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| 1 | · | 1 | ·96b25c388cdab2d1f1d20ddaf510edab·1039072·doc·optional·libhtsjdk-java-doc_3.0.4+dfsg-2_all.deb |
| 2 | ·3375151baf60e103b9d2d83d44ecd7ab·1813244·java·optional·libhtsjdk-java_3.0.4+dfsg-2_all.deb | 2 | ·3375151baf60e103b9d2d83d44ecd7ab·1813244·java·optional·libhtsjdk-java_3.0.4+dfsg-2_all.deb |
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| 1 | -rw-r--r--···0········0········0········4·2023-01-24·03:16:14.000000·debian-binary | 1 | -rw-r--r--···0········0········0········4·2023-01-24·03:16:14.000000·debian-binary |
| 2 | -rw-r--r--···0········0········0····26364·2023-01-24·03:16:14.000000·control.tar.xz | 2 | -rw-r--r--···0········0········0····26364·2023-01-24·03:16:14.000000·control.tar.xz |
| 3 | -rw-r--r--···0········0········0··10125 | 3 | -rw-r--r--···0········0········0··1012516·2023-01-24·03:16:14.000000·data.tar.xz |
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| 1 | Package:·libhtsjdk-java-doc | 1 | Package:·libhtsjdk-java-doc |
| 2 | Source:·htsjdk | 2 | Source:·htsjdk |
| 3 | Version:·3.0.4+dfsg-2 | 3 | Version:·3.0.4+dfsg-2 |
| 4 | Architecture:·all | 4 | Architecture:·all |
| 5 | Maintainer:·Debian·Med·Packaging·Team·<debian-med-packaging@lists.alioth.debian.org> | 5 | Maintainer:·Debian·Med·Packaging·Team·<debian-med-packaging@lists.alioth.debian.org> |
| 6 | Installed-Size:·2509 | 6 | Installed-Size:·25093 |
| 7 | Section:·doc | 7 | Section:·doc |
| 8 | Priority:·optional | 8 | Priority:·optional |
| 9 | Multi-Arch:·foreign | 9 | Multi-Arch:·foreign |
| 10 | Homepage:·https://samtools.github.io/htsjdk/ | 10 | Homepage:·https://samtools.github.io/htsjdk/ |
| 11 | Description:·Documentation·for·the·java·HTSJDK·library | 11 | Description:·Documentation·for·the·java·HTSJDK·library |
| 12 | ·HTSJDK·is·an·implementation·of·a·unified·Java·library·for·accessing·common | 12 | ·HTSJDK·is·an·implementation·of·a·unified·Java·library·for·accessing·common |
| 13 | ·file·formats,·such·as·SAM·(Sequence·Alignment/Map)·and·VCF,·used·for | 13 | ·file·formats,·such·as·SAM·(Sequence·Alignment/Map)·and·VCF,·used·for |
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| 1100 | -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 | 1100 | -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 |
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| 6640 | <div·class="block">Scans·the·classpath·for·classes·within·the·specified·package·and·sub-packages·that | 6640 | <div·class="block">Scans·the·classpath·for·classes·within·the·specified·package·and·sub-packages·that |
| 6641 | ·extend·the·parentType.</div> | 6641 | ·extend·the·parentType.</div> |
| 6642 | </dd> | 6642 | </dd> |
| 6643 | <dt><a·href="htsjdk/samtools/cram/CRAIIndex.html#find(java.util.List,int,int,int)"·class="member-name-link">find(List<CRAIEntry>,·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> | 6643 | <dt><a·href="htsjdk/samtools/cram/CRAIIndex.html#find(java.util.List,int,int,int)"·class="member-name-link">find(List<CRAIEntry>,·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> |
| 6644 | <dd> | 6644 | <dd> |
| 6645 | <div·class="block">Currently·unused,·but·retained·for·the·native·rai·query·implementation</div> | 6645 | <div·class="block">Currently·unused,·but·retained·for·the·native·rai·query·implementation</div> |
| 6646 | </dd> | 6646 | </dd> |
| 6647 | <dt><a·href="htsjdk/samtools/reference/ | 6647 | <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"·[·...·truncated·by·diffoscope;·len:·43,·SHA:·9832d6daa99ce18d19be19afada0d48aabd38401dc8c38b270a9de0aeecf58e2·...·]IndexedFastaSequenceFile</a></dt> |
| 6648 | <dd> | 6648 | <dd> |
| 6649 | <div·class="block">Attempts·to·find·and·load·the·sequence·dictionary·if·present.</div> | 6649 | <div·class="block">Attempts·to·find·and·load·the·sequence·dictionary·if·present.</div> |
| 6650 | </dd> | 6650 | </dd> |
| 6651 | <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> | 6651 | <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> |
| 6652 | <dd> | 6652 | <dd> |
| 6653 | <div·class="block">Find·the·nth·interval·in·the·tree.</div> | 6653 | <div·class="block">Find·the·nth·interval·in·the·tree.</div> |
| 6654 | </dd> | 6654 | </dd> |
| 6655 | <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> | 6655 | <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> |
| 6656 | <dd> </dd> | 6656 | <dd> </dd> |
| 6657 | <dt><a·href="htsjdk/samtools/reference/ | 6657 | <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.[·...·truncated·by·diffoscope;·len:·20,·SHA:·30696af0ede087a681bbbafc995ecacac8028cf890111d73858dfbafa99e08a9·...·]IndexedFastaSequenceFile</a></dt> |
| 6658 | <dd> </dd> | 6658 | <dd> </dd> |
| 6659 | <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> | 6659 | <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> |
| 6660 | <dd> | 6660 | <dd> |
| 6661 | <div·class="block">Finds·the·index·file·associated·with·the·provided·SAM·file.</div> | 6661 | <div·class="block">Finds·the·index·file·associated·with·the·provided·SAM·file.</div> |
| 6662 | </dd> | 6662 | </dd> |
| 6663 | <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> | 6663 | <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> |
| 6664 | <dd> | 6664 | <dd> |
| Offset 6670, 23 lines modified | Offset 6670, 23 lines modified | ||
| 6670 | </dd> | 6670 | </dd> |
| 6671 | <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> | 6671 | <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> |
| 6672 | <dd> </dd> | 6672 | <dd> </dd> |
| 6673 | <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> | 6673 | <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> |
| 6674 | <dd> | 6674 | <dd> |
| 6675 | <div·class="block">Implements·phred-style·quality·trimming.</div> | 6675 | <div·class="block">Implements·phred-style·quality·trimming.</div> |
| 6676 | </dd> | 6676 | </dd> |
| 6677 | <dt><a·href="htsjdk/samtools/reference/ | 6677 | <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"[·...·truncated·by·diffoscope;·len:·44,·SHA:·f7110c951b7f965ba34157619a6ba935c8387c1d77730335790d14639f2cd195·...·]IndexedFastaSequenceFile</a></dt> |
| 6678 | <dd> </dd> | 6678 | <dd> </dd> |
| 6679 | <dt><a·href="htsjdk/samtools/reference/ | 6679 | <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·[·...·truncated·by·diffoscope;·len:·30,·SHA:·b7416a6e1e4aa0603690323abe021ec3bf0e74da2c196c88435e603c1f8b91c1·...·]IndexedFastaSequenceFile</a></dt> |
| 6680 | <dd> | 6680 | <dd> |
| 6681 | <div·class="deprecation-block"><span·class="deprecated-label">Deprecated.</span> | 6681 | <div·class="deprecation-block"><span·class="deprecated-label">Deprecated.</span> |
| 6682 | <div·class="deprecation-comment">use·findSequenceDictionary(Path)·instead.</div> | 6682 | <div·class="deprecation-comment">use·findSequenceDictionary(Path)·instead.</div> |
| 6683 | </div> | 6683 | </div> |
| 6684 | </dd> | 6684 | </dd> |
| 6685 | <dt><a·href="htsjdk/samtools/reference/ | 6685 | <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="[·...·truncated·by·diffoscope;·len:·36,·SHA:·5862a24fb90f3f96c906a1f40f98e29ec2c95d4b14905d2d834c14faa942229e·...·]IndexedFastaSequenceFile</a></dt> |
| 6686 | <dd> | 6686 | <dd> |
| 6687 | <div·class="block">Attempts·to·locate·the·sequence·dictionary·file·adjacent·to·the·reference·fasta·file.</div> | 6687 | <div·class="block">Attempts·to·locate·the·sequence·dictionary·file·adjacent·to·the·reference·fasta·file.</div> |
| 6688 | </dd> | 6688 | </dd> |
| 6689 | <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> | 6689 | <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> |
| 6690 | <dd> | 6690 | <dd> |
| 6691 | <div·class="block">Returns·the·virtual·file·offset·of·the·first·record·in·a·BAM·file·-·i.e.</div> | 6691 | <div·class="block">Returns·the·virtual·file·offset·of·the·first·record·in·a·BAM·file·-·i.e.</div> |
| 6692 | </dd> | 6692 | </dd> |
| Offset 7377, 15 lines modified | Offset 7377, 15 lines modified | ||
| 7377 | <dd> | 7377 | <dd> |
| 7378 | <div·class="block">Retrieves·the·bin·associated·with·the·given·key.</div> | 7378 | <div·class="block">Retrieves·the·bin·associated·with·the·given·key.</div> |
| 7379 | </dd> | 7379 | </dd> |
| 7380 | <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> | 7380 | <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> |
| 7381 | <dd> | 7381 | <dd> |
| 7382 | <div·class="block">Return·an·existing·value,·or·create·a·new·one·if·necessary.</div> | 7382 | <div·class="block">Return·an·existing·value,·or·create·a·new·one·if·necessary.</div> |
| 7383 | </dd> | 7383 | </dd> |
| 7384 | <dt><a·href="htsjdk/samtools/reference/ | 7384 | <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> |
| 7385 | <dd> | 7385 | <dd> |
| 7386 | <div·class="block">Returns·the·full·path·to·the·reference·file.</div> | 7386 | <div·class="block">Returns·the·full·path·to·the·reference·file.</div> |
| 7387 | </dd> | 7387 | </dd> |
| 7388 | <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> | 7388 | <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> |
| 7389 | <dd> | 7389 | <dd> |
| 7390 | <div·class="block">Returns·the·number·of·records·returned·since·creation·of·the·last·call·to·resetStatistics.</div> | 7390 | <div·class="block">Returns·the·number·of·records·returned·since·creation·of·the·last·call·to·resetStatistics.</div> |
| 7391 | </dd> | 7391 | </dd> |
| Offset 9343, 15 lines modified | Offset 9343, 15 lines modified | ||
| 9343 | <dd> </dd> | 9343 | <dd> </dd> |
| 9344 | <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> | 9344 | <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> |
| 9345 | <dd> </dd> | 9345 | <dd> </dd> |
| 9346 | <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> | 9346 | <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> |
| 9347 | <dd> | 9347 | <dd> |
| 9348 | <div·class="block">Always·null·as·htsget·sources·do·not·have·indices</div> | 9348 | <div·class="block">Always·null·as·htsget·sources·do·not·have·indices</div> |
| 9349 | </dd> | 9349 | </dd> |
| 9350 | <dt><a·href="htsjdk/samtools/reference/ | 9350 | <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> |
| 9351 | <dd> </dd> | 9351 | <dd> </dd> |
| 9352 | <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> | 9352 | <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> |
| 9353 | <dd> | 9353 | <dd> |
| 9354 | <div·class="block">Retrieves·the·index·for·the·given·file·type.</div> | 9354 | <div·class="block">Retrieves·the·index·for·the·given·file·type.</div> |
| 9355 | </dd> | 9355 | </dd> |
| 9356 | <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> | 9356 | <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> |
| 9357 | <dd> </dd> | 9357 | <dd> </dd> |
| Offset 10247, 15 lines modified | Offset 10247, 15 lines modified | ||
| 10247 | </dd> | 10247 | </dd> |
| 10248 | <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> | 10248 | <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> |
| 10249 | <dd> </dd> | 10249 | <dd> </dd> |
| 10250 | <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> | 10250 | <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> |
| 10251 | <dd> | 10251 | <dd> |
| 10252 | <div·class="block">Get·the·patch·version·integer·for·this·version.</div> | 10252 | <div·class="block">Get·the·patch·version·integer·for·this·version.</div> |
| 10253 | </dd> | 10253 | </dd> |
| 10254 | <dt><a·href="htsjdk/samtools/reference/ | 10254 | <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> |
| 10255 | <dd> | 10255 | <dd> |
| 10256 | <div·class="block">Returns·the·path·to·the·reference·file.</div> | 10256 | <div·class="block">Returns·the·path·to·the·reference·file.</div> |
| 10257 | </dd> | 10257 | </dd> |
| 10258 | <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> | 10258 | <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> |
| 10259 | <dd> | 10259 | <dd> |
| 10260 | <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> | 10260 | <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> |
| 10261 | </dd> | 10261 | </dd> |
| Offset 11086, 15 lines modified | Offset 11086, 15 lines modified | ||
| 11086 | </dd> | 11086 | </dd> |
| 11087 | <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> | 11087 | <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> |
| 11088 | <dd> </dd> | 11088 | <dd> </dd> |
| 11089 | <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> | 11089 | <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> |
| 11090 | <dd> | 11090 | <dd> |
| 11091 | <div·class="block">default·implementation·--·override·if·index·is·supported</div> | 11091 | <div·class="block">default·implementation·--·override·if·index·is·supported</div> |
| 11092 | </dd> | 11092 | </dd> |
| 11093 | <dt><a·href="htsjdk/samtools/reference/ | 11093 | <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.refe[·...·truncated·by·diffoscope;·len:·7,·SHA:·f70838aa4ab9bd6bab9856e2cdfccc4460d8b3946a46a683c95c8aad8cc48334·...·]IndexedFastaSequenceFile</a></dt> |
| 11094 | <dd> | 11094 | <dd> |
| 11095 | <div·class="block">Retrieves·the·complete·sequence·described·by·this·contig.</div> | 11095 | <div·class="block">Retrieves·the·complete·sequence·described·by·this·contig.</div> |
| 11096 | </dd> | 11096 | </dd> |
| 11097 | <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> | 11097 | <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> |
| 11098 | <dd> | 11098 | <dd> |
| 11099 | <div·class="block">Retrieves·the·complete·sequence·described·by·this·contig.</div> | 11099 | <div·class="block">Retrieves·the·complete·sequence·described·by·this·contig.</div> |
| 11100 | </dd> | 11100 | </dd> |
| Offset 11102, 15 lines modified | Offset 11102, 15 lines modified | ||
| 11102 | <dd> | 11102 | <dd> |
| 11103 | <div·class="block">Look·up·sequence·record·by·name.</div> | 11103 | <div·class="block">Look·up·sequence·record·by·name.</div> |
| 11104 | </dd> | 11104 | </dd> |
| 11105 | <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> | 11105 | <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> |
| 11106 | <dd> </dd> | 11106 | <dd> </dd> |
| 11107 | <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> | 11107 | <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> |
| 11108 | <dd> </dd> | 11108 | <dd> </dd> |
| 11109 | <dt><a·href="htsjdk/samtools/reference/ | 11109 | <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.refere[·...·truncated·by·diffoscope;·len:·5,·SHA:·7e079755f1001d6b4db984815661c71136125657733d93ac018e4327f491be4c·...·]IndexedFastaSequenceFile</a></dt> |
| 11110 | <dd> | 11110 | <dd> |
| 11111 | <div·class="block">Returns·the·list·of·sequence·records·associated·with·the·reference·sequence·if·found | 11111 | <div·class="block">Returns·the·list·of·sequence·records·associated·with·the·reference·sequence·if·found |
| 11112 | ·otherwise·null.</div> | 11112 | ·otherwise·null.</div> |
| 11113 | </dd> | 11113 | </dd> |
| 11114 | <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> | 11114 | <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> |
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| Offset 5328, 22 lines modified | Offset 5328, 22 lines modified | ||
| 5328 | ··find(String,_Class<?>)·-·Method·in·class·htsjdk.utils.ClassFinder | 5328 | ··find(String,_Class<?>)·-·Method·in·class·htsjdk.utils.ClassFinder |
| 5329 | ······Scans·the·classpath·for·classes·within·the·specified·package·and·sub- | 5329 | ······Scans·the·classpath·for·classes·within·the·specified·package·and·sub- |
| 5330 | ······packages·that·extend·the·parentType. | 5330 | ······packages·that·extend·the·parentType. |
| 5331 | ··find(List<CRAIEntry>,_int,_int,_int)·-·Static·method·in·class | 5331 | ··find(List<CRAIEntry>,_int,_int,_int)·-·Static·method·in·class |
| 5332 | ··htsjdk.samtools.cram.CRAIIndex | 5332 | ··htsjdk.samtools.cram.CRAIIndex |
| 5333 | ······Currently·unused,·but·retained·for·the·native·rai·query·implementation | 5333 | ······Currently·unused,·but·retained·for·the·native·rai·query·implementation |
| 5334 | ··findAndLoadSequenceDictionary(Path)·-·Method·in·class | 5334 | ··findAndLoadSequenceDictionary(Path)·-·Method·in·class |
| 5335 | ··htsjdk.samtools.reference. | 5335 | ··htsjdk.samtools.reference.IndexedFastaSequenceFile |
| 5336 | ······Attempts·to·find·and·load·the·sequence·dictionary·if·present. | 5336 | ······Attempts·to·find·and·load·the·sequence·dictionary·if·present. |
| 5337 | ··findByIndex(int)·-·Method·in·class·htsjdk.samtools.util.IntervalTree | 5337 | ··findByIndex(int)·-·Method·in·class·htsjdk.samtools.util.IntervalTree |
| 5338 | ······Find·the·nth·interval·in·the·tree. | 5338 | ······Find·the·nth·interval·in·the·tree. |
| 5339 | ··findByName(String)·-·Static·method·in·enum·class·htsjdk.samtools.SAMFlag | 5339 | ··findByName(String)·-·Static·method·in·enum·class·htsjdk.samtools.SAMFlag |
| 5340 | ······ | 5340 | ······ |
| 5341 | ··findFastaIndex(Path)·-·Static·method·in·class | 5341 | ··findFastaIndex(Path)·-·Static·method·in·class |
| 5342 | ··htsjdk.samtools.reference. | 5342 | ··htsjdk.samtools.reference.IndexedFastaSequenceFile |
| 5343 | ······ | 5343 | ······ |
| 5344 | ··findIndex(File)·-·Static·method·in·class·htsjdk.samtools.SamFiles | 5344 | ··findIndex(File)·-·Static·method·in·class·htsjdk.samtools.SamFiles |
| 5345 | ······Finds·the·index·file·associated·with·the·provided·SAM·file. | 5345 | ······Finds·the·index·file·associated·with·the·provided·SAM·file. |
| 5346 | ··findIndex(Path)·-·Static·method·in·class·htsjdk.samtools.SamFiles | 5346 | ··findIndex(Path)·-·Static·method·in·class·htsjdk.samtools.SamFiles |
| 5347 | ······Finds·the·index·file·associated·with·the·provided·SAM·file. | 5347 | ······Finds·the·index·file·associated·with·the·provided·SAM·file. |
| 5348 | ··findLastAlignedEntry(List<CRAIEntry>)·-·Static·method·in·class | 5348 | ··findLastAlignedEntry(List<CRAIEntry>)·-·Static·method·in·class |
| 5349 | ··htsjdk.samtools.cram.CRAIIndex | 5349 | ··htsjdk.samtools.cram.CRAIIndex |
| Offset 5351, 22 lines modified | Offset 5351, 22 lines modified | ||
| 5351 | ··findOverlapping(Interval)·-·Method·in·class | 5351 | ··findOverlapping(Interval)·-·Method·in·class |
| 5352 | ··htsjdk.tribble.index.interval.IntervalTree | 5352 | ··htsjdk.tribble.index.interval.IntervalTree |
| 5353 | ······ | 5353 | ······ |
| 5354 | ··findQualityTrimPoint(byte[],_int)·-·Static·method·in·class | 5354 | ··findQualityTrimPoint(byte[],_int)·-·Static·method·in·class |
| 5355 | ··htsjdk.samtools.util.TrimmingUtil | 5355 | ··htsjdk.samtools.util.TrimmingUtil |
| 5356 | ······Implements·phred-style·quality·trimming. | 5356 | ······Implements·phred-style·quality·trimming. |
| 5357 | ··findRequiredFastaIndexFile(Path)·-·Static·method·in·class | 5357 | ··findRequiredFastaIndexFile(Path)·-·Static·method·in·class |
| 5358 | ··htsjdk.samtools.reference. | 5358 | ··htsjdk.samtools.reference.IndexedFastaSequenceFile |
| 5359 | ······ | 5359 | ······ |
| 5360 | ··findSequenceDictionary(File)·-·Static·method·in·class | 5360 | ··findSequenceDictionary(File)·-·Static·method·in·class |
| 5361 | ··htsjdk.samtools.reference. | 5361 | ··htsjdk.samtools.reference.IndexedFastaSequenceFile |
| 5362 | ······Deprecated. | 5362 | ······Deprecated. |
| 5363 | ······use·findSequenceDictionary(Path)·instead. | 5363 | ······use·findSequenceDictionary(Path)·instead. |
| 5364 | ··findSequenceDictionary(Path)·-·Static·method·in·class | 5364 | ··findSequenceDictionary(Path)·-·Static·method·in·class |
| 5365 | ··htsjdk.samtools.reference. | 5365 | ··htsjdk.samtools.reference.IndexedFastaSequenceFile |
| 5366 | ······Attempts·to·locate·the·sequence·dictionary·file·adjacent·to·the·reference | 5366 | ······Attempts·to·locate·the·sequence·dictionary·file·adjacent·to·the·reference |
| 5367 | ······fasta·file. | 5367 | ······fasta·file. |
| 5368 | ··findVirtualOffsetOfFirstRecordInBam(SeekableStream)·-·Static·method·in·class | 5368 | ··findVirtualOffsetOfFirstRecordInBam(SeekableStream)·-·Static·method·in·class |
| 5369 | ··htsjdk.samtools.SAMUtils | 5369 | ··htsjdk.samtools.SAMUtils |
| 5370 | ······Returns·the·virtual·file·offset·of·the·first·record·in·a·BAM·file·-·i.e. | 5370 | ······Returns·the·virtual·file·offset·of·the·first·record·in·a·BAM·file·-·i.e. |
| 5371 | ··findVirtualOffsetOfFirstRecordInBam(File)·-·Static·method·in·class | 5371 | ··findVirtualOffsetOfFirstRecordInBam(File)·-·Static·method·in·class |
| 5372 | ··htsjdk.samtools.SAMUtils | 5372 | ··htsjdk.samtools.SAMUtils |
| Offset 5945, 15 lines modified | Offset 5945, 15 lines modified | ||
| 5945 | ··get(String)·-·Method·in·class·htsjdk.variant.variantcontext.GenotypesContext | 5945 | ··get(String)·-·Method·in·class·htsjdk.variant.variantcontext.GenotypesContext |
| 5946 | ······Gets·sample·associated·with·this·sampleName,·or·null·if·none·is·found | 5946 | ······Gets·sample·associated·with·this·sampleName,·or·null·if·none·is·found |
| 5947 | ··get(K)·-·Method·in·class·htsjdk.samtools.util.Histogram | 5947 | ··get(K)·-·Method·in·class·htsjdk.samtools.util.Histogram |
| 5948 | ······Retrieves·the·bin·associated·with·the·given·key. | 5948 | ······Retrieves·the·bin·associated·with·the·given·key. |
| 5949 | ··get(Key)·-·Method·in·class·htsjdk.samtools.util.ResourceLimitedMap | 5949 | ··get(Key)·-·Method·in·class·htsjdk.samtools.util.ResourceLimitedMap |
| 5950 | ······Return·an·existing·value,·or·create·a·new·one·if·necessary. | 5950 | ······Return·an·existing·value,·or·create·a·new·one·if·necessary. |
| 5951 | ··getAbsolutePath()·-·Method·in·class | 5951 | ··getAbsolutePath()·-·Method·in·class |
| 5952 | ··htsjdk.samtools.reference. | 5952 | ··htsjdk.samtools.reference.IndexedFastaSequenceFile |
| 5953 | ······Returns·the·full·path·to·the·reference·file. | 5953 | ······Returns·the·full·path·to·the·reference·file. |
| 5954 | ··getAcceptedCount()·-·Method·in·class·htsjdk.samtools.DownsamplingIterator | 5954 | ··getAcceptedCount()·-·Method·in·class·htsjdk.samtools.DownsamplingIterator |
| 5955 | ······Returns·the·number·of·records·returned·since·creation·of·the·last·call·to | 5955 | ······Returns·the·number·of·records·returned·since·creation·of·the·last·call·to |
| 5956 | ······resetStatistics. | 5956 | ······resetStatistics. |
| 5957 | ··getAcceptedFraction()·-·Method·in·class·htsjdk.samtools.DownsamplingIterator | 5957 | ··getAcceptedFraction()·-·Method·in·class·htsjdk.samtools.DownsamplingIterator |
| 5958 | ······Gets·the·fraction·of·records·accepted·since·creation·or·the·last·call·to | 5958 | ······Gets·the·fraction·of·records·accepted·since·creation·or·the·last·call·to |
| 5959 | ······resetStatistics(). | 5959 | ······resetStatistics(). |
| Offset 7725, 15 lines modified | Offset 7725, 15 lines modified | ||
| 7725 | ··getIndex()·-·Method·in·class·htsjdk.samtools.cram.structure.ReadTag | 7725 | ··getIndex()·-·Method·in·class·htsjdk.samtools.cram.structure.ReadTag |
| 7726 | ······ | 7726 | ······ |
| 7727 | ··getIndex()·-·Method·in·class·htsjdk.samtools.CRAMFileReader | 7727 | ··getIndex()·-·Method·in·class·htsjdk.samtools.CRAMFileReader |
| 7728 | ······ | 7728 | ······ |
| 7729 | ··getIndex()·-·Method·in·class·htsjdk.samtools.HtsgetBAMFileReader | 7729 | ··getIndex()·-·Method·in·class·htsjdk.samtools.HtsgetBAMFileReader |
| 7730 | ······Always·null·as·htsget·sources·do·not·have·indices | 7730 | ······Always·null·as·htsget·sources·do·not·have·indices |
| 7731 | ··getIndex()·-·Method·in·class | 7731 | ··getIndex()·-·Method·in·class |
| 7732 | ··htsjdk.samtools.reference. | 7732 | ··htsjdk.samtools.reference.IndexedFastaSequenceFile |
| 7733 | ······ | 7733 | ······ |
| 7734 | ··getIndex()·-·Method·in·interface·htsjdk.samtools.SamReader.Indexing | 7734 | ··getIndex()·-·Method·in·interface·htsjdk.samtools.SamReader.Indexing |
| 7735 | ······Retrieves·the·index·for·the·given·file·type. | 7735 | ······Retrieves·the·index·for·the·given·file·type. |
| 7736 | ··getIndex()·-·Method·in·interface·htsjdk.samtools.SamReader.PrimitiveSamReader | 7736 | ··getIndex()·-·Method·in·interface·htsjdk.samtools.SamReader.PrimitiveSamReader |
| 7737 | ······ | 7737 | ······ |
| 7738 | ··getIndex()·-·Method·in·class | 7738 | ··getIndex()·-·Method·in·class |
| 7739 | ··htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter | 7739 | ··htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter |
| Offset 8493, 15 lines modified | Offset 8493, 15 lines modified | ||
| 8493 | ······ | 8493 | ······ |
| 8494 | ··getPassword()·-·Method·in·interface | 8494 | ··getPassword()·-·Method·in·interface |
| 8495 | ··htsjdk.samtools.seekablestream.UserPasswordInput | 8495 | ··htsjdk.samtools.seekablestream.UserPasswordInput |
| 8496 | ······ | 8496 | ······ |
| 8497 | ··getPatchVersion()·-·Method·in·class·htsjdk.beta.plugin.HtsVersion | 8497 | ··getPatchVersion()·-·Method·in·class·htsjdk.beta.plugin.HtsVersion |
| 8498 | ······Get·the·patch·version·integer·for·this·version. | 8498 | ······Get·the·patch·version·integer·for·this·version. |
| 8499 | ··getPath()·-·Method·in·class | 8499 | ··getPath()·-·Method·in·class |
| 8500 | ··htsjdk.samtools.reference. | 8500 | ··htsjdk.samtools.reference.IndexedFastaSequenceFile |
| 8501 | ······Returns·the·path·to·the·reference·file. | 8501 | ······Returns·the·path·to·the·reference·file. |
| 8502 | ··getPath(String)·-·Static·method·in·class·htsjdk.samtools.util.IOUtil | 8502 | ··getPath(String)·-·Static·method·in·class·htsjdk.samtools.util.IOUtil |
| 8503 | ······Converts·the·given·URI·to·a·Path·object. | 8503 | ······Converts·the·given·URI·to·a·Path·object. |
| 8504 | ··getPaths(List<String>)·-·Static·method·in·class·htsjdk.samtools.util.IOUtil | 8504 | ··getPaths(List<String>)·-·Static·method·in·class·htsjdk.samtools.util.IOUtil |
| 8505 | ······ | 8505 | ······ |
| 8506 | ··getPathToDataFile(String)·-·Method·in·interface·htsjdk.tribble.FeatureCodec | 8506 | ··getPathToDataFile(String)·-·Method·in·interface·htsjdk.tribble.FeatureCodec |
| 8507 | ······Codecs·may·override·this·method·if·the·file·that·they·recognize·with | 8507 | ······Codecs·may·override·this·method·if·the·file·that·they·recognize·with |
| Offset 9219, 28 lines modified | Offset 9219, 28 lines modified | ||
| 9219 | ······Look·up·a·sequence·record·by·index. | 9219 | ······Look·up·a·sequence·record·by·index. |
| 9220 | ··getSequence(int)·-·Method·in·class·htsjdk.samtools.SAMSequenceDictionary | 9220 | ··getSequence(int)·-·Method·in·class·htsjdk.samtools.SAMSequenceDictionary |
| 9221 | ······ | 9221 | ······ |
| 9222 | ··getSequence(String)·-·Method·in·class | 9222 | ··getSequence(String)·-·Method·in·class |
| 9223 | ··htsjdk.samtools.reference.FastaSequenceFile | 9223 | ··htsjdk.samtools.reference.FastaSequenceFile |
| 9224 | ······default·implementation·--·override·if·index·is·supported | 9224 | ······default·implementation·--·override·if·index·is·supported |
| 9225 | ··getSequence(String)·-·Method·in·class | 9225 | ··getSequence(String)·-·Method·in·class |
| 9226 | ··htsjdk.samtools.reference. | 9226 | ··htsjdk.samtools.reference.IndexedFastaSequenceFile |
| 9227 | ······Retrieves·the·complete·sequence·described·by·this·contig. | 9227 | ······Retrieves·the·complete·sequence·described·by·this·contig. |
| 9228 | ··getSequence(String)·-·Method·in·interface | 9228 | ··getSequence(String)·-·Method·in·interface |
| 9229 | ··htsjdk.samtools.reference.ReferenceSequenceFile | 9229 | ··htsjdk.samtools.reference.ReferenceSequenceFile |
| 9230 | ······Retrieves·the·complete·sequence·described·by·this·contig. | 9230 | ······Retrieves·the·complete·sequence·described·by·this·contig. |
| 9231 | ··getSequence(String)·-·Method·in·class·htsjdk.samtools.SAMFileHeader | 9231 | ··getSequence(String)·-·Method·in·class·htsjdk.samtools.SAMFileHeader |
| 9232 | ······Look·up·sequence·record·by·name. | 9232 | ······Look·up·sequence·record·by·name. |
| 9233 | ··getSequence(String)·-·Method·in·class·htsjdk.samtools.SAMSequenceDictionary | 9233 | ··getSequence(String)·-·Method·in·class·htsjdk.samtools.SAMSequenceDictionary |
| 9234 | ······ | 9234 | ······ |
| 9235 | ··getSequence(String)·-·Method·in·class | 9235 | ··getSequence(String)·-·Method·in·class |
| 9236 | ··htsjdk.samtools.sra.SRAIndexedSequenceFile | 9236 | ··htsjdk.samtools.sra.SRAIndexedSequenceFile |
| 9237 | ······ | 9237 | ······ |
| 9238 | ··getSequenceDictionary()·-·Method·in·class | 9238 | ··getSequenceDictionary()·-·Method·in·class |
| 9239 | ··htsjdk.samtools.reference. | 9239 | ··htsjdk.samtools.reference.IndexedFastaSequenceFile |
| 9240 | ······Returns·the·list·of·sequence·records·associated·with·the·reference | 9240 | ······Returns·the·list·of·sequence·records·associated·with·the·reference |
| 9241 | ······sequence·if·found·otherwise·null. | 9241 | ······sequence·if·found·otherwise·null. |
| 9242 | ··getSequenceDictionary()·-·Method·in·interface | 9242 | ··getSequenceDictionary()·-·Method·in·interface |
| 9243 | ··htsjdk.samtools.reference.ReferenceSequenceFile | 9243 | ··htsjdk.samtools.reference.ReferenceSequenceFile |
| 9244 | ······Must·return·a·sequence·dictionary·with·at·least·the·following·fields | 9244 | ······Must·return·a·sequence·dictionary·with·at·least·the·following·fields |
| 9245 | ······completed·for·each·sequence:·name,·length. | 9245 | ······completed·for·each·sequence:·name,·length. |
| 9246 | ··getSequenceDictionary()·-·Method·in·class | 9246 | ··getSequenceDictionary()·-·Method·in·class |
| Offset 9478, 15 lines modified | Offset 9478, 15 lines modified | ||
| 9478 | ··getSortOrder()·-·Method·in·class·htsjdk.samtools.SAMFileHeader | 9478 | ··getSortOrder()·-·Method·in·class·htsjdk.samtools.SAMFileHeader |
| 9479 | ······ | 9479 | ······ |
| 9480 | ··getSortOrder()·-·Method·in·class·htsjdk.samtools.SAMFileWriterImpl | 9480 | ··getSortOrder()·-·Method·in·class·htsjdk.samtools.SAMFileWriterImpl |
| 9481 | ······Must·be·called·after·calling·setHeader(). | 9481 | ······Must·be·called·after·calling·setHeader(). |
| Max diff block lines reached; 5332/12449 bytes (42.83%) of diff not shown. | |||
| Offset 8131, 29 lines modified | Offset 8131, 29 lines modified | ||
| 8131 | },·{ | 8131 | },·{ |
| 8132 | ····"p":·"htsjdk.utils", | 8132 | ····"p":·"htsjdk.utils", |
| 8133 | ····"c":·"ClassFinder", | 8133 | ····"c":·"ClassFinder", |
| 8134 | ····"l":·"find(String,·Class<?>)", | 8134 | ····"l":·"find(String,·Class<?>)", |
| 8135 | ····"u":·"find(java.lang.String,java.lang.Class)" | 8135 | ····"u":·"find(java.lang.String,java.lang.Class)" |
| 8136 | },·{ | 8136 | },·{ |
| 8137 | ····"p":·"htsjdk.samtools.reference", | 8137 | ····"p":·"htsjdk.samtools.reference", |
| 8138 | ····"c":·" | 8138 | ····"c":·"IndexedFastaSequenceFile", |
| 8139 | ····"l":·"findAndLoadSequenceDictionary(Path)", | 8139 | ····"l":·"findAndLoadSequenceDictionary(Path)", |
| 8140 | ····"u":·"findAndLoadSequenceDictionary(java.nio.file.Path)" | 8140 | ····"u":·"findAndLoadSequenceDictionary(java.nio.file.Path)" |
| 8141 | },·{ | 8141 | },·{ |
| 8142 | ····"p":·"htsjdk.samtools.util", | 8142 | ····"p":·"htsjdk.samtools.util", |
| 8143 | ····"c":·"IntervalTree", | 8143 | ····"c":·"IntervalTree", |
| 8144 | ····"l":·"findByIndex(int)" | 8144 | ····"l":·"findByIndex(int)" |
| 8145 | },·{ | 8145 | },·{ |
| 8146 | ····"p":·"htsjdk.samtools", | 8146 | ····"p":·"htsjdk.samtools", |
| 8147 | ····"c":·"SAMFlag", | 8147 | ····"c":·"SAMFlag", |
| 8148 | ····"l":·"findByName(String)", | 8148 | ····"l":·"findByName(String)", |
| 8149 | ····"u":·"findByName(java.lang.String)" | 8149 | ····"u":·"findByName(java.lang.String)" |
| 8150 | },·{ | 8150 | },·{ |
| 8151 | ····"p":·"htsjdk.samtools.reference", | 8151 | ····"p":·"htsjdk.samtools.reference", |
| 8152 | ····"c":·" | 8152 | ····"c":·"IndexedFastaSequenceFile", |
| 8153 | ····"l":·"findFastaIndex(Path)", | 8153 | ····"l":·"findFastaIndex(Path)", |
| 8154 | ····"u":·"findFastaIndex(java.nio.file.Path)" | 8154 | ····"u":·"findFastaIndex(java.nio.file.Path)" |
| 8155 | },·{ | 8155 | },·{ |
| 8156 | ····"p":·"htsjdk.samtools", | 8156 | ····"p":·"htsjdk.samtools", |
| 8157 | ····"c":·"SamFiles", | 8157 | ····"c":·"SamFiles", |
| 8158 | ····"l":·"findIndex(File)", | 8158 | ····"l":·"findIndex(File)", |
| 8159 | ····"u":·"findIndex(java.io.File)" | 8159 | ····"u":·"findIndex(java.io.File)" |
| Offset 8175, 25 lines modified | Offset 8175, 25 lines modified | ||
| 8175 | },·{ | 8175 | },·{ |
| 8176 | ····"p":·"htsjdk.samtools.util", | 8176 | ····"p":·"htsjdk.samtools.util", |
| 8177 | ····"c":·"TrimmingUtil", | 8177 | ····"c":·"TrimmingUtil", |
| 8178 | ····"l":·"findQualityTrimPoint(byte[],·int)", | 8178 | ····"l":·"findQualityTrimPoint(byte[],·int)", |
| 8179 | ····"u":·"findQualityTrimPoint(byte[],int)" | 8179 | ····"u":·"findQualityTrimPoint(byte[],int)" |
| 8180 | },·{ | 8180 | },·{ |
| 8181 | ····"p":·"htsjdk.samtools.reference", | 8181 | ····"p":·"htsjdk.samtools.reference", |
| 8182 | ····"c":·" | 8182 | ····"c":·"IndexedFastaSequenceFile", |
| 8183 | ····"l":·"findRequiredFastaIndexFile(Path)", | 8183 | ····"l":·"findRequiredFastaIndexFile(Path)", |
| 8184 | ····"u":·"findRequiredFastaIndexFile(java.nio.file.Path)" | 8184 | ····"u":·"findRequiredFastaIndexFile(java.nio.file.Path)" |
| 8185 | },·{ | 8185 | },·{ |
| 8186 | ····"p":·"htsjdk.samtools.reference", | 8186 | ····"p":·"htsjdk.samtools.reference", |
| 8187 | ····"c":·" | 8187 | ····"c":·"IndexedFastaSequenceFile", |
| 8188 | ····"l":·"findSequenceDictionary(File)", | 8188 | ····"l":·"findSequenceDictionary(File)", |
| 8189 | ····"u":·"findSequenceDictionary(java.io.File)" | 8189 | ····"u":·"findSequenceDictionary(java.io.File)" |
| 8190 | },·{ | 8190 | },·{ |
| 8191 | ····"p":·"htsjdk.samtools.reference", | 8191 | ····"p":·"htsjdk.samtools.reference", |
| 8192 | ····"c":·" | 8192 | ····"c":·"IndexedFastaSequenceFile", |
| 8193 | ····"l":·"findSequenceDictionary(Path)", | 8193 | ····"l":·"findSequenceDictionary(Path)", |
| 8194 | ····"u":·"findSequenceDictionary(java.nio.file.Path)" | 8194 | ····"u":·"findSequenceDictionary(java.nio.file.Path)" |
| 8195 | },·{ | 8195 | },·{ |
| 8196 | ····"p":·"htsjdk.samtools", | 8196 | ····"p":·"htsjdk.samtools", |
| 8197 | ····"c":·"SAMUtils", | 8197 | ····"c":·"SAMUtils", |
| 8198 | ····"l":·"findVirtualOffsetOfFirstRecordInBam(File)", | 8198 | ····"l":·"findVirtualOffsetOfFirstRecordInBam(File)", |
| 8199 | ····"u":·"findVirtualOffsetOfFirstRecordInBam(java.io.File)" | 8199 | ····"u":·"findVirtualOffsetOfFirstRecordInBam(java.io.File)" |
| Offset 9020, 15 lines modified | Offset 9020, 15 lines modified | ||
| 9020 | },·{ | 9020 | },·{ |
| 9021 | ····"p":·"htsjdk.variant.variantcontext", | 9021 | ····"p":·"htsjdk.variant.variantcontext", |
| 9022 | ····"c":·"GenotypesContext", | 9022 | ····"c":·"GenotypesContext", |
| 9023 | ····"l":·"get(String)", | 9023 | ····"l":·"get(String)", |
| 9024 | ····"u":·"get(java.lang.String)" | 9024 | ····"u":·"get(java.lang.String)" |
| 9025 | },·{ | 9025 | },·{ |
| 9026 | ····"p":·"htsjdk.samtools.reference", | 9026 | ····"p":·"htsjdk.samtools.reference", |
| 9027 | ····"c":·" | 9027 | ····"c":·"IndexedFastaSequenceFile", |
| 9028 | ····"l":·"getAbsolutePath()" | 9028 | ····"l":·"getAbsolutePath()" |
| 9029 | },·{ | 9029 | },·{ |
| 9030 | ····"p":·"htsjdk.samtools", | 9030 | ····"p":·"htsjdk.samtools", |
| 9031 | ····"c":·"DownsamplingIterator", | 9031 | ····"c":·"DownsamplingIterator", |
| 9032 | ····"l":·"getAcceptedCount()" | 9032 | ····"l":·"getAcceptedCount()" |
| 9033 | },·{ | 9033 | },·{ |
| 9034 | ····"p":·"htsjdk.samtools", | 9034 | ····"p":·"htsjdk.samtools", |
| Offset 11937, 15 lines modified | Offset 11937, 15 lines modified | ||
| 11937 | ····"l":·"getIndex()" | 11937 | ····"l":·"getIndex()" |
| 11938 | },·{ | 11938 | },·{ |
| 11939 | ····"p":·"htsjdk.samtools", | 11939 | ····"p":·"htsjdk.samtools", |
| 11940 | ····"c":·"HtsgetBAMFileReader", | 11940 | ····"c":·"HtsgetBAMFileReader", |
| 11941 | ····"l":·"getIndex()" | 11941 | ····"l":·"getIndex()" |
| 11942 | },·{ | 11942 | },·{ |
| 11943 | ····"p":·"htsjdk.samtools.reference", | 11943 | ····"p":·"htsjdk.samtools.reference", |
| 11944 | ····"c":·" | 11944 | ····"c":·"IndexedFastaSequenceFile", |
| 11945 | ····"l":·"getIndex()" | 11945 | ····"l":·"getIndex()" |
| 11946 | },·{ | 11946 | },·{ |
| 11947 | ····"p":·"htsjdk.samtools", | 11947 | ····"p":·"htsjdk.samtools", |
| 11948 | ····"c":·"SamReader.Indexing", | 11948 | ····"c":·"SamReader.Indexing", |
| 11949 | ····"l":·"getIndex()" | 11949 | ····"l":·"getIndex()" |
| 11950 | },·{ | 11950 | },·{ |
| 11951 | ····"p":·"htsjdk.samtools", | 11951 | ····"p":·"htsjdk.samtools", |
| Offset 13222, 15 lines modified | Offset 13222, 15 lines modified | ||
| 13222 | ····"l":·"getPassword()" | 13222 | ····"l":·"getPassword()" |
| 13223 | },·{ | 13223 | },·{ |
| 13224 | ····"p":·"htsjdk.beta.plugin", | 13224 | ····"p":·"htsjdk.beta.plugin", |
| 13225 | ····"c":·"HtsVersion", | 13225 | ····"c":·"HtsVersion", |
| 13226 | ····"l":·"getPatchVersion()" | 13226 | ····"l":·"getPatchVersion()" |
| 13227 | },·{ | 13227 | },·{ |
| 13228 | ····"p":·"htsjdk.samtools.reference", | 13228 | ····"p":·"htsjdk.samtools.reference", |
| 13229 | ····"c":·" | 13229 | ····"c":·"IndexedFastaSequenceFile", |
| 13230 | ····"l":·"getPath()" | 13230 | ····"l":·"getPath()" |
| 13231 | },·{ | 13231 | },·{ |
| 13232 | ····"p":·"htsjdk.samtools.util", | 13232 | ····"p":·"htsjdk.samtools.util", |
| 13233 | ····"c":·"IOUtil", | 13233 | ····"c":·"IOUtil", |
| 13234 | ····"l":·"getPath(String)", | 13234 | ····"l":·"getPath(String)", |
| 13235 | ····"u":·"getPath(java.lang.String)" | 13235 | ····"u":·"getPath(java.lang.String)" |
| 13236 | },·{ | 13236 | },·{ |
| Offset 14349, 15 lines modified | Offset 14349, 15 lines modified | ||
| 14349 | },·{ | 14349 | },·{ |
| 14350 | ····"p":·"htsjdk.samtools.reference", | 14350 | ····"p":·"htsjdk.samtools.reference", |
| 14351 | ····"c":·"FastaSequenceFile", | 14351 | ····"c":·"FastaSequenceFile", |
| 14352 | ····"l":·"getSequence(String)", | 14352 | ····"l":·"getSequence(String)", |
| 14353 | ····"u":·"getSequence(java.lang.String)" | 14353 | ····"u":·"getSequence(java.lang.String)" |
| 14354 | },·{ | 14354 | },·{ |
| 14355 | ····"p":·"htsjdk.samtools.reference", | 14355 | ····"p":·"htsjdk.samtools.reference", |
| 14356 | ····"c":·" | 14356 | ····"c":·"IndexedFastaSequenceFile", |
| 14357 | ····"l":·"getSequence(String)", | 14357 | ····"l":·"getSequence(String)", |
| 14358 | ····"u":·"getSequence(java.lang.String)" | 14358 | ····"u":·"getSequence(java.lang.String)" |
| 14359 | },·{ | 14359 | },·{ |
| 14360 | ····"p":·"htsjdk.samtools.reference", | 14360 | ····"p":·"htsjdk.samtools.reference", |
| 14361 | ····"c":·"ReferenceSequenceFile", | 14361 | ····"c":·"ReferenceSequenceFile", |
| 14362 | ····"l":·"getSequence(String)", | 14362 | ····"l":·"getSequence(String)", |
| 14363 | ····"u":·"getSequence(java.lang.String)" | 14363 | ····"u":·"getSequence(java.lang.String)" |
| Offset 14374, 15 lines modified | Offset 14374, 15 lines modified | ||
| 14374 | },·{ | 14374 | },·{ |
| 14375 | ····"p":·"htsjdk.samtools.sra", | 14375 | ····"p":·"htsjdk.samtools.sra", |
| 14376 | ····"c":·"SRAIndexedSequenceFile", | 14376 | ····"c":·"SRAIndexedSequenceFile", |
| 14377 | ····"l":·"getSequence(String)", | 14377 | ····"l":·"getSequence(String)", |
| 14378 | ····"u":·"getSequence(java.lang.String)" | 14378 | ····"u":·"getSequence(java.lang.String)" |
| 14379 | },·{ | 14379 | },·{ |
| 14380 | ····"p":·"htsjdk.samtools.reference", | 14380 | ····"p":·"htsjdk.samtools.reference", |
| Max diff block lines reached; 3924/8172 bytes (48.02%) of diff not shown. | |||