio.file.Path)" class="member-name-link">findRequiredFastaIndexFile(Path)</a> - Static method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#findRequiredFastaIndexFile(java.nio.file.Path)" class="member-name-link">findRequiredFastaIndexFile(Path)</a> - Static method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#findSequenceDictionary(java.io.File)" class="member-name-link">findSequenceDictionary(File)</a> - Static method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#findSequenceDictionary(java.io.File)" class="member-name-link">findSequenceDictionary(File)</a> - Static method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="deprecation-block"><span class="deprecated-label">Deprecated.</span>
│ │ │ │  <div class="deprecation-comment">use findSequenceDictionary(Path) instead.</div>
│ │ │ │  </div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#findSequenceDictionary(java.nio.file.Path)" class="member-name-link">findSequenceDictionary(Path)</a> - Static method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#findSequenceDictionary(java.nio.file.Path)" class="member-name-link">findSequenceDictionary(Path)</a> - Static method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Attempts to locate the sequence dictionary file adjacent to the reference fasta file.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SAMUtils.html#findVirtualOffsetOfFirstRecordInBam(htsjdk.samtools.seekablestream.SeekableStream)" class="member-name-link">findVirtualOffsetOfFirstRecordInBam(SeekableStream)</a> - Static method in class htsjdk.samtools.<a href="htsjdk/samtools/SAMUtils.html" title="class in htsjdk.samtools">SAMUtils</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Returns the virtual file offset of the first record in a BAM file - i.e.</div>
│ │ │ │  </dd>
│ │ │ │ @@ -7377,15 +7377,15 @@
│ │ │ │  <dd>
│ │ │ │  <div class="block">Retrieves the bin associated with the given key.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/util/ResourceLimitedMap.html#get(Key)" class="member-name-link">get(Key)</a> - Method in class htsjdk.samtools.util.<a href="htsjdk/samtools/util/ResourceLimitedMap.html" title="class in htsjdk.samtools.util">ResourceLimitedMap</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Return an existing value, or create a new one if necessary.</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#getAbsolutePath()" class="member-name-link">getAbsolutePath()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#getAbsolutePath()" class="member-name-link">getAbsolutePath()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Returns the full path to the reference file.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/DownsamplingIterator.html#getAcceptedCount()" class="member-name-link">getAcceptedCount()</a> - Method in class htsjdk.samtools.<a href="htsjdk/samtools/DownsamplingIterator.html" title="class in htsjdk.samtools">DownsamplingIterator</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Returns the number of records returned since creation of the last call to resetStatistics.</div>
│ │ │ │  </dd>
│ │ │ │ @@ -9343,15 +9343,15 @@
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/CRAMFileReader.html#getIndex()" class="member-name-link">getIndex()</a> - Method in class htsjdk.samtools.<a href="htsjdk/samtools/CRAMFileReader.html" title="class in htsjdk.samtools">CRAMFileReader</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/HtsgetBAMFileReader.html#getIndex()" class="member-name-link">getIndex()</a> - Method in class htsjdk.samtools.<a href="htsjdk/samtools/HtsgetBAMFileReader.html" title="class in htsjdk.samtools">HtsgetBAMFileReader</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Always null as htsget sources do not have indices</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#getIndex()" class="member-name-link">getIndex()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#getIndex()" class="member-name-link">getIndex()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SamReader.Indexing.html#getIndex()" class="member-name-link">getIndex()</a> - Method in interface htsjdk.samtools.<a href="htsjdk/samtools/SamReader.Indexing.html" title="interface in htsjdk.samtools">SamReader.Indexing</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Retrieves the index for the given file type.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SamReader.PrimitiveSamReader.html#getIndex()" class="member-name-link">getIndex()</a> - Method in interface htsjdk.samtools.<a href="htsjdk/samtools/SamReader.PrimitiveSamReader.html" title="interface in htsjdk.samtools">SamReader.PrimitiveSamReader</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ @@ -10247,15 +10247,15 @@
│ │ │ │  &nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/seekablestream/UserPasswordInput.html#getPassword()" class="member-name-link">getPassword()</a> - Method in interface htsjdk.samtools.seekablestream.<a href="htsjdk/samtools/seekablestream/UserPasswordInput.html" title="interface in htsjdk.samtools.seekablestream">UserPasswordInput</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/beta/plugin/HtsVersion.html#getPatchVersion()" class="member-name-link">getPatchVersion()</a> - Method in class htsjdk.beta.plugin.<a href="htsjdk/beta/plugin/HtsVersion.html" title="class in htsjdk.beta.plugin">HtsVersion</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Get the patch version integer for this version.</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#getPath()" class="member-name-link">getPath()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#getPath()" class="member-name-link">getPath()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Returns the path to the reference file.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/util/IOUtil.html#getPath(java.lang.String)" class="member-name-link">getPath(String)</a> - Static method in class htsjdk.samtools.util.<a href="htsjdk/samtools/util/IOUtil.html" title="class in htsjdk.samtools.util">IOUtil</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Converts the given URI to a <a href="file:///usr/share/doc/default-jdk/api/java.base/java/nio/file/Path.html" title="class or interface in java.nio.file" class="external-link"><code>Path</code></a> object.</div>
│ │ │ │  </dd>
│ │ │ │ @@ -11086,15 +11086,15 @@
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SAMSequenceDictionary.html#getSequence(int)" class="member-name-link">getSequence(int)</a> - Method in class htsjdk.samtools.<a href="htsjdk/samtools/SAMSequenceDictionary.html" title="class in htsjdk.samtools">SAMSequenceDictionary</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/reference/FastaSequenceFile.html#getSequence(java.lang.String)" class="member-name-link">getSequence(String)</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/FastaSequenceFile.html" title="class in htsjdk.samtools.reference">FastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">default implementation -- override if index is supported</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#getSequence(java.lang.String)" class="member-name-link">getSequence(String)</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#getSequence(java.lang.String)" class="member-name-link">getSequence(String)</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Retrieves the complete sequence described by this contig.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/reference/ReferenceSequenceFile.html#getSequence(java.lang.String)" class="member-name-link">getSequence(String)</a> - Method in interface htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/ReferenceSequenceFile.html" title="interface in htsjdk.samtools.reference">ReferenceSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Retrieves the complete sequence described by this contig.</div>
│ │ │ │  </dd>
│ │ │ │ @@ -11102,15 +11102,15 @@
│ │ │ │  <dd>
│ │ │ │  <div class="block">Look up sequence record by name.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SAMSequenceDictionary.html#getSequence(java.lang.String)" class="member-name-link">getSequence(String)</a> - Method in class htsjdk.samtools.<a href="htsjdk/samtools/SAMSequenceDictionary.html" title="class in htsjdk.samtools">SAMSequenceDictionary</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/sra/SRAIndexedSequenceFile.html#getSequence(java.lang.String)" class="member-name-link">getSequence(String)</a> - Method in class htsjdk.samtools.sra.<a href="htsjdk/samtools/sra/SRAIndexedSequenceFile.html" title="class in htsjdk.samtools.sra">SRAIndexedSequenceFile</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#getSequenceDictionary()" class="member-name-link">getSequenceDictionary()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#getSequenceDictionary()" class="member-name-link">getSequenceDictionary()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Returns the list of sequence records associated with the reference sequence if found
│ │ │ │   otherwise null.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/reference/ReferenceSequenceFile.html#getSequenceDictionary()" class="member-name-link">getSequenceDictionary()</a> - Method in interface htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/ReferenceSequenceFile.html" title="interface in htsjdk.samtools.reference">ReferenceSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Must return a sequence dictionary with at least the following fields completed
│ │ │ │ @@ -11352,15 +11352,15 @@
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SAMFileWriterImpl.html#getSortOrder()" class="member-name-link">getSortOrder()</a> - Method in class htsjdk.samtools.<a href="htsjdk/samtools/SAMFileWriterImpl.html" title="class in htsjdk.samtools">SAMFileWriterImpl</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Must be called after calling setHeader().</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SAMSortOrderChecker.html#getSortOrder()" class="member-name-link">getSortOrder()</a> - Method in class htsjdk.samtools.<a href="htsjdk/samtools/SAMSortOrderChecker.html" title="class in htsjdk.samtools">SAMSortOrderChecker</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#getSource()" class="member-name-link">getSource()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#getSource()" class="member-name-link">getSource()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Returns the named source of the reference file.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SAMValidationError.html#getSource()" class="member-name-link">getSource()</a> - Method in class htsjdk.samtools.<a href="htsjdk/samtools/SAMValidationError.html" title="class in htsjdk.samtools">SAMValidationError</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/seekablestream/ByteArraySeekableStream.html#getSource()" class="member-name-link">getSource()</a> - Method in class htsjdk.samtools.seekablestream.<a href="htsjdk/samtools/seekablestream/ByteArraySeekableStream.html" title="class in htsjdk.samtools.seekablestream">ByteArraySeekableStream</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ @@ -11527,15 +11527,15 @@
│ │ │ │  <dd>
│ │ │ │  <div class="block">Search for the INFO=SVTYPE and return the type of Structural Variant</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/reference/FastaSequenceFile.html#getSubsequenceAt(java.lang.String,long,long)" class="member-name-link">getSubsequenceAt(String, long, long)</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/FastaSequenceFile.html" title="class in htsjdk.samtools.reference">FastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">default implementation -- override if index is supported</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#getSubsequenceAt(java.lang.String,long,long)" class="member-name-link">getSubsequenceAt(String, long, long)</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#getSubsequenceAt(java.lang.String,long,long)" class="member-name-link">getSubsequenceAt(String, long, long)</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Gets the subsequence of the contig in the range [start,stop]</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/reference/ReferenceSequenceFile.html#getSubsequenceAt(java.lang.String,long,long)" class="member-name-link">getSubsequenceAt(String, long, long)</a> - Method in interface htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/ReferenceSequenceFile.html" title="interface in htsjdk.samtools.reference">ReferenceSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Gets the subsequence of the contig in the range [start,stop]</div>
│ │ │ │  </dd>
│ │ │ │ @@ -14625,15 +14625,15 @@
│ │ │ │  <dd>
│ │ │ │  <div class="block">Returns true if the operator is a Skipped Region Insertion or Deletion operator</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/reference/FastaSequenceFile.html#isIndexed()" class="member-name-link">isIndexed()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/FastaSequenceFile.html" title="class in htsjdk.samtools.reference">FastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">default implementation -- override if index is supported</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#isIndexed()" class="member-name-link">isIndexed()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#isIndexed()" class="member-name-link">isIndexed()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/reference/ReferenceSequenceFile.html#isIndexed()" class="member-name-link">isIndexed()</a> - Method in interface htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/ReferenceSequenceFile.html" title="interface in htsjdk.samtools.reference">ReferenceSequenceFile</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/sra/SRAIndexedSequenceFile.html#isIndexed()" class="member-name-link">isIndexed()</a> - Method in class htsjdk.samtools.sra.<a href="htsjdk/samtools/sra/SRAIndexedSequenceFile.html" title="class in htsjdk.samtools.sra">SRAIndexedSequenceFile</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/util/Lazy.html#isInitialized()" class="member-name-link">isInitialized()</a> - Method in class htsjdk.samtools.util.<a href="htsjdk/samtools/util/Lazy.html" title="class in htsjdk.samtools.util">Lazy</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ @@ -16769,15 +16769,15 @@
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/util/ReferenceSequenceMask.html#nextPosition(int,int)" class="member-name-link">nextPosition(int, int)</a> - Method in interface htsjdk.samtools.util.<a href="htsjdk/samtools/util/ReferenceSequenceMask.html" title="interface in htsjdk.samtools.util">ReferenceSequenceMask</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.html#nextPosition(int,int)" class="member-name-link">nextPosition(int, int)</a> - Method in class htsjdk.samtools.util.<a href="htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.html" title="class in htsjdk.samtools.util">WholeGenomeReferenceSequenceMask</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#nextSequence()" class="member-name-link">nextSequence()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#nextSequence()" class="member-name-link">nextSequence()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Gets the next sequence if available, or null if not present.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/reference/FastaSequenceFile.html#nextSequence()" class="member-name-link">nextSequence()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/FastaSequenceFile.html" title="class in htsjdk.samtools.reference">FastaSequenceFile</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/reference/ReferenceSequenceFile.html#nextSequence()" class="member-name-link">nextSequence()</a> - Method in interface htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/ReferenceSequenceFile.html" title="interface in htsjdk.samtools.reference">ReferenceSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │ @@ -19541,15 +19541,15 @@
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/cram/io/CountingInputStream.html#reset()" class="member-name-link">reset()</a> - Method in class htsjdk.samtools.cram.io.<a href="htsjdk/samtools/cram/io/CountingInputStream.html" title="class in htsjdk.samtools.cram.io">CountingInputStream</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/cram/io/CRC32InputStream.html#reset()" class="member-name-link">reset()</a> - Method in class htsjdk.samtools.cram.io.<a href="htsjdk/samtools/cram/io/CRC32InputStream.html" title="class in htsjdk.samtools.cram.io">CRC32InputStream</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/cram/io/DefaultBitInputStream.html#reset()" class="member-name-link">reset()</a> - Method in class htsjdk.samtools.cram.io.<a href="htsjdk/samtools/cram/io/DefaultBitInputStream.html" title="class in htsjdk.samtools.cram.io">DefaultBitInputStream</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#reset()" class="member-name-link">reset()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#reset()" class="member-name-link">reset()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Reset the iterator over the index.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/reference/FastaSequenceFile.html#reset()" class="member-name-link">reset()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/FastaSequenceFile.html" title="class in htsjdk.samtools.reference">FastaSequenceFile</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/reference/ReferenceSequenceFile.html#reset()" class="member-name-link">reset()</a> - Method in interface htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/ReferenceSequenceFile.html" title="interface in htsjdk.samtools.reference">ReferenceSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │ @@ -20516,15 +20516,15 @@
│ │ │ │  <dd>
│ │ │ │  <div class="block">Construct a SAMValidationError with possibly-known record number.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SAMValidationError.Severity.html" class="type-name-link" title="enum class in htsjdk.samtools">SAMValidationError.Severity</a> - Enum Class in <a href="htsjdk/samtools/package-summary.html">htsjdk.samtools</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SAMValidationError.Type.html" class="type-name-link" title="enum class in htsjdk.samtools">SAMValidationError.Type</a> - Enum Class in <a href="htsjdk/samtools/package-summary.html">htsjdk.samtools</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#sanityCheckDictionaryAgainstIndex(java.lang.String,htsjdk.samtools.SAMSequenceDictionary,htsjdk.samtools.reference.FastaSequenceIndex)" class="member-name-link">sanityCheckDictionaryAgainstIndex(String, SAMSequenceDictionary, FastaSequenceIndex)</a> - Static method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#sanityCheckDictionaryAgainstIndex(java.lang.String,htsjdk.samtools.SAMSequenceDictionary,htsjdk.samtools.reference.FastaSequenceIndex)" class="member-name-link">sanityCheckDictionaryAgainstIndex(String, SAMSequenceDictionary, FastaSequenceIndex)</a> - Static method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Do some basic checking to make sure the dictionary and the index match.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/SAMTestUtil.SanityCheckFailedException.html#%3Cinit%3E(java.lang.String)" class="member-name-link">SanityCheckFailedException(String)</a> - Constructor for exception htsjdk.samtools.<a href="htsjdk/samtools/SAMTestUtil.SanityCheckFailedException.html" title="class in htsjdk.samtools">SAMTestUtil.SanityCheckFailedException</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/util/FileExtensions.html#SBI" class="member-name-link">SBI</a> - Static variable in class htsjdk.samtools.util.<a href="htsjdk/samtools/util/FileExtensions.html" title="class in htsjdk.samtools.util">FileExtensions</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ @@ -23599,15 +23599,15 @@
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/metrics/StringHeader.html#toString()" class="member-name-link">toString()</a> - Method in class htsjdk.samtools.metrics.<a href="htsjdk/samtools/metrics/StringHeader.html" title="class in htsjdk.samtools.metrics">StringHeader</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/metrics/VersionHeader.html#toString()" class="member-name-link">toString()</a> - Method in class htsjdk.samtools.metrics.<a href="htsjdk/samtools/metrics/VersionHeader.html" title="class in htsjdk.samtools.metrics">VersionHeader</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <dt><a href="htsjdk/samtools/QueryInterval.html#toString()" class="member-name-link">toString()</a> - Method in class htsjdk.samtools.<a href="htsjdk/samtools/QueryInterval.html" title="class in htsjdk.samtools">QueryInterval</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#toString()" class="member-name-link">toString()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">BlockCompressedIndexedFastaSequenceFile</a></dt>
│ │ │ │ +<dt><a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#toString()" class="member-name-link">toString()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html" title="class in htsjdk.samtools.reference">IndexedFastaSequenceFile</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Returns the full path to the reference file, or the source if no path was specified.</div>
│ │ │ │  </dd>
│ │ │ │  <dt><a href="htsjdk/samtools/reference/FastaSequenceIndexEntry.html#toString()" class="member-name-link">toString()</a> - Method in class htsjdk.samtools.reference.<a href="htsjdk/samtools/reference/FastaSequenceIndexEntry.html" title="class in htsjdk.samtools.reference">FastaSequenceIndexEntry</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">For debugging.</div>
│ │ │ │  </dd>
│ │ │ │ ├── html2text {}
│ │ │ │ │ @@ -5328,22 +5328,22 @@
│ │ │ │ │    find(String,_Class<?>) - Method in class htsjdk.utils.ClassFinder
│ │ │ │ │        Scans the classpath for classes within the specified package and sub-
│ │ │ │ │        packages that extend the parentType.
│ │ │ │ │    find(List<CRAIEntry>,_int,_int,_int) - Static method in class
│ │ │ │ │    htsjdk.samtools.cram.CRAIIndex
│ │ │ │ │        Currently unused, but retained for the native rai query implementation
│ │ │ │ │    findAndLoadSequenceDictionary(Path) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Attempts to find and load the sequence dictionary if present.
│ │ │ │ │    findByIndex(int) - Method in class htsjdk.samtools.util.IntervalTree
│ │ │ │ │        Find the nth interval in the tree.
│ │ │ │ │    findByName(String) - Static method in enum class htsjdk.samtools.SAMFlag
│ │ │ │ │         
│ │ │ │ │    findFastaIndex(Path) - Static method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │         
│ │ │ │ │    findIndex(File) - Static method in class htsjdk.samtools.SamFiles
│ │ │ │ │        Finds the index file associated with the provided SAM file.
│ │ │ │ │    findIndex(Path) - Static method in class htsjdk.samtools.SamFiles
│ │ │ │ │        Finds the index file associated with the provided SAM file.
│ │ │ │ │    findLastAlignedEntry(List<CRAIEntry>) - Static method in class
│ │ │ │ │    htsjdk.samtools.cram.CRAIIndex
│ │ │ │ │ @@ -5351,22 +5351,22 @@
│ │ │ │ │    findOverlapping(Interval) - Method in class
│ │ │ │ │    htsjdk.tribble.index.interval.IntervalTree
│ │ │ │ │         
│ │ │ │ │    findQualityTrimPoint(byte[],_int) - Static method in class
│ │ │ │ │    htsjdk.samtools.util.TrimmingUtil
│ │ │ │ │        Implements phred-style quality trimming.
│ │ │ │ │    findRequiredFastaIndexFile(Path) - Static method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │         
│ │ │ │ │    findSequenceDictionary(File) - Static method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Deprecated.
│ │ │ │ │        use findSequenceDictionary(Path) instead.
│ │ │ │ │    findSequenceDictionary(Path) - Static method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Attempts to locate the sequence dictionary file adjacent to the reference
│ │ │ │ │        fasta file.
│ │ │ │ │    findVirtualOffsetOfFirstRecordInBam(SeekableStream) - Static method in class
│ │ │ │ │    htsjdk.samtools.SAMUtils
│ │ │ │ │        Returns the virtual file offset of the first record in a BAM file - i.e.
│ │ │ │ │    findVirtualOffsetOfFirstRecordInBam(File) - Static method in class
│ │ │ │ │    htsjdk.samtools.SAMUtils
│ │ │ │ │ @@ -5945,15 +5945,15 @@
│ │ │ │ │    get(String) - Method in class htsjdk.variant.variantcontext.GenotypesContext
│ │ │ │ │        Gets sample associated with this sampleName, or null if none is found
│ │ │ │ │    get(K) - Method in class htsjdk.samtools.util.Histogram
│ │ │ │ │        Retrieves the bin associated with the given key.
│ │ │ │ │    get(Key) - Method in class htsjdk.samtools.util.ResourceLimitedMap
│ │ │ │ │        Return an existing value, or create a new one if necessary.
│ │ │ │ │    getAbsolutePath() - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Returns the full path to the reference file.
│ │ │ │ │    getAcceptedCount() - Method in class htsjdk.samtools.DownsamplingIterator
│ │ │ │ │        Returns the number of records returned since creation of the last call to
│ │ │ │ │        resetStatistics.
│ │ │ │ │    getAcceptedFraction() - Method in class htsjdk.samtools.DownsamplingIterator
│ │ │ │ │        Gets the fraction of records accepted since creation or the last call to
│ │ │ │ │        resetStatistics().
│ │ │ │ │ @@ -7725,15 +7725,15 @@
│ │ │ │ │    getIndex() - Method in class htsjdk.samtools.cram.structure.ReadTag
│ │ │ │ │         
│ │ │ │ │    getIndex() - Method in class htsjdk.samtools.CRAMFileReader
│ │ │ │ │         
│ │ │ │ │    getIndex() - Method in class htsjdk.samtools.HtsgetBAMFileReader
│ │ │ │ │        Always null as htsget sources do not have indices
│ │ │ │ │    getIndex() - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │         
│ │ │ │ │    getIndex() - Method in interface htsjdk.samtools.SamReader.Indexing
│ │ │ │ │        Retrieves the index for the given file type.
│ │ │ │ │    getIndex() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
│ │ │ │ │         
│ │ │ │ │    getIndex() - Method in class
│ │ │ │ │    htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter
│ │ │ │ │ @@ -8493,15 +8493,15 @@
│ │ │ │ │         
│ │ │ │ │    getPassword() - Method in interface
│ │ │ │ │    htsjdk.samtools.seekablestream.UserPasswordInput
│ │ │ │ │         
│ │ │ │ │    getPatchVersion() - Method in class htsjdk.beta.plugin.HtsVersion
│ │ │ │ │        Get the patch version integer for this version.
│ │ │ │ │    getPath() - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Returns the path to the reference file.
│ │ │ │ │    getPath(String) - Static method in class htsjdk.samtools.util.IOUtil
│ │ │ │ │        Converts the given URI to a Path object.
│ │ │ │ │    getPaths(List<String>) - Static method in class htsjdk.samtools.util.IOUtil
│ │ │ │ │         
│ │ │ │ │    getPathToDataFile(String) - Method in interface htsjdk.tribble.FeatureCodec
│ │ │ │ │        Codecs may override this method if the file that they recognize with
│ │ │ │ │ @@ -9219,28 +9219,28 @@
│ │ │ │ │        Look up a sequence record by index.
│ │ │ │ │    getSequence(int) - Method in class htsjdk.samtools.SAMSequenceDictionary
│ │ │ │ │         
│ │ │ │ │    getSequence(String) - Method in class
│ │ │ │ │    htsjdk.samtools.reference.FastaSequenceFile
│ │ │ │ │        default implementation -- override if index is supported
│ │ │ │ │    getSequence(String) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Retrieves the complete sequence described by this contig.
│ │ │ │ │    getSequence(String) - Method in interface
│ │ │ │ │    htsjdk.samtools.reference.ReferenceSequenceFile
│ │ │ │ │        Retrieves the complete sequence described by this contig.
│ │ │ │ │    getSequence(String) - Method in class htsjdk.samtools.SAMFileHeader
│ │ │ │ │        Look up sequence record by name.
│ │ │ │ │    getSequence(String) - Method in class htsjdk.samtools.SAMSequenceDictionary
│ │ │ │ │         
│ │ │ │ │    getSequence(String) - Method in class
│ │ │ │ │    htsjdk.samtools.sra.SRAIndexedSequenceFile
│ │ │ │ │         
│ │ │ │ │    getSequenceDictionary() - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Returns the list of sequence records associated with the reference
│ │ │ │ │        sequence if found otherwise null.
│ │ │ │ │    getSequenceDictionary() - Method in interface
│ │ │ │ │    htsjdk.samtools.reference.ReferenceSequenceFile
│ │ │ │ │        Must return a sequence dictionary with at least the following fields
│ │ │ │ │        completed for each sequence: name, length.
│ │ │ │ │    getSequenceDictionary() - Method in class
│ │ │ │ │ @@ -9478,15 +9478,15 @@
│ │ │ │ │    getSortOrder() - Method in class htsjdk.samtools.SAMFileHeader
│ │ │ │ │         
│ │ │ │ │    getSortOrder() - Method in class htsjdk.samtools.SAMFileWriterImpl
│ │ │ │ │        Must be called after calling setHeader().
│ │ │ │ │    getSortOrder() - Method in class htsjdk.samtools.SAMSortOrderChecker
│ │ │ │ │         
│ │ │ │ │    getSource() - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Returns the named source of the reference file.
│ │ │ │ │    getSource() - Method in class htsjdk.samtools.SAMValidationError
│ │ │ │ │         
│ │ │ │ │    getSource() - Method in class
│ │ │ │ │    htsjdk.samtools.seekablestream.ByteArraySeekableStream
│ │ │ │ │         
│ │ │ │ │    getSource() - Method in class
│ │ │ │ │ @@ -9637,15 +9637,15 @@
│ │ │ │ │    getStructuralVariantType() - Method in class
│ │ │ │ │    htsjdk.variant.variantcontext.VariantContext
│ │ │ │ │        Search for the INFO=SVTYPE and return the type of Structural Variant
│ │ │ │ │    getSubsequenceAt(String,_long,_long) - Method in class
│ │ │ │ │    htsjdk.samtools.reference.FastaSequenceFile
│ │ │ │ │        default implementation -- override if index is supported
│ │ │ │ │    getSubsequenceAt(String,_long,_long) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Gets the subsequence of the contig in the range [start,stop]
│ │ │ │ │    getSubsequenceAt(String,_long,_long) - Method in interface
│ │ │ │ │    htsjdk.samtools.reference.ReferenceSequenceFile
│ │ │ │ │        Gets the subsequence of the contig in the range [start,stop]
│ │ │ │ │    getSubsequenceAt(String,_long,_long) - Method in class
│ │ │ │ │    htsjdk.samtools.sra.SRAIndexedSequenceFile
│ │ │ │ │         
│ │ │ │ │ @@ -12507,15 +12507,15 @@
│ │ │ │ │        convenience method for indels
│ │ │ │ │    isIndelOrSkippedRegion() - Method in enum class htsjdk.samtools.CigarOperator
│ │ │ │ │        Returns true if the operator is a Skipped Region Insertion or Deletion
│ │ │ │ │        operator
│ │ │ │ │    isIndexed() - Method in class htsjdk.samtools.reference.FastaSequenceFile
│ │ │ │ │        default implementation -- override if index is supported
│ │ │ │ │    isIndexed() - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │         
│ │ │ │ │    isIndexed() - Method in interface
│ │ │ │ │    htsjdk.samtools.reference.ReferenceSequenceFile
│ │ │ │ │         
│ │ │ │ │    isIndexed() - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile
│ │ │ │ │         
│ │ │ │ │    isInitialized() - Method in class htsjdk.samtools.util.Lazy
│ │ │ │ │ @@ -14357,15 +14357,15 @@
│ │ │ │ │    htsjdk.samtools.util.ReferenceSequenceMask
│ │ │ │ │        It is required that sequenceIndex is >= any previous sequenceIndex passed
│ │ │ │ │        to this class.
│ │ │ │ │    nextPosition(int,_int) - Method in class
│ │ │ │ │    htsjdk.samtools.util.WholeGenomeReferenceSequenceMask
│ │ │ │ │         
│ │ │ │ │    nextSequence() - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Gets the next sequence if available, or null if not present.
│ │ │ │ │    nextSequence() - Method in class htsjdk.samtools.reference.FastaSequenceFile
│ │ │ │ │         
│ │ │ │ │    nextSequence() - Method in interface
│ │ │ │ │    htsjdk.samtools.reference.ReferenceSequenceFile
│ │ │ │ │        Retrieves the next whole sequences from the file.
│ │ │ │ │    nextSequence() - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile
│ │ │ │ │ @@ -16793,16 +16793,15 @@
│ │ │ │ │         
│ │ │ │ │    reset() - Method in class htsjdk.samtools.cram.io.CountingInputStream
│ │ │ │ │         
│ │ │ │ │    reset() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
│ │ │ │ │         
│ │ │ │ │    reset() - Method in class htsjdk.samtools.cram.io.DefaultBitInputStream
│ │ │ │ │         
│ │ │ │ │ -  reset() - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  reset() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Reset the iterator over the index.
│ │ │ │ │    reset() - Method in class htsjdk.samtools.reference.FastaSequenceFile
│ │ │ │ │         
│ │ │ │ │    reset() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
│ │ │ │ │        Resets the ReferenceSequenceFile so that the next call to nextSequence()
│ │ │ │ │        will return the first sequence in the file.
│ │ │ │ │    reset() - Method in class htsjdk.samtools.seekablestream.SeekableStream
│ │ │ │ │ @@ -17603,15 +17602,15 @@
│ │ │ │ │        Construct a SAMValidationError with possibly-known record number.
│ │ │ │ │    SAMValidationError.Severity - Enum Class in htsjdk.samtools
│ │ │ │ │         
│ │ │ │ │    SAMValidationError.Type - Enum Class in htsjdk.samtools
│ │ │ │ │         
│ │ │ │ │    sanityCheckDictionaryAgainstIndex(String,_SAMSequenceDictionary,
│ │ │ │ │    FastaSequenceIndex) - Static method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Do some basic checking to make sure the dictionary and the index match.
│ │ │ │ │    SanityCheckFailedException(String) - Constructor for exception
│ │ │ │ │    htsjdk.samtools.SAMTestUtil.SanityCheckFailedException
│ │ │ │ │         
│ │ │ │ │    SBI - Static variable in class htsjdk.samtools.util.FileExtensions
│ │ │ │ │         
│ │ │ │ │    SBIIndex - Class in htsjdk.samtools
│ │ │ │ │ @@ -20415,15 +20414,15 @@
│ │ │ │ │    toString() - Method in class htsjdk.samtools.metrics.StringHeader
│ │ │ │ │         
│ │ │ │ │    toString() - Method in class htsjdk.samtools.metrics.VersionHeader
│ │ │ │ │         
│ │ │ │ │    toString() - Method in class htsjdk.samtools.QueryInterval
│ │ │ │ │         
│ │ │ │ │    toString() - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
│ │ │ │ │ +  htsjdk.samtools.reference.IndexedFastaSequenceFile
│ │ │ │ │        Returns the full path to the reference file, or the source if no path was
│ │ │ │ │        specified.
│ │ │ │ │    toString() - Method in class
│ │ │ │ │    htsjdk.samtools.reference.FastaSequenceIndexEntry
│ │ │ │ │        For debugging.
│ │ │ │ │    toString() - Method in class htsjdk.samtools.reference.ReferenceSequence
│ │ │ ├── ./usr/share/doc/libhtsjdk-java/api/member-search-index.js
│ │ │ │ ├── js-beautify {}
│ │ │ │ │ @@ -8131,29 +8131,29 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.utils",
│ │ │ │ │      "c": "ClassFinder",
│ │ │ │ │      "l": "find(String, Class<?>)",
│ │ │ │ │      "u": "find(java.lang.String,java.lang.Class)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "findAndLoadSequenceDictionary(Path)",
│ │ │ │ │      "u": "findAndLoadSequenceDictionary(java.nio.file.Path)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.util",
│ │ │ │ │      "c": "IntervalTree",
│ │ │ │ │      "l": "findByIndex(int)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SAMFlag",
│ │ │ │ │      "l": "findByName(String)",
│ │ │ │ │      "u": "findByName(java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "findFastaIndex(Path)",
│ │ │ │ │      "u": "findFastaIndex(java.nio.file.Path)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SamFiles",
│ │ │ │ │      "l": "findIndex(File)",
│ │ │ │ │      "u": "findIndex(java.io.File)"
│ │ │ │ │ @@ -8175,25 +8175,25 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.util",
│ │ │ │ │      "c": "TrimmingUtil",
│ │ │ │ │      "l": "findQualityTrimPoint(byte[], int)",
│ │ │ │ │      "u": "findQualityTrimPoint(byte[],int)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "findRequiredFastaIndexFile(Path)",
│ │ │ │ │      "u": "findRequiredFastaIndexFile(java.nio.file.Path)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "findSequenceDictionary(File)",
│ │ │ │ │      "u": "findSequenceDictionary(java.io.File)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "findSequenceDictionary(Path)",
│ │ │ │ │      "u": "findSequenceDictionary(java.nio.file.Path)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SAMUtils",
│ │ │ │ │      "l": "findVirtualOffsetOfFirstRecordInBam(File)",
│ │ │ │ │      "u": "findVirtualOffsetOfFirstRecordInBam(java.io.File)"
│ │ │ │ │ @@ -9020,15 +9020,15 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.variant.variantcontext",
│ │ │ │ │      "c": "GenotypesContext",
│ │ │ │ │      "l": "get(String)",
│ │ │ │ │      "u": "get(java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "getAbsolutePath()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "DownsamplingIterator",
│ │ │ │ │      "l": "getAcceptedCount()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │ @@ -11937,15 +11937,15 @@
│ │ │ │ │      "l": "getIndex()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "HtsgetBAMFileReader",
│ │ │ │ │      "l": "getIndex()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "getIndex()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SamReader.Indexing",
│ │ │ │ │      "l": "getIndex()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │ @@ -13222,15 +13222,15 @@
│ │ │ │ │      "l": "getPassword()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.beta.plugin",
│ │ │ │ │      "c": "HtsVersion",
│ │ │ │ │      "l": "getPatchVersion()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "getPath()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.util",
│ │ │ │ │      "c": "IOUtil",
│ │ │ │ │      "l": "getPath(String)",
│ │ │ │ │      "u": "getPath(java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │ @@ -14349,15 +14349,15 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "FastaSequenceFile",
│ │ │ │ │      "l": "getSequence(String)",
│ │ │ │ │      "u": "getSequence(java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "getSequence(String)",
│ │ │ │ │      "u": "getSequence(java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "ReferenceSequenceFile",
│ │ │ │ │      "l": "getSequence(String)",
│ │ │ │ │      "u": "getSequence(java.lang.String)"
│ │ │ │ │ @@ -14374,15 +14374,15 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.sra",
│ │ │ │ │      "c": "SRAIndexedSequenceFile",
│ │ │ │ │      "l": "getSequence(String)",
│ │ │ │ │      "u": "getSequence(java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "getSequenceDictionary()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "ReferenceSequenceFile",
│ │ │ │ │      "l": "getSequenceDictionary()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ @@ -14769,15 +14769,15 @@
│ │ │ │ │      "l": "getSortOrder()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SAMSortOrderChecker",
│ │ │ │ │      "l": "getSortOrder()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "getSource()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SAMValidationError",
│ │ │ │ │      "l": "getSource()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.seekablestream",
│ │ │ │ │ @@ -15054,15 +15054,15 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "FastaSequenceFile",
│ │ │ │ │      "l": "getSubsequenceAt(String, long, long)",
│ │ │ │ │      "u": "getSubsequenceAt(java.lang.String,long,long)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "getSubsequenceAt(String, long, long)",
│ │ │ │ │      "u": "getSubsequenceAt(java.lang.String,long,long)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "ReferenceSequenceFile",
│ │ │ │ │      "l": "getSubsequenceAt(String, long, long)",
│ │ │ │ │      "u": "getSubsequenceAt(java.lang.String,long,long)"
│ │ │ │ │ @@ -18815,15 +18815,15 @@
│ │ │ │ │      "l": "isIndelOrSkippedRegion()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "FastaSequenceFile",
│ │ │ │ │      "l": "isIndexed()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "isIndexed()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "ReferenceSequenceFile",
│ │ │ │ │      "l": "isIndexed()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.sra",
│ │ │ │ │ @@ -21493,15 +21493,15 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.util",
│ │ │ │ │      "c": "WholeGenomeReferenceSequenceMask",
│ │ │ │ │      "l": "nextPosition(int, int)",
│ │ │ │ │      "u": "nextPosition(int,int)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "nextSequence()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "FastaSequenceFile",
│ │ │ │ │      "l": "nextSequence()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ @@ -25182,15 +25182,15 @@
│ │ │ │ │      "l": "reset()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.cram.io",
│ │ │ │ │      "c": "DefaultBitInputStream",
│ │ │ │ │      "l": "reset()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "reset()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "FastaSequenceFile",
│ │ │ │ │      "l": "reset()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ @@ -26130,15 +26130,15 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SAMValidationError",
│ │ │ │ │      "l": "SAMValidationError(SAMValidationError.Type, String, String, long)",
│ │ │ │ │      "u": "%3Cinit%3E(htsjdk.samtools.SAMValidationError.Type,java.lang.String,java.lang.String,long)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "sanityCheckDictionaryAgainstIndex(String, SAMSequenceDictionary, FastaSequenceIndex)",
│ │ │ │ │      "u": "sanityCheckDictionaryAgainstIndex(java.lang.String,htsjdk.samtools.SAMSequenceDictionary,htsjdk.samtools.reference.FastaSequenceIndex)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SAMTestUtil.SanityCheckFailedException",
│ │ │ │ │      "l": "SanityCheckFailedException(String)",
│ │ │ │ │      "u": "%3Cinit%3E(java.lang.String)"
│ │ │ │ │ @@ -30221,15 +30221,15 @@
│ │ │ │ │      "l": "toString()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "QueryInterval",
│ │ │ │ │      "l": "toString()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "IndexedFastaSequenceFile",
│ │ │ │ │      "l": "toString()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "FastaSequenceIndexEntry",
│ │ │ │ │      "l": "toString()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",