--- /srv/reproducible-results/rbuild-debian/r-b-build.D63VSAQ0/b1/htsjdk_4.1.0+dfsg-1_amd64.changes
+++ /srv/reproducible-results/rbuild-debian/r-b-build.D63VSAQ0/b2/htsjdk_4.1.0+dfsg-1_amd64.changes
├── Files
│ @@ -1,3 +1,3 @@
│  
│ - b78f9d715d094b93946f568e5f8f5d8d 1043544 doc optional libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb
│ + bb86e98fcd1925ed39f4fe2360f7eb44 1043536 doc optional libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb
│   e2a525d9d62d110f9137837762113747 1832576 java optional libhtsjdk-java_4.1.0+dfsg-1_all.deb
├── libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb
│ ├── file list
│ │ @@ -1,3 +1,3 @@
│ │  -rw-r--r--   0        0        0        4 2024-02-11 21:41:39.000000 debian-binary
│ │  -rw-r--r--   0        0        0    26368 2024-02-11 21:41:39.000000 control.tar.xz
│ │ --rw-r--r--   0        0        0  1016984 2024-02-11 21:41:39.000000 data.tar.xz
│ │ +-rw-r--r--   0        0        0  1016976 2024-02-11 21:41:39.000000 data.tar.xz
│ ├── control.tar.xz
│ │ ├── control.tar
│ │ │ ├── ./control
│ │ │ │ @@ -1,13 +1,13 @@
│ │ │ │  Package: libhtsjdk-java-doc
│ │ │ │  Source: htsjdk
│ │ │ │  Version: 4.1.0+dfsg-1
│ │ │ │  Architecture: all
│ │ │ │  Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
│ │ │ │ -Installed-Size: 25146
│ │ │ │ +Installed-Size: 25147
│ │ │ │  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
│ │ │ │ @@ -1080,22 +1080,22 @@
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    10867 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    32388 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    29765 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     9958 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFTextTransformer.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    28441 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFUtils.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    14736 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-summary.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    13991 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-tree.html
│ │ │ │ --rw-r--r--   0 root         (0) root         (0)  3133098 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/index-all.html
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)  3133863 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/index-all.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    25187 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/index.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1498 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/jquery-ui.overrides.css
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/legal/
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1522 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/legal/ASSEMBLY_EXCEPTION
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     2936 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/legal/jquery.md
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1870 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/legal/jqueryUI.md
│ │ │ │ --rw-r--r--   0 root         (0) root         (0)   804015 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/member-search-index.js
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)   804270 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/member-search-index.js
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)       45 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/module-search-index.js
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      826 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/overview-summary.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)   237598 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/overview-tree.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     3152 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/package-search-index.js
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/resources/
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      499 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/resources/glass.png
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      394 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/resources/x.png
│ │ │ ├── ./usr/share/doc/libhtsjdk-java/api/index-all.html
│ │ │ │ @@ -6667,25 +6667,25 @@
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <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>
│ │ │ │ @@ -6697,23 +6697,23 @@
│ │ │ │  </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/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>
│ │ │ │ +<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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<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>
│ │ │ │ +<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>
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <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>
│ │ │ │ @@ -7411,15 +7411,15 @@
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <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>
│ │ │ │ @@ -9377,15 +9377,15 @@
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <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>
│ │ │ │ @@ -10281,15 +10281,15 @@
│ │ │ │  &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/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>
│ │ │ │ +<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>
│ │ │ │  <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>
│ │ │ │ @@ -11120,15 +11120,15 @@
│ │ │ │  </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/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>
│ │ │ │ +<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>
│ │ │ │  <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>
│ │ │ │ @@ -11136,15 +11136,15 @@
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <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
│ │ │ │ @@ -11386,15 +11386,15 @@
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <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>
│ │ │ │ @@ -11561,15 +11561,15 @@
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <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>
│ │ │ │ @@ -14670,15 +14670,15 @@
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <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>
│ │ │ │ @@ -16820,15 +16820,15 @@
│ │ │ │  </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/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>
│ │ │ │ +<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>
│ │ │ │  <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>
│ │ │ │ @@ -19601,15 +19601,15 @@
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <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>
│ │ │ │ @@ -20576,15 +20576,15 @@
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <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>
│ │ │ │ @@ -23659,15 +23659,15 @@
│ │ │ │  </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/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>
│ │ │ │ +<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>
│ │ │ │  <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 {}
│ │ │ │ │ @@ -5342,22 +5342,22 @@
│ │ │ │ │    _f_i_n_d_(_S_t_r_i_n_g_,_ _C_l_a_s_s_<_?_>_) - Method in class htsjdk.utils._C_l_a_s_s_F_i_n_d_e_r
│ │ │ │ │        Scans the classpath for classes within the specified package and sub-
│ │ │ │ │        packages that extend the parentType.
│ │ │ │ │    _f_i_n_d_(_L_i_s_t_<_C_R_A_I_E_n_t_r_y_>_,_ _i_n_t_,_ _i_n_t_,_ _i_n_t_) - Static method in class
│ │ │ │ │    htsjdk.samtools.cram._C_R_A_I_I_n_d_e_x
│ │ │ │ │        Currently unused, but retained for the native rai query implementation
│ │ │ │ │    _f_i_n_d_A_n_d_L_o_a_d_S_e_q_u_e_n_c_e_D_i_c_t_i_o_n_a_r_y_(_P_a_t_h_) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Attempts to find and load the sequence dictionary if present.
│ │ │ │ │    _f_i_n_d_B_y_I_n_d_e_x_(_i_n_t_) - Method in class htsjdk.samtools.util._I_n_t_e_r_v_a_l_T_r_e_e
│ │ │ │ │        Find the nth interval in the tree.
│ │ │ │ │    _f_i_n_d_B_y_N_a_m_e_(_S_t_r_i_n_g_) - Static method in enum class htsjdk.samtools._S_A_M_F_l_a_g
│ │ │ │ │         
│ │ │ │ │    _f_i_n_d_F_a_s_t_a_I_n_d_e_x_(_P_a_t_h_) - Static method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │         
│ │ │ │ │    _f_i_n_d_I_n_d_e_x_(_F_i_l_e_) - Static method in class htsjdk.samtools._S_a_m_F_i_l_e_s
│ │ │ │ │        Finds the index file associated with the provided SAM file.
│ │ │ │ │    _f_i_n_d_I_n_d_e_x_(_P_a_t_h_) - Static method in class htsjdk.samtools._S_a_m_F_i_l_e_s
│ │ │ │ │        Finds the index file associated with the provided SAM file.
│ │ │ │ │    _f_i_n_d_L_a_s_t_A_l_i_g_n_e_d_E_n_t_r_y_(_L_i_s_t_<_C_R_A_I_E_n_t_r_y_>_) - Static method in class
│ │ │ │ │    htsjdk.samtools.cram._C_R_A_I_I_n_d_e_x
│ │ │ │ │ @@ -5365,22 +5365,22 @@
│ │ │ │ │    _f_i_n_d_O_v_e_r_l_a_p_p_i_n_g_(_I_n_t_e_r_v_a_l_) - Method in class
│ │ │ │ │    htsjdk.tribble.index.interval._I_n_t_e_r_v_a_l_T_r_e_e
│ │ │ │ │         
│ │ │ │ │    _f_i_n_d_Q_u_a_l_i_t_y_T_r_i_m_P_o_i_n_t_(_b_y_t_e_[_]_,_ _i_n_t_) - Static method in class
│ │ │ │ │    htsjdk.samtools.util._T_r_i_m_m_i_n_g_U_t_i_l
│ │ │ │ │        Implements phred-style quality trimming.
│ │ │ │ │    _f_i_n_d_R_e_q_u_i_r_e_d_F_a_s_t_a_I_n_d_e_x_F_i_l_e_(_P_a_t_h_) - Static method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │         
│ │ │ │ │    _f_i_n_d_S_e_q_u_e_n_c_e_D_i_c_t_i_o_n_a_r_y_(_F_i_l_e_) - Static method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Deprecated.
│ │ │ │ │        use findSequenceDictionary(Path) instead.
│ │ │ │ │    _f_i_n_d_S_e_q_u_e_n_c_e_D_i_c_t_i_o_n_a_r_y_(_P_a_t_h_) - Static method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Attempts to locate the sequence dictionary file adjacent to the reference
│ │ │ │ │        fasta file.
│ │ │ │ │    _f_i_n_d_V_i_r_t_u_a_l_O_f_f_s_e_t_O_f_F_i_r_s_t_R_e_c_o_r_d_I_n_B_a_m_(_S_e_e_k_a_b_l_e_S_t_r_e_a_m_) - Static method in class
│ │ │ │ │    htsjdk.samtools._S_A_M_U_t_i_l_s
│ │ │ │ │        Returns the virtual file offset of the first record in a BAM file - i.e.
│ │ │ │ │    _f_i_n_d_V_i_r_t_u_a_l_O_f_f_s_e_t_O_f_F_i_r_s_t_R_e_c_o_r_d_I_n_B_a_m_(_F_i_l_e_) - Static method in class
│ │ │ │ │    htsjdk.samtools._S_A_M_U_t_i_l_s
│ │ │ │ │ @@ -5965,15 +5965,15 @@
│ │ │ │ │    _g_e_t_(_S_t_r_i_n_g_) - Method in class htsjdk.variant.variantcontext._G_e_n_o_t_y_p_e_s_C_o_n_t_e_x_t
│ │ │ │ │        Gets sample associated with this sampleName, or null if none is found
│ │ │ │ │    _g_e_t_(_K_) - Method in class htsjdk.samtools.util._H_i_s_t_o_g_r_a_m
│ │ │ │ │        Retrieves the bin associated with the given key.
│ │ │ │ │    _g_e_t_(_K_e_y_) - Method in class htsjdk.samtools.util._R_e_s_o_u_r_c_e_L_i_m_i_t_e_d_M_a_p
│ │ │ │ │        Return an existing value, or create a new one if necessary.
│ │ │ │ │    _g_e_t_A_b_s_o_l_u_t_e_P_a_t_h_(_) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Returns the full path to the reference file.
│ │ │ │ │    _g_e_t_A_c_c_e_p_t_e_d_C_o_u_n_t_(_) - Method in class htsjdk.samtools._D_o_w_n_s_a_m_p_l_i_n_g_I_t_e_r_a_t_o_r
│ │ │ │ │        Returns the number of records returned since creation of the last call to
│ │ │ │ │        resetStatistics.
│ │ │ │ │    _g_e_t_A_c_c_e_p_t_e_d_F_r_a_c_t_i_o_n_(_) - Method in class htsjdk.samtools._D_o_w_n_s_a_m_p_l_i_n_g_I_t_e_r_a_t_o_r
│ │ │ │ │        Gets the fraction of records accepted since creation or the last call to
│ │ │ │ │        resetStatistics().
│ │ │ │ │ @@ -7745,15 +7745,15 @@
│ │ │ │ │    _g_e_t_I_n_d_e_x_(_) - Method in class htsjdk.samtools.cram.structure._R_e_a_d_T_a_g
│ │ │ │ │         
│ │ │ │ │    _g_e_t_I_n_d_e_x_(_) - Method in class htsjdk.samtools._C_R_A_M_F_i_l_e_R_e_a_d_e_r
│ │ │ │ │         
│ │ │ │ │    _g_e_t_I_n_d_e_x_(_) - Method in class htsjdk.samtools._H_t_s_g_e_t_B_A_M_F_i_l_e_R_e_a_d_e_r
│ │ │ │ │        Always null as htsget sources do not have indices
│ │ │ │ │    _g_e_t_I_n_d_e_x_(_) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │         
│ │ │ │ │    _g_e_t_I_n_d_e_x_(_) - Method in interface htsjdk.samtools._S_a_m_R_e_a_d_e_r_._I_n_d_e_x_i_n_g
│ │ │ │ │        Retrieves the index for the given file type.
│ │ │ │ │    _g_e_t_I_n_d_e_x_(_) - Method in interface htsjdk.samtools._S_a_m_R_e_a_d_e_r_._P_r_i_m_i_t_i_v_e_S_a_m_R_e_a_d_e_r
│ │ │ │ │         
│ │ │ │ │    _g_e_t_I_n_d_e_x_(_) - Method in class
│ │ │ │ │    htsjdk.samtools._S_a_m_R_e_a_d_e_r_._P_r_i_m_i_t_i_v_e_S_a_m_R_e_a_d_e_r_T_o_S_a_m_R_e_a_d_e_r_A_d_a_p_t_e_r
│ │ │ │ │ @@ -8513,15 +8513,15 @@
│ │ │ │ │         
│ │ │ │ │    _g_e_t_P_a_s_s_w_o_r_d_(_) - Method in interface
│ │ │ │ │    htsjdk.samtools.seekablestream._U_s_e_r_P_a_s_s_w_o_r_d_I_n_p_u_t
│ │ │ │ │         
│ │ │ │ │    _g_e_t_P_a_t_c_h_V_e_r_s_i_o_n_(_) - Method in class htsjdk.beta.plugin._H_t_s_V_e_r_s_i_o_n
│ │ │ │ │        Get the patch version integer for this version.
│ │ │ │ │    _g_e_t_P_a_t_h_(_) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Returns the path to the reference file.
│ │ │ │ │    _g_e_t_P_a_t_h_(_S_t_r_i_n_g_) - Static method in class htsjdk.samtools.util._I_O_U_t_i_l
│ │ │ │ │        Converts the given URI to a _P_a_t_h object.
│ │ │ │ │    _g_e_t_P_a_t_h_s_(_L_i_s_t_<_S_t_r_i_n_g_>_) - Static method in class htsjdk.samtools.util._I_O_U_t_i_l
│ │ │ │ │         
│ │ │ │ │    _g_e_t_P_a_t_h_T_o_D_a_t_a_F_i_l_e_(_S_t_r_i_n_g_) - Method in interface htsjdk.tribble._F_e_a_t_u_r_e_C_o_d_e_c
│ │ │ │ │        Codecs may override this method if the file that they recognize with
│ │ │ │ │ @@ -9239,28 +9239,28 @@
│ │ │ │ │        Look up a sequence record by index.
│ │ │ │ │    _g_e_t_S_e_q_u_e_n_c_e_(_i_n_t_) - Method in class htsjdk.samtools._S_A_M_S_e_q_u_e_n_c_e_D_i_c_t_i_o_n_a_r_y
│ │ │ │ │         
│ │ │ │ │    _g_e_t_S_e_q_u_e_n_c_e_(_S_t_r_i_n_g_) - Method in class
│ │ │ │ │    htsjdk.samtools.reference._F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        default implementation -- override if index is supported
│ │ │ │ │    _g_e_t_S_e_q_u_e_n_c_e_(_S_t_r_i_n_g_) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Retrieves the complete sequence described by this contig.
│ │ │ │ │    _g_e_t_S_e_q_u_e_n_c_e_(_S_t_r_i_n_g_) - Method in interface
│ │ │ │ │    htsjdk.samtools.reference._R_e_f_e_r_e_n_c_e_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Retrieves the complete sequence described by this contig.
│ │ │ │ │    _g_e_t_S_e_q_u_e_n_c_e_(_S_t_r_i_n_g_) - Method in class htsjdk.samtools._S_A_M_F_i_l_e_H_e_a_d_e_r
│ │ │ │ │        Look up sequence record by name.
│ │ │ │ │    _g_e_t_S_e_q_u_e_n_c_e_(_S_t_r_i_n_g_) - Method in class htsjdk.samtools._S_A_M_S_e_q_u_e_n_c_e_D_i_c_t_i_o_n_a_r_y
│ │ │ │ │         
│ │ │ │ │    _g_e_t_S_e_q_u_e_n_c_e_(_S_t_r_i_n_g_) - Method in class
│ │ │ │ │    htsjdk.samtools.sra._S_R_A_I_n_d_e_x_e_d_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │         
│ │ │ │ │    _g_e_t_S_e_q_u_e_n_c_e_D_i_c_t_i_o_n_a_r_y_(_) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Returns the list of sequence records associated with the reference
│ │ │ │ │        sequence if found otherwise null.
│ │ │ │ │    _g_e_t_S_e_q_u_e_n_c_e_D_i_c_t_i_o_n_a_r_y_(_) - Method in interface
│ │ │ │ │    htsjdk.samtools.reference._R_e_f_e_r_e_n_c_e_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Must return a sequence dictionary with at least the following fields
│ │ │ │ │        completed for each sequence: name, length.
│ │ │ │ │    _g_e_t_S_e_q_u_e_n_c_e_D_i_c_t_i_o_n_a_r_y_(_) - Method in class
│ │ │ │ │ @@ -9498,15 +9498,15 @@
│ │ │ │ │    _g_e_t_S_o_r_t_O_r_d_e_r_(_) - Method in class htsjdk.samtools._S_A_M_F_i_l_e_H_e_a_d_e_r
│ │ │ │ │         
│ │ │ │ │    _g_e_t_S_o_r_t_O_r_d_e_r_(_) - Method in class htsjdk.samtools._S_A_M_F_i_l_e_W_r_i_t_e_r_I_m_p_l
│ │ │ │ │        Must be called after calling setHeader().
│ │ │ │ │    _g_e_t_S_o_r_t_O_r_d_e_r_(_) - Method in class htsjdk.samtools._S_A_M_S_o_r_t_O_r_d_e_r_C_h_e_c_k_e_r
│ │ │ │ │         
│ │ │ │ │    _g_e_t_S_o_u_r_c_e_(_) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Returns the named source of the reference file.
│ │ │ │ │    _g_e_t_S_o_u_r_c_e_(_) - Method in class htsjdk.samtools._S_A_M_V_a_l_i_d_a_t_i_o_n_E_r_r_o_r
│ │ │ │ │         
│ │ │ │ │    _g_e_t_S_o_u_r_c_e_(_) - Method in class
│ │ │ │ │    htsjdk.samtools.seekablestream._B_y_t_e_A_r_r_a_y_S_e_e_k_a_b_l_e_S_t_r_e_a_m
│ │ │ │ │         
│ │ │ │ │    _g_e_t_S_o_u_r_c_e_(_) - Method in class
│ │ │ │ │ @@ -9657,15 +9657,15 @@
│ │ │ │ │    _g_e_t_S_t_r_u_c_t_u_r_a_l_V_a_r_i_a_n_t_T_y_p_e_(_) - Method in class
│ │ │ │ │    htsjdk.variant.variantcontext._V_a_r_i_a_n_t_C_o_n_t_e_x_t
│ │ │ │ │        Search for the INFO=SVTYPE and return the type of Structural Variant
│ │ │ │ │    _g_e_t_S_u_b_s_e_q_u_e_n_c_e_A_t_(_S_t_r_i_n_g_,_ _l_o_n_g_,_ _l_o_n_g_) - Method in class
│ │ │ │ │    htsjdk.samtools.reference._F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        default implementation -- override if index is supported
│ │ │ │ │    _g_e_t_S_u_b_s_e_q_u_e_n_c_e_A_t_(_S_t_r_i_n_g_,_ _l_o_n_g_,_ _l_o_n_g_) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Gets the subsequence of the contig in the range [start,stop]
│ │ │ │ │    _g_e_t_S_u_b_s_e_q_u_e_n_c_e_A_t_(_S_t_r_i_n_g_,_ _l_o_n_g_,_ _l_o_n_g_) - Method in interface
│ │ │ │ │    htsjdk.samtools.reference._R_e_f_e_r_e_n_c_e_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Gets the subsequence of the contig in the range [start,stop]
│ │ │ │ │    _g_e_t_S_u_b_s_e_q_u_e_n_c_e_A_t_(_S_t_r_i_n_g_,_ _l_o_n_g_,_ _l_o_n_g_) - Method in class
│ │ │ │ │    htsjdk.samtools.sra._S_R_A_I_n_d_e_x_e_d_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │         
│ │ │ │ │ @@ -12538,15 +12538,15 @@
│ │ │ │ │        convenience method for indels
│ │ │ │ │    _i_s_I_n_d_e_l_O_r_S_k_i_p_p_e_d_R_e_g_i_o_n_(_) - Method in enum class htsjdk.samtools._C_i_g_a_r_O_p_e_r_a_t_o_r
│ │ │ │ │        Returns true if the operator is a Skipped Region Insertion or Deletion
│ │ │ │ │        operator
│ │ │ │ │    _i_s_I_n_d_e_x_e_d_(_) - Method in class htsjdk.samtools.reference._F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        default implementation -- override if index is supported
│ │ │ │ │    _i_s_I_n_d_e_x_e_d_(_) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │         
│ │ │ │ │    _i_s_I_n_d_e_x_e_d_(_) - Method in interface
│ │ │ │ │    htsjdk.samtools.reference._R_e_f_e_r_e_n_c_e_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │         
│ │ │ │ │    _i_s_I_n_d_e_x_e_d_(_) - Method in class htsjdk.samtools.sra._S_R_A_I_n_d_e_x_e_d_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │         
│ │ │ │ │    _i_s_I_n_i_t_i_a_l_i_z_e_d_(_) - Method in class htsjdk.samtools.util._L_a_z_y
│ │ │ │ │ @@ -14392,15 +14392,15 @@
│ │ │ │ │    htsjdk.samtools.util._R_e_f_e_r_e_n_c_e_S_e_q_u_e_n_c_e_M_a_s_k
│ │ │ │ │        It is required that sequenceIndex is >= any previous sequenceIndex passed
│ │ │ │ │        to this class.
│ │ │ │ │    _n_e_x_t_P_o_s_i_t_i_o_n_(_i_n_t_,_ _i_n_t_) - Method in class
│ │ │ │ │    htsjdk.samtools.util._W_h_o_l_e_G_e_n_o_m_e_R_e_f_e_r_e_n_c_e_S_e_q_u_e_n_c_e_M_a_s_k
│ │ │ │ │         
│ │ │ │ │    _n_e_x_t_S_e_q_u_e_n_c_e_(_) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Gets the next sequence if available, or null if not present.
│ │ │ │ │    _n_e_x_t_S_e_q_u_e_n_c_e_(_) - Method in class htsjdk.samtools.reference._F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │         
│ │ │ │ │    _n_e_x_t_S_e_q_u_e_n_c_e_(_) - Method in interface
│ │ │ │ │    htsjdk.samtools.reference._R_e_f_e_r_e_n_c_e_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Retrieves the next whole sequences from the file.
│ │ │ │ │    _n_e_x_t_S_e_q_u_e_n_c_e_(_) - Method in class htsjdk.samtools.sra._S_R_A_I_n_d_e_x_e_d_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ @@ -16836,15 +16836,16 @@
│ │ │ │ │         
│ │ │ │ │    _r_e_s_e_t_(_) - Method in class htsjdk.samtools.cram.io._C_o_u_n_t_i_n_g_I_n_p_u_t_S_t_r_e_a_m
│ │ │ │ │         
│ │ │ │ │    _r_e_s_e_t_(_) - Method in class htsjdk.samtools.cram.io._C_R_C_3_2_I_n_p_u_t_S_t_r_e_a_m
│ │ │ │ │         
│ │ │ │ │    _r_e_s_e_t_(_) - Method in class htsjdk.samtools.cram.io._D_e_f_a_u_l_t_B_i_t_I_n_p_u_t_S_t_r_e_a_m
│ │ │ │ │         
│ │ │ │ │ -  _r_e_s_e_t_(_) - Method in class htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  _r_e_s_e_t_(_) - Method in class
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Reset the iterator over the index.
│ │ │ │ │    _r_e_s_e_t_(_) - Method in class htsjdk.samtools.reference._F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │         
│ │ │ │ │    _r_e_s_e_t_(_) - Method in interface htsjdk.samtools.reference._R_e_f_e_r_e_n_c_e_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Resets the ReferenceSequenceFile so that the next call to nextSequence()
│ │ │ │ │        will return the first sequence in the file.
│ │ │ │ │    _r_e_s_e_t_(_) - Method in class htsjdk.samtools.seekablestream._S_e_e_k_a_b_l_e_S_t_r_e_a_m
│ │ │ │ │ @@ -17645,15 +17646,15 @@
│ │ │ │ │        Construct a SAMValidationError with possibly-known record number.
│ │ │ │ │    _S_A_M_V_a_l_i_d_a_t_i_o_n_E_r_r_o_r_._S_e_v_e_r_i_t_y - Enum Class in _h_t_s_j_d_k_._s_a_m_t_o_o_l_s
│ │ │ │ │         
│ │ │ │ │    _S_A_M_V_a_l_i_d_a_t_i_o_n_E_r_r_o_r_._T_y_p_e - Enum Class in _h_t_s_j_d_k_._s_a_m_t_o_o_l_s
│ │ │ │ │         
│ │ │ │ │    _s_a_n_i_t_y_C_h_e_c_k_D_i_c_t_i_o_n_a_r_y_A_g_a_i_n_s_t_I_n_d_e_x_(_S_t_r_i_n_g_,_ _S_A_M_S_e_q_u_e_n_c_e_D_i_c_t_i_o_n_a_r_y_,
│ │ │ │ │    _F_a_s_t_a_S_e_q_u_e_n_c_e_I_n_d_e_x_) - Static method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Do some basic checking to make sure the dictionary and the index match.
│ │ │ │ │    _S_a_n_i_t_y_C_h_e_c_k_F_a_i_l_e_d_E_x_c_e_p_t_i_o_n_(_S_t_r_i_n_g_) - Constructor for exception
│ │ │ │ │    htsjdk.samtools._S_A_M_T_e_s_t_U_t_i_l_._S_a_n_i_t_y_C_h_e_c_k_F_a_i_l_e_d_E_x_c_e_p_t_i_o_n
│ │ │ │ │         
│ │ │ │ │    _S_B_I - Static variable in class htsjdk.samtools.util._F_i_l_e_E_x_t_e_n_s_i_o_n_s
│ │ │ │ │         
│ │ │ │ │    _S_B_I_I_n_d_e_x - Class in _h_t_s_j_d_k_._s_a_m_t_o_o_l_s
│ │ │ │ │ @@ -20457,15 +20458,15 @@
│ │ │ │ │    _t_o_S_t_r_i_n_g_(_) - Method in class htsjdk.samtools.metrics._S_t_r_i_n_g_H_e_a_d_e_r
│ │ │ │ │         
│ │ │ │ │    _t_o_S_t_r_i_n_g_(_) - Method in class htsjdk.samtools.metrics._V_e_r_s_i_o_n_H_e_a_d_e_r
│ │ │ │ │         
│ │ │ │ │    _t_o_S_t_r_i_n_g_(_) - Method in class htsjdk.samtools._Q_u_e_r_y_I_n_t_e_r_v_a_l
│ │ │ │ │         
│ │ │ │ │    _t_o_S_t_r_i_n_g_(_) - Method in class
│ │ │ │ │ -  htsjdk.samtools.reference._I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │ +  htsjdk.samtools.reference._B_l_o_c_k_C_o_m_p_r_e_s_s_e_d_I_n_d_e_x_e_d_F_a_s_t_a_S_e_q_u_e_n_c_e_F_i_l_e
│ │ │ │ │        Returns the full path to the reference file, or the source if no path was
│ │ │ │ │        specified.
│ │ │ │ │    _t_o_S_t_r_i_n_g_(_) - Method in class
│ │ │ │ │    htsjdk.samtools.reference._F_a_s_t_a_S_e_q_u_e_n_c_e_I_n_d_e_x_E_n_t_r_y
│ │ │ │ │        For debugging.
│ │ │ │ │    _t_o_S_t_r_i_n_g_(_) - Method in class htsjdk.samtools.reference._R_e_f_e_r_e_n_c_e_S_e_q_u_e_n_c_e
│ │ │ ├── ./usr/share/doc/libhtsjdk-java/api/member-search-index.js
│ │ │ │ ├── js-beautify {}
│ │ │ │ │ @@ -8165,29 +8165,29 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.utils",
│ │ │ │ │      "c": "ClassFinder",
│ │ │ │ │      "l": "find(String, Class<?>)",
│ │ │ │ │      "u": "find(java.lang.String,java.lang.Class)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "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": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "findFastaIndex(Path)",
│ │ │ │ │      "u": "findFastaIndex(java.nio.file.Path)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SamFiles",
│ │ │ │ │      "l": "findIndex(File)",
│ │ │ │ │      "u": "findIndex(java.io.File)"
│ │ │ │ │ @@ -8209,25 +8209,25 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.util",
│ │ │ │ │      "c": "TrimmingUtil",
│ │ │ │ │      "l": "findQualityTrimPoint(byte[], int)",
│ │ │ │ │      "u": "findQualityTrimPoint(byte[],int)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "findRequiredFastaIndexFile(Path)",
│ │ │ │ │      "u": "findRequiredFastaIndexFile(java.nio.file.Path)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "findSequenceDictionary(File)",
│ │ │ │ │      "u": "findSequenceDictionary(java.io.File)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "findSequenceDictionary(Path)",
│ │ │ │ │      "u": "findSequenceDictionary(java.nio.file.Path)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SAMUtils",
│ │ │ │ │      "l": "findVirtualOffsetOfFirstRecordInBam(File)",
│ │ │ │ │      "u": "findVirtualOffsetOfFirstRecordInBam(java.io.File)"
│ │ │ │ │ @@ -9064,15 +9064,15 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.variant.variantcontext",
│ │ │ │ │      "c": "GenotypesContext",
│ │ │ │ │      "l": "get(String)",
│ │ │ │ │      "u": "get(java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "getAbsolutePath()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "DownsamplingIterator",
│ │ │ │ │      "l": "getAcceptedCount()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │ @@ -11981,15 +11981,15 @@
│ │ │ │ │      "l": "getIndex()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "HtsgetBAMFileReader",
│ │ │ │ │      "l": "getIndex()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "getIndex()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SamReader.Indexing",
│ │ │ │ │      "l": "getIndex()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │ @@ -13266,15 +13266,15 @@
│ │ │ │ │      "l": "getPassword()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.beta.plugin",
│ │ │ │ │      "c": "HtsVersion",
│ │ │ │ │      "l": "getPatchVersion()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "getPath()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.util",
│ │ │ │ │      "c": "IOUtil",
│ │ │ │ │      "l": "getPath(String)",
│ │ │ │ │      "u": "getPath(java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │ @@ -14393,15 +14393,15 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "FastaSequenceFile",
│ │ │ │ │      "l": "getSequence(String)",
│ │ │ │ │      "u": "getSequence(java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "getSequence(String)",
│ │ │ │ │      "u": "getSequence(java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "ReferenceSequenceFile",
│ │ │ │ │      "l": "getSequence(String)",
│ │ │ │ │      "u": "getSequence(java.lang.String)"
│ │ │ │ │ @@ -14418,15 +14418,15 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.sra",
│ │ │ │ │      "c": "SRAIndexedSequenceFile",
│ │ │ │ │      "l": "getSequence(String)",
│ │ │ │ │      "u": "getSequence(java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "getSequenceDictionary()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "ReferenceSequenceFile",
│ │ │ │ │      "l": "getSequenceDictionary()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ @@ -14813,15 +14813,15 @@
│ │ │ │ │      "l": "getSortOrder()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SAMSortOrderChecker",
│ │ │ │ │      "l": "getSortOrder()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "getSource()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "SAMValidationError",
│ │ │ │ │      "l": "getSource()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.seekablestream",
│ │ │ │ │ @@ -15098,15 +15098,15 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "FastaSequenceFile",
│ │ │ │ │      "l": "getSubsequenceAt(String, long, long)",
│ │ │ │ │      "u": "getSubsequenceAt(java.lang.String,long,long)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "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)"
│ │ │ │ │ @@ -18872,15 +18872,15 @@
│ │ │ │ │      "l": "isIndelOrSkippedRegion()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "FastaSequenceFile",
│ │ │ │ │      "l": "isIndexed()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "isIndexed()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "ReferenceSequenceFile",
│ │ │ │ │      "l": "isIndexed()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.sra",
│ │ │ │ │ @@ -21554,15 +21554,15 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.util",
│ │ │ │ │      "c": "WholeGenomeReferenceSequenceMask",
│ │ │ │ │      "l": "nextPosition(int, int)",
│ │ │ │ │      "u": "nextPosition(int,int)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "nextSequence()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "FastaSequenceFile",
│ │ │ │ │      "l": "nextSequence()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ @@ -25256,15 +25256,15 @@
│ │ │ │ │      "l": "reset()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.cram.io",
│ │ │ │ │      "c": "DefaultBitInputStream",
│ │ │ │ │      "l": "reset()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "reset()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "FastaSequenceFile",
│ │ │ │ │      "l": "reset()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ @@ -26204,15 +26204,15 @@
│ │ │ │ │  }, {
│ │ │ │ │      "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": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "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)"
│ │ │ │ │ @@ -30294,15 +30294,15 @@
│ │ │ │ │      "l": "toString()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools",
│ │ │ │ │      "c": "QueryInterval",
│ │ │ │ │      "l": "toString()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │ -    "c": "IndexedFastaSequenceFile",
│ │ │ │ │ +    "c": "BlockCompressedIndexedFastaSequenceFile",
│ │ │ │ │      "l": "toString()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",
│ │ │ │ │      "c": "FastaSequenceIndexEntry",
│ │ │ │ │      "l": "toString()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "htsjdk.samtools.reference",