{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.D63VSAQ0/b1/htsjdk_4.1.0+dfsg-1_amd64.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.D63VSAQ0/b2/htsjdk_4.1.0+dfsg-1_amd64.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,3 +1,3 @@\n \n- b78f9d715d094b93946f568e5f8f5d8d 1043544 doc optional libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb\n+ bb86e98fcd1925ed39f4fe2360f7eb44 1043536 doc optional libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb\n e2a525d9d62d110f9137837762113747 1832576 java optional libhtsjdk-java_4.1.0+dfsg-1_all.deb\n"}, {"source1": "libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb", "source2": "libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1,3 +1,3 @@\n -rw-r--r-- 0 0 0 4 2024-02-11 21:41:39.000000 debian-binary\n -rw-r--r-- 0 0 0 26368 2024-02-11 21:41:39.000000 control.tar.xz\n--rw-r--r-- 0 0 0 1016984 2024-02-11 21:41:39.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 1016976 2024-02-11 21:41:39.000000 data.tar.xz\n"}, {"source1": "control.tar.xz", "source2": "control.tar.xz", "unified_diff": null, "details": [{"source1": "control.tar", "source2": "control.tar", "unified_diff": null, "details": [{"source1": "./control", "source2": "./control", "unified_diff": "@@ -1,13 +1,13 @@\n Package: libhtsjdk-java-doc\n Source: htsjdk\n Version: 4.1.0+dfsg-1\n Architecture: all\n Maintainer: Debian Med Packaging Team \n-Installed-Size: 25146\n+Installed-Size: 25147\n Section: doc\n Priority: optional\n Multi-Arch: foreign\n Homepage: https://samtools.github.io/htsjdk/\n Description: Documentation for the java HTSJDK library\n HTSJDK is an implementation of a unified Java library for accessing common\n file formats, such as SAM (Sequence Alignment/Map) and VCF, used for\n"}, {"source1": "./md5sums", "source2": "./md5sums", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "comments": ["Files differ"], "unified_diff": null}]}]}]}, {"source1": "data.tar.xz", "source2": "data.tar.xz", "unified_diff": null, "details": [{"source1": "data.tar", "source2": "data.tar", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1080,22 +1080,22 @@\n -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\n -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\n -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\n -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\n -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\n -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\n -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\n--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\n+-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\n -rw-r--r-- 0 root (0) root (0) 25187 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/index.html\n -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\n drwxr-xr-x 0 root (0) root (0) 0 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/legal/\n -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\n -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\n -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\n--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\n+-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\n -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\n -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\n -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\n -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\n drwxr-xr-x 0 root (0) root (0) 0 2024-02-11 21:41:39.000000 ./usr/share/doc/libhtsjdk-java/api/resources/\n -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\n -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\n"}, {"source1": "./usr/share/doc/libhtsjdk-java/api/index-all.html", "source2": "./usr/share/doc/libhtsjdk-java/api/index-all.html", "unified_diff": "@@ -6667,25 +6667,25 @@\n
Scans the classpath for classes within the specified package and sub-packages that\n extend the parentType.
\n \n
find(List<CRAIEntry>, int, int, int) - Static method in class htsjdk.samtools.cram.CRAIIndex
\n
\n
Currently unused, but retained for the native rai query implementation
\n
\n-
findAndLoadSequenceDictionary(Path) - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
findAndLoadSequenceDictionary(Path) - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Attempts to find and load the sequence dictionary if present.
\n
\n
findByIndex(int) - Method in class htsjdk.samtools.util.IntervalTree
\n
\n
Find the nth interval in the tree.
\n
\n
findByName(String) - Static method in enum class htsjdk.samtools.SAMFlag
\n
 
\n-
findFastaIndex(Path) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
findFastaIndex(Path) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
 
\n
findIndex(File) - Static method in class htsjdk.samtools.SamFiles
\n
\n
Finds the index file associated with the provided SAM file.
\n
\n
findIndex(Path) - Static method in class htsjdk.samtools.SamFiles
\n
\n@@ -6697,23 +6697,23 @@\n
\n
findOverlapping(Interval) - Method in class htsjdk.tribble.index.interval.IntervalTree
\n
 
\n
findQualityTrimPoint(byte[], int) - Static method in class htsjdk.samtools.util.TrimmingUtil
\n
\n
Implements phred-style quality trimming.
\n
\n-
findRequiredFastaIndexFile(Path) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
findRequiredFastaIndexFile(Path) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
 
\n-
findSequenceDictionary(File) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
findSequenceDictionary(File) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Deprecated.\n
use findSequenceDictionary(Path) instead.
\n
\n
\n-
findSequenceDictionary(Path) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
findSequenceDictionary(Path) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Attempts to locate the sequence dictionary file adjacent to the reference fasta file.
\n
\n
findVirtualOffsetOfFirstRecordInBam(SeekableStream) - Static method in class htsjdk.samtools.SAMUtils
\n
\n
Returns the virtual file offset of the first record in a BAM file - i.e.
\n
\n@@ -7411,15 +7411,15 @@\n
\n
Retrieves the bin associated with the given key.
\n
\n
get(Key) - Method in class htsjdk.samtools.util.ResourceLimitedMap
\n
\n
Return an existing value, or create a new one if necessary.
\n
\n-
getAbsolutePath() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
getAbsolutePath() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Returns the full path to the reference file.
\n
\n
getAcceptedCount() - Method in class htsjdk.samtools.DownsamplingIterator
\n
\n
Returns the number of records returned since creation of the last call to resetStatistics.
\n
\n@@ -9377,15 +9377,15 @@\n
 
\n
getIndex() - Method in class htsjdk.samtools.CRAMFileReader
\n
 
\n
getIndex() - Method in class htsjdk.samtools.HtsgetBAMFileReader
\n
\n
Always null as htsget sources do not have indices
\n
\n-
getIndex() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
getIndex() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
 
\n
getIndex() - Method in interface htsjdk.samtools.SamReader.Indexing
\n
\n
Retrieves the index for the given file type.
\n
\n
getIndex() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader
\n
 
\n@@ -10281,15 +10281,15 @@\n  \n
getPassword() - Method in interface htsjdk.samtools.seekablestream.UserPasswordInput
\n
 
\n
getPatchVersion() - Method in class htsjdk.beta.plugin.HtsVersion
\n
\n
Get the patch version integer for this version.
\n
\n-
getPath() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
getPath() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Returns the path to the reference file.
\n
\n
getPath(String) - Static method in class htsjdk.samtools.util.IOUtil
\n
\n
Converts the given URI to a Path object.
\n
\n@@ -11120,15 +11120,15 @@\n \n
getSequence(int) - Method in class htsjdk.samtools.SAMSequenceDictionary
\n
 
\n
getSequence(String) - Method in class htsjdk.samtools.reference.FastaSequenceFile
\n
\n
default implementation -- override if index is supported
\n
\n-
getSequence(String) - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
getSequence(String) - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Retrieves the complete sequence described by this contig.
\n
\n
getSequence(String) - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
\n
\n
Retrieves the complete sequence described by this contig.
\n
\n@@ -11136,15 +11136,15 @@\n
\n
Look up sequence record by name.
\n
\n
getSequence(String) - Method in class htsjdk.samtools.SAMSequenceDictionary
\n
 
\n
getSequence(String) - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile
\n
 
\n-
getSequenceDictionary() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
getSequenceDictionary() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Returns the list of sequence records associated with the reference sequence if found\n otherwise null.
\n
\n
getSequenceDictionary() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
\n
\n
Must return a sequence dictionary with at least the following fields completed\n@@ -11386,15 +11386,15 @@\n
 
\n
getSortOrder() - Method in class htsjdk.samtools.SAMFileWriterImpl
\n
\n
Must be called after calling setHeader().
\n
\n
getSortOrder() - Method in class htsjdk.samtools.SAMSortOrderChecker
\n
 
\n-
getSource() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
getSource() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Returns the named source of the reference file.
\n
\n
getSource() - Method in class htsjdk.samtools.SAMValidationError
\n
 
\n
getSource() - Method in class htsjdk.samtools.seekablestream.ByteArraySeekableStream
\n
 
\n@@ -11561,15 +11561,15 @@\n
\n
Search for the INFO=SVTYPE and return the type of Structural Variant
\n
\n
getSubsequenceAt(String, long, long) - Method in class htsjdk.samtools.reference.FastaSequenceFile
\n
\n
default implementation -- override if index is supported
\n
\n-
getSubsequenceAt(String, long, long) - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
getSubsequenceAt(String, long, long) - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Gets the subsequence of the contig in the range [start,stop]
\n
\n
getSubsequenceAt(String, long, long) - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
\n
\n
Gets the subsequence of the contig in the range [start,stop]
\n
\n@@ -14670,15 +14670,15 @@\n
\n
Returns true if the operator is a Skipped Region Insertion or Deletion operator
\n
\n
isIndexed() - Method in class htsjdk.samtools.reference.FastaSequenceFile
\n
\n
default implementation -- override if index is supported
\n
\n-
isIndexed() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
isIndexed() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
 
\n
isIndexed() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
\n
 
\n
isIndexed() - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile
\n
 
\n
isInitialized() - Method in class htsjdk.samtools.util.Lazy
\n
 
\n@@ -16820,15 +16820,15 @@\n \n
nextPosition(int, int) - Method in interface htsjdk.samtools.util.ReferenceSequenceMask
\n
\n
It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
\n
\n
nextPosition(int, int) - Method in class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask
\n
 
\n-
nextSequence() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
nextSequence() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Gets the next sequence if available, or null if not present.
\n
\n
nextSequence() - Method in class htsjdk.samtools.reference.FastaSequenceFile
\n
 
\n
nextSequence() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
\n
\n@@ -19601,15 +19601,15 @@\n
 
\n
reset() - Method in class htsjdk.samtools.cram.io.CountingInputStream
\n
 
\n
reset() - Method in class htsjdk.samtools.cram.io.CRC32InputStream
\n
 
\n
reset() - Method in class htsjdk.samtools.cram.io.DefaultBitInputStream
\n
 
\n-
reset() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
reset() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Reset the iterator over the index.
\n
\n
reset() - Method in class htsjdk.samtools.reference.FastaSequenceFile
\n
 
\n
reset() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile
\n
\n@@ -20576,15 +20576,15 @@\n
\n
Construct a SAMValidationError with possibly-known record number.
\n
\n
SAMValidationError.Severity - Enum Class in htsjdk.samtools
\n
 
\n
SAMValidationError.Type - Enum Class in htsjdk.samtools
\n
 
\n-
sanityCheckDictionaryAgainstIndex(String, SAMSequenceDictionary, FastaSequenceIndex) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
sanityCheckDictionaryAgainstIndex(String, SAMSequenceDictionary, FastaSequenceIndex) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Do some basic checking to make sure the dictionary and the index match.
\n
\n
SanityCheckFailedException(String) - Constructor for exception htsjdk.samtools.SAMTestUtil.SanityCheckFailedException
\n
 
\n
SBI - Static variable in class htsjdk.samtools.util.FileExtensions
\n
 
\n@@ -23659,15 +23659,15 @@\n \n
toString() - Method in class htsjdk.samtools.metrics.StringHeader
\n
 
\n
toString() - Method in class htsjdk.samtools.metrics.VersionHeader
\n
 
\n
toString() - Method in class htsjdk.samtools.QueryInterval
\n
 
\n-
toString() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n+
toString() - Method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n
\n
Returns the full path to the reference file, or the source if no path was specified.
\n
\n
toString() - Method in class htsjdk.samtools.reference.FastaSequenceIndexEntry
\n
\n
For debugging.
\n
\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -5342,22 +5342,22 @@\n _\bf_\bi_\bn_\bd_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bC_\bl_\ba_\bs_\bs_\b<_\b?_\b>_\b) - Method in class htsjdk.utils._\bC_\bl_\ba_\bs_\bs_\bF_\bi_\bn_\bd_\be_\br\n Scans the classpath for classes within the specified package and sub-\n packages that extend the parentType.\n _\bf_\bi_\bn_\bd_\b(_\bL_\bi_\bs_\bt_\b<_\bC_\bR_\bA_\bI_\bE_\bn_\bt_\br_\by_\b>_\b,_\b _\bi_\bn_\bt_\b,_\b _\bi_\bn_\bt_\b,_\b _\bi_\bn_\bt_\b) - Static method in class\n htsjdk.samtools.cram._\bC_\bR_\bA_\bI_\bI_\bn_\bd_\be_\bx\n Currently unused, but retained for the native rai query implementation\n _\bf_\bi_\bn_\bd_\bA_\bn_\bd_\bL_\bo_\ba_\bd_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bD_\bi_\bc_\bt_\bi_\bo_\bn_\ba_\br_\by_\b(_\bP_\ba_\bt_\bh_\b) - Method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Attempts to find and load the sequence dictionary if present.\n _\bf_\bi_\bn_\bd_\bB_\by_\bI_\bn_\bd_\be_\bx_\b(_\bi_\bn_\bt_\b) - Method in class htsjdk.samtools.util._\bI_\bn_\bt_\be_\br_\bv_\ba_\bl_\bT_\br_\be_\be\n Find the nth interval in the tree.\n _\bf_\bi_\bn_\bd_\bB_\by_\bN_\ba_\bm_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Static method in enum class htsjdk.samtools._\bS_\bA_\bM_\bF_\bl_\ba_\bg\n \u00a0\n _\bf_\bi_\bn_\bd_\bF_\ba_\bs_\bt_\ba_\bI_\bn_\bd_\be_\bx_\b(_\bP_\ba_\bt_\bh_\b) - Static method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n \u00a0\n _\bf_\bi_\bn_\bd_\bI_\bn_\bd_\be_\bx_\b(_\bF_\bi_\bl_\be_\b) - Static method in class htsjdk.samtools._\bS_\ba_\bm_\bF_\bi_\bl_\be_\bs\n Finds the index file associated with the provided SAM file.\n _\bf_\bi_\bn_\bd_\bI_\bn_\bd_\be_\bx_\b(_\bP_\ba_\bt_\bh_\b) - Static method in class htsjdk.samtools._\bS_\ba_\bm_\bF_\bi_\bl_\be_\bs\n Finds the index file associated with the provided SAM file.\n _\bf_\bi_\bn_\bd_\bL_\ba_\bs_\bt_\bA_\bl_\bi_\bg_\bn_\be_\bd_\bE_\bn_\bt_\br_\by_\b(_\bL_\bi_\bs_\bt_\b<_\bC_\bR_\bA_\bI_\bE_\bn_\bt_\br_\by_\b>_\b) - Static method in class\n htsjdk.samtools.cram._\bC_\bR_\bA_\bI_\bI_\bn_\bd_\be_\bx\n@@ -5365,22 +5365,22 @@\n _\bf_\bi_\bn_\bd_\bO_\bv_\be_\br_\bl_\ba_\bp_\bp_\bi_\bn_\bg_\b(_\bI_\bn_\bt_\be_\br_\bv_\ba_\bl_\b) - Method in class\n htsjdk.tribble.index.interval._\bI_\bn_\bt_\be_\br_\bv_\ba_\bl_\bT_\br_\be_\be\n \u00a0\n _\bf_\bi_\bn_\bd_\bQ_\bu_\ba_\bl_\bi_\bt_\by_\bT_\br_\bi_\bm_\bP_\bo_\bi_\bn_\bt_\b(_\bb_\by_\bt_\be_\b[_\b]_\b,_\b _\bi_\bn_\bt_\b) - Static method in class\n htsjdk.samtools.util._\bT_\br_\bi_\bm_\bm_\bi_\bn_\bg_\bU_\bt_\bi_\bl\n Implements phred-style quality trimming.\n _\bf_\bi_\bn_\bd_\bR_\be_\bq_\bu_\bi_\br_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bI_\bn_\bd_\be_\bx_\bF_\bi_\bl_\be_\b(_\bP_\ba_\bt_\bh_\b) - Static method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n \u00a0\n _\bf_\bi_\bn_\bd_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bD_\bi_\bc_\bt_\bi_\bo_\bn_\ba_\br_\by_\b(_\bF_\bi_\bl_\be_\b) - Static method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Deprecated.\n use findSequenceDictionary(Path) instead.\n _\bf_\bi_\bn_\bd_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bD_\bi_\bc_\bt_\bi_\bo_\bn_\ba_\br_\by_\b(_\bP_\ba_\bt_\bh_\b) - Static method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Attempts to locate the sequence dictionary file adjacent to the reference\n fasta file.\n _\bf_\bi_\bn_\bd_\bV_\bi_\br_\bt_\bu_\ba_\bl_\bO_\bf_\bf_\bs_\be_\bt_\bO_\bf_\bF_\bi_\br_\bs_\bt_\bR_\be_\bc_\bo_\br_\bd_\bI_\bn_\bB_\ba_\bm_\b(_\bS_\be_\be_\bk_\ba_\bb_\bl_\be_\bS_\bt_\br_\be_\ba_\bm_\b) - Static method in class\n htsjdk.samtools._\bS_\bA_\bM_\bU_\bt_\bi_\bl_\bs\n Returns the virtual file offset of the first record in a BAM file - i.e.\n _\bf_\bi_\bn_\bd_\bV_\bi_\br_\bt_\bu_\ba_\bl_\bO_\bf_\bf_\bs_\be_\bt_\bO_\bf_\bF_\bi_\br_\bs_\bt_\bR_\be_\bc_\bo_\br_\bd_\bI_\bn_\bB_\ba_\bm_\b(_\bF_\bi_\bl_\be_\b) - Static method in class\n htsjdk.samtools._\bS_\bA_\bM_\bU_\bt_\bi_\bl_\bs\n@@ -5965,15 +5965,15 @@\n _\bg_\be_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class htsjdk.variant.variantcontext._\bG_\be_\bn_\bo_\bt_\by_\bp_\be_\bs_\bC_\bo_\bn_\bt_\be_\bx_\bt\n Gets sample associated with this sampleName, or null if none is found\n _\bg_\be_\bt_\b(_\bK_\b) - Method in class htsjdk.samtools.util._\bH_\bi_\bs_\bt_\bo_\bg_\br_\ba_\bm\n Retrieves the bin associated with the given key.\n _\bg_\be_\bt_\b(_\bK_\be_\by_\b) - Method in class htsjdk.samtools.util._\bR_\be_\bs_\bo_\bu_\br_\bc_\be_\bL_\bi_\bm_\bi_\bt_\be_\bd_\bM_\ba_\bp\n Return an existing value, or create a new one if necessary.\n _\bg_\be_\bt_\bA_\bb_\bs_\bo_\bl_\bu_\bt_\be_\bP_\ba_\bt_\bh_\b(_\b) - Method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Returns the full path to the reference file.\n _\bg_\be_\bt_\bA_\bc_\bc_\be_\bp_\bt_\be_\bd_\bC_\bo_\bu_\bn_\bt_\b(_\b) - Method in class htsjdk.samtools._\bD_\bo_\bw_\bn_\bs_\ba_\bm_\bp_\bl_\bi_\bn_\bg_\bI_\bt_\be_\br_\ba_\bt_\bo_\br\n Returns the number of records returned since creation of the last call to\n resetStatistics.\n _\bg_\be_\bt_\bA_\bc_\bc_\be_\bp_\bt_\be_\bd_\bF_\br_\ba_\bc_\bt_\bi_\bo_\bn_\b(_\b) - Method in class htsjdk.samtools._\bD_\bo_\bw_\bn_\bs_\ba_\bm_\bp_\bl_\bi_\bn_\bg_\bI_\bt_\be_\br_\ba_\bt_\bo_\br\n Gets the fraction of records accepted since creation or the last call to\n resetStatistics().\n@@ -7745,15 +7745,15 @@\n _\bg_\be_\bt_\bI_\bn_\bd_\be_\bx_\b(_\b) - Method in class htsjdk.samtools.cram.structure._\bR_\be_\ba_\bd_\bT_\ba_\bg\n \u00a0\n _\bg_\be_\bt_\bI_\bn_\bd_\be_\bx_\b(_\b) - Method in class htsjdk.samtools._\bC_\bR_\bA_\bM_\bF_\bi_\bl_\be_\bR_\be_\ba_\bd_\be_\br\n \u00a0\n _\bg_\be_\bt_\bI_\bn_\bd_\be_\bx_\b(_\b) - Method in class htsjdk.samtools._\bH_\bt_\bs_\bg_\be_\bt_\bB_\bA_\bM_\bF_\bi_\bl_\be_\bR_\be_\ba_\bd_\be_\br\n Always null as htsget sources do not have indices\n _\bg_\be_\bt_\bI_\bn_\bd_\be_\bx_\b(_\b) - Method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n \u00a0\n _\bg_\be_\bt_\bI_\bn_\bd_\be_\bx_\b(_\b) - Method in interface htsjdk.samtools._\bS_\ba_\bm_\bR_\be_\ba_\bd_\be_\br_\b._\bI_\bn_\bd_\be_\bx_\bi_\bn_\bg\n Retrieves the index for the given file type.\n _\bg_\be_\bt_\bI_\bn_\bd_\be_\bx_\b(_\b) - Method in interface htsjdk.samtools._\bS_\ba_\bm_\bR_\be_\ba_\bd_\be_\br_\b._\bP_\br_\bi_\bm_\bi_\bt_\bi_\bv_\be_\bS_\ba_\bm_\bR_\be_\ba_\bd_\be_\br\n \u00a0\n _\bg_\be_\bt_\bI_\bn_\bd_\be_\bx_\b(_\b) - Method in class\n htsjdk.samtools._\bS_\ba_\bm_\bR_\be_\ba_\bd_\be_\br_\b._\bP_\br_\bi_\bm_\bi_\bt_\bi_\bv_\be_\bS_\ba_\bm_\bR_\be_\ba_\bd_\be_\br_\bT_\bo_\bS_\ba_\bm_\bR_\be_\ba_\bd_\be_\br_\bA_\bd_\ba_\bp_\bt_\be_\br\n@@ -8513,15 +8513,15 @@\n \u00a0\n _\bg_\be_\bt_\bP_\ba_\bs_\bs_\bw_\bo_\br_\bd_\b(_\b) - Method in interface\n htsjdk.samtools.seekablestream._\bU_\bs_\be_\br_\bP_\ba_\bs_\bs_\bw_\bo_\br_\bd_\bI_\bn_\bp_\bu_\bt\n \u00a0\n _\bg_\be_\bt_\bP_\ba_\bt_\bc_\bh_\bV_\be_\br_\bs_\bi_\bo_\bn_\b(_\b) - Method in class htsjdk.beta.plugin._\bH_\bt_\bs_\bV_\be_\br_\bs_\bi_\bo_\bn\n Get the patch version integer for this version.\n _\bg_\be_\bt_\bP_\ba_\bt_\bh_\b(_\b) - Method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Returns the path to the reference file.\n _\bg_\be_\bt_\bP_\ba_\bt_\bh_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Static method in class htsjdk.samtools.util._\bI_\bO_\bU_\bt_\bi_\bl\n Converts the given URI to a _\bP_\ba_\bt_\bh object.\n _\bg_\be_\bt_\bP_\ba_\bt_\bh_\bs_\b(_\bL_\bi_\bs_\bt_\b<_\bS_\bt_\br_\bi_\bn_\bg_\b>_\b) - Static method in class htsjdk.samtools.util._\bI_\bO_\bU_\bt_\bi_\bl\n \u00a0\n _\bg_\be_\bt_\bP_\ba_\bt_\bh_\bT_\bo_\bD_\ba_\bt_\ba_\bF_\bi_\bl_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in interface htsjdk.tribble._\bF_\be_\ba_\bt_\bu_\br_\be_\bC_\bo_\bd_\be_\bc\n Codecs may override this method if the file that they recognize with\n@@ -9239,28 +9239,28 @@\n Look up a sequence record by index.\n _\bg_\be_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b(_\bi_\bn_\bt_\b) - Method in class htsjdk.samtools._\bS_\bA_\bM_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bD_\bi_\bc_\bt_\bi_\bo_\bn_\ba_\br_\by\n \u00a0\n _\bg_\be_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n htsjdk.samtools.reference._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n default implementation -- override if index is supported\n _\bg_\be_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Retrieves the complete sequence described by this contig.\n _\bg_\be_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in interface\n htsjdk.samtools.reference._\bR_\be_\bf_\be_\br_\be_\bn_\bc_\be_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Retrieves the complete sequence described by this contig.\n _\bg_\be_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class htsjdk.samtools._\bS_\bA_\bM_\bF_\bi_\bl_\be_\bH_\be_\ba_\bd_\be_\br\n Look up sequence record by name.\n _\bg_\be_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class htsjdk.samtools._\bS_\bA_\bM_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bD_\bi_\bc_\bt_\bi_\bo_\bn_\ba_\br_\by\n \u00a0\n _\bg_\be_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n htsjdk.samtools.sra._\bS_\bR_\bA_\bI_\bn_\bd_\be_\bx_\be_\bd_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n \u00a0\n _\bg_\be_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bD_\bi_\bc_\bt_\bi_\bo_\bn_\ba_\br_\by_\b(_\b) - Method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Returns the list of sequence records associated with the reference\n sequence if found otherwise null.\n _\bg_\be_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bD_\bi_\bc_\bt_\bi_\bo_\bn_\ba_\br_\by_\b(_\b) - Method in interface\n htsjdk.samtools.reference._\bR_\be_\bf_\be_\br_\be_\bn_\bc_\be_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Must return a sequence dictionary with at least the following fields\n completed for each sequence: name, length.\n _\bg_\be_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bD_\bi_\bc_\bt_\bi_\bo_\bn_\ba_\br_\by_\b(_\b) - Method in class\n@@ -9498,15 +9498,15 @@\n _\bg_\be_\bt_\bS_\bo_\br_\bt_\bO_\br_\bd_\be_\br_\b(_\b) - Method in class htsjdk.samtools._\bS_\bA_\bM_\bF_\bi_\bl_\be_\bH_\be_\ba_\bd_\be_\br\n \u00a0\n _\bg_\be_\bt_\bS_\bo_\br_\bt_\bO_\br_\bd_\be_\br_\b(_\b) - Method in class htsjdk.samtools._\bS_\bA_\bM_\bF_\bi_\bl_\be_\bW_\br_\bi_\bt_\be_\br_\bI_\bm_\bp_\bl\n Must be called after calling setHeader().\n _\bg_\be_\bt_\bS_\bo_\br_\bt_\bO_\br_\bd_\be_\br_\b(_\b) - Method in class htsjdk.samtools._\bS_\bA_\bM_\bS_\bo_\br_\bt_\bO_\br_\bd_\be_\br_\bC_\bh_\be_\bc_\bk_\be_\br\n \u00a0\n _\bg_\be_\bt_\bS_\bo_\bu_\br_\bc_\be_\b(_\b) - Method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Returns the named source of the reference file.\n _\bg_\be_\bt_\bS_\bo_\bu_\br_\bc_\be_\b(_\b) - Method in class htsjdk.samtools._\bS_\bA_\bM_\bV_\ba_\bl_\bi_\bd_\ba_\bt_\bi_\bo_\bn_\bE_\br_\br_\bo_\br\n \u00a0\n _\bg_\be_\bt_\bS_\bo_\bu_\br_\bc_\be_\b(_\b) - Method in class\n htsjdk.samtools.seekablestream._\bB_\by_\bt_\be_\bA_\br_\br_\ba_\by_\bS_\be_\be_\bk_\ba_\bb_\bl_\be_\bS_\bt_\br_\be_\ba_\bm\n \u00a0\n _\bg_\be_\bt_\bS_\bo_\bu_\br_\bc_\be_\b(_\b) - Method in class\n@@ -9657,15 +9657,15 @@\n _\bg_\be_\bt_\bS_\bt_\br_\bu_\bc_\bt_\bu_\br_\ba_\bl_\bV_\ba_\br_\bi_\ba_\bn_\bt_\bT_\by_\bp_\be_\b(_\b) - Method in class\n htsjdk.variant.variantcontext._\bV_\ba_\br_\bi_\ba_\bn_\bt_\bC_\bo_\bn_\bt_\be_\bx_\bt\n Search for the INFO=SVTYPE and return the type of Structural Variant\n _\bg_\be_\bt_\bS_\bu_\bb_\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\bA_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bl_\bo_\bn_\bg_\b,_\b _\bl_\bo_\bn_\bg_\b) - Method in class\n htsjdk.samtools.reference._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n default implementation -- override if index is supported\n _\bg_\be_\bt_\bS_\bu_\bb_\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\bA_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bl_\bo_\bn_\bg_\b,_\b _\bl_\bo_\bn_\bg_\b) - Method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Gets the subsequence of the contig in the range [start,stop]\n _\bg_\be_\bt_\bS_\bu_\bb_\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\bA_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bl_\bo_\bn_\bg_\b,_\b _\bl_\bo_\bn_\bg_\b) - Method in interface\n htsjdk.samtools.reference._\bR_\be_\bf_\be_\br_\be_\bn_\bc_\be_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Gets the subsequence of the contig in the range [start,stop]\n _\bg_\be_\bt_\bS_\bu_\bb_\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\bA_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bl_\bo_\bn_\bg_\b,_\b _\bl_\bo_\bn_\bg_\b) - Method in class\n htsjdk.samtools.sra._\bS_\bR_\bA_\bI_\bn_\bd_\be_\bx_\be_\bd_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n \u00a0\n@@ -12538,15 +12538,15 @@\n convenience method for indels\n _\bi_\bs_\bI_\bn_\bd_\be_\bl_\bO_\br_\bS_\bk_\bi_\bp_\bp_\be_\bd_\bR_\be_\bg_\bi_\bo_\bn_\b(_\b) - Method in enum class htsjdk.samtools._\bC_\bi_\bg_\ba_\br_\bO_\bp_\be_\br_\ba_\bt_\bo_\br\n Returns true if the operator is a Skipped Region Insertion or Deletion\n operator\n _\bi_\bs_\bI_\bn_\bd_\be_\bx_\be_\bd_\b(_\b) - Method in class htsjdk.samtools.reference._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n default implementation -- override if index is supported\n _\bi_\bs_\bI_\bn_\bd_\be_\bx_\be_\bd_\b(_\b) - Method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n \u00a0\n _\bi_\bs_\bI_\bn_\bd_\be_\bx_\be_\bd_\b(_\b) - Method in interface\n htsjdk.samtools.reference._\bR_\be_\bf_\be_\br_\be_\bn_\bc_\be_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n \u00a0\n _\bi_\bs_\bI_\bn_\bd_\be_\bx_\be_\bd_\b(_\b) - Method in class htsjdk.samtools.sra._\bS_\bR_\bA_\bI_\bn_\bd_\be_\bx_\be_\bd_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n \u00a0\n _\bi_\bs_\bI_\bn_\bi_\bt_\bi_\ba_\bl_\bi_\bz_\be_\bd_\b(_\b) - Method in class htsjdk.samtools.util._\bL_\ba_\bz_\by\n@@ -14392,15 +14392,15 @@\n htsjdk.samtools.util._\bR_\be_\bf_\be_\br_\be_\bn_\bc_\be_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bM_\ba_\bs_\bk\n It is required that sequenceIndex is >= any previous sequenceIndex passed\n to this class.\n _\bn_\be_\bx_\bt_\bP_\bo_\bs_\bi_\bt_\bi_\bo_\bn_\b(_\bi_\bn_\bt_\b,_\b _\bi_\bn_\bt_\b) - Method in class\n htsjdk.samtools.util._\bW_\bh_\bo_\bl_\be_\bG_\be_\bn_\bo_\bm_\be_\bR_\be_\bf_\be_\br_\be_\bn_\bc_\be_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bM_\ba_\bs_\bk\n \u00a0\n _\bn_\be_\bx_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b(_\b) - Method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Gets the next sequence if available, or null if not present.\n _\bn_\be_\bx_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b(_\b) - Method in class htsjdk.samtools.reference._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n \u00a0\n _\bn_\be_\bx_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b(_\b) - Method in interface\n htsjdk.samtools.reference._\bR_\be_\bf_\be_\br_\be_\bn_\bc_\be_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Retrieves the next whole sequences from the file.\n _\bn_\be_\bx_\bt_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b(_\b) - Method in class htsjdk.samtools.sra._\bS_\bR_\bA_\bI_\bn_\bd_\be_\bx_\be_\bd_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n@@ -16836,15 +16836,16 @@\n \u00a0\n _\br_\be_\bs_\be_\bt_\b(_\b) - Method in class htsjdk.samtools.cram.io._\bC_\bo_\bu_\bn_\bt_\bi_\bn_\bg_\bI_\bn_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm\n \u00a0\n _\br_\be_\bs_\be_\bt_\b(_\b) - Method in class htsjdk.samtools.cram.io._\bC_\bR_\bC_\b3_\b2_\bI_\bn_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm\n \u00a0\n _\br_\be_\bs_\be_\bt_\b(_\b) - Method in class htsjdk.samtools.cram.io._\bD_\be_\bf_\ba_\bu_\bl_\bt_\bB_\bi_\bt_\bI_\bn_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm\n \u00a0\n- _\br_\be_\bs_\be_\bt_\b(_\b) - Method in class htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ _\br_\be_\bs_\be_\bt_\b(_\b) - Method in class\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Reset the iterator over the index.\n _\br_\be_\bs_\be_\bt_\b(_\b) - Method in class htsjdk.samtools.reference._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n \u00a0\n _\br_\be_\bs_\be_\bt_\b(_\b) - Method in interface htsjdk.samtools.reference._\bR_\be_\bf_\be_\br_\be_\bn_\bc_\be_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Resets the ReferenceSequenceFile so that the next call to nextSequence()\n will return the first sequence in the file.\n _\br_\be_\bs_\be_\bt_\b(_\b) - Method in class htsjdk.samtools.seekablestream._\bS_\be_\be_\bk_\ba_\bb_\bl_\be_\bS_\bt_\br_\be_\ba_\bm\n@@ -17645,15 +17646,15 @@\n Construct a SAMValidationError with possibly-known record number.\n _\bS_\bA_\bM_\bV_\ba_\bl_\bi_\bd_\ba_\bt_\bi_\bo_\bn_\bE_\br_\br_\bo_\br_\b._\bS_\be_\bv_\be_\br_\bi_\bt_\by - Enum Class in _\bh_\bt_\bs_\bj_\bd_\bk_\b._\bs_\ba_\bm_\bt_\bo_\bo_\bl_\bs\n \u00a0\n _\bS_\bA_\bM_\bV_\ba_\bl_\bi_\bd_\ba_\bt_\bi_\bo_\bn_\bE_\br_\br_\bo_\br_\b._\bT_\by_\bp_\be - Enum Class in _\bh_\bt_\bs_\bj_\bd_\bk_\b._\bs_\ba_\bm_\bt_\bo_\bo_\bl_\bs\n \u00a0\n _\bs_\ba_\bn_\bi_\bt_\by_\bC_\bh_\be_\bc_\bk_\bD_\bi_\bc_\bt_\bi_\bo_\bn_\ba_\br_\by_\bA_\bg_\ba_\bi_\bn_\bs_\bt_\bI_\bn_\bd_\be_\bx_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bA_\bM_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bD_\bi_\bc_\bt_\bi_\bo_\bn_\ba_\br_\by_\b,\n _\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bI_\bn_\bd_\be_\bx_\b) - Static method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Do some basic checking to make sure the dictionary and the index match.\n _\bS_\ba_\bn_\bi_\bt_\by_\bC_\bh_\be_\bc_\bk_\bF_\ba_\bi_\bl_\be_\bd_\bE_\bx_\bc_\be_\bp_\bt_\bi_\bo_\bn_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Constructor for exception\n htsjdk.samtools._\bS_\bA_\bM_\bT_\be_\bs_\bt_\bU_\bt_\bi_\bl_\b._\bS_\ba_\bn_\bi_\bt_\by_\bC_\bh_\be_\bc_\bk_\bF_\ba_\bi_\bl_\be_\bd_\bE_\bx_\bc_\be_\bp_\bt_\bi_\bo_\bn\n \u00a0\n _\bS_\bB_\bI - Static variable in class htsjdk.samtools.util._\bF_\bi_\bl_\be_\bE_\bx_\bt_\be_\bn_\bs_\bi_\bo_\bn_\bs\n \u00a0\n _\bS_\bB_\bI_\bI_\bn_\bd_\be_\bx - Class in _\bh_\bt_\bs_\bj_\bd_\bk_\b._\bs_\ba_\bm_\bt_\bo_\bo_\bl_\bs\n@@ -20457,15 +20458,15 @@\n _\bt_\bo_\bS_\bt_\br_\bi_\bn_\bg_\b(_\b) - Method in class htsjdk.samtools.metrics._\bS_\bt_\br_\bi_\bn_\bg_\bH_\be_\ba_\bd_\be_\br\n \u00a0\n _\bt_\bo_\bS_\bt_\br_\bi_\bn_\bg_\b(_\b) - Method in class htsjdk.samtools.metrics._\bV_\be_\br_\bs_\bi_\bo_\bn_\bH_\be_\ba_\bd_\be_\br\n \u00a0\n _\bt_\bo_\bS_\bt_\br_\bi_\bn_\bg_\b(_\b) - Method in class htsjdk.samtools._\bQ_\bu_\be_\br_\by_\bI_\bn_\bt_\be_\br_\bv_\ba_\bl\n \u00a0\n _\bt_\bo_\bS_\bt_\br_\bi_\bn_\bg_\b(_\b) - Method in class\n- htsjdk.samtools.reference._\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n+ htsjdk.samtools.reference._\bB_\bl_\bo_\bc_\bk_\bC_\bo_\bm_\bp_\br_\be_\bs_\bs_\be_\bd_\bI_\bn_\bd_\be_\bx_\be_\bd_\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bF_\bi_\bl_\be\n Returns the full path to the reference file, or the source if no path was\n specified.\n _\bt_\bo_\bS_\bt_\br_\bi_\bn_\bg_\b(_\b) - Method in class\n htsjdk.samtools.reference._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bI_\bn_\bd_\be_\bx_\bE_\bn_\bt_\br_\by\n For debugging.\n _\bt_\bo_\bS_\bt_\br_\bi_\bn_\bg_\b(_\b) - Method in class htsjdk.samtools.reference._\bR_\be_\bf_\be_\br_\be_\bn_\bc_\be_\bS_\be_\bq_\bu_\be_\bn_\bc_\be\n \u00a0\n"}]}, {"source1": "./usr/share/doc/libhtsjdk-java/api/member-search-index.js", "source2": "./usr/share/doc/libhtsjdk-java/api/member-search-index.js", "unified_diff": null, "details": [{"source1": "js-beautify {}", "source2": "js-beautify {}", "unified_diff": "@@ -8165,29 +8165,29 @@\n }, {\n \"p\": \"htsjdk.utils\",\n \"c\": \"ClassFinder\",\n \"l\": \"find(String, Class)\",\n \"u\": \"find(java.lang.String,java.lang.Class)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"findAndLoadSequenceDictionary(Path)\",\n \"u\": \"findAndLoadSequenceDictionary(java.nio.file.Path)\"\n }, {\n \"p\": \"htsjdk.samtools.util\",\n \"c\": \"IntervalTree\",\n \"l\": \"findByIndex(int)\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"SAMFlag\",\n \"l\": \"findByName(String)\",\n \"u\": \"findByName(java.lang.String)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"findFastaIndex(Path)\",\n \"u\": \"findFastaIndex(java.nio.file.Path)\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"SamFiles\",\n \"l\": \"findIndex(File)\",\n \"u\": \"findIndex(java.io.File)\"\n@@ -8209,25 +8209,25 @@\n }, {\n \"p\": \"htsjdk.samtools.util\",\n \"c\": \"TrimmingUtil\",\n \"l\": \"findQualityTrimPoint(byte[], int)\",\n \"u\": \"findQualityTrimPoint(byte[],int)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"findRequiredFastaIndexFile(Path)\",\n \"u\": \"findRequiredFastaIndexFile(java.nio.file.Path)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"findSequenceDictionary(File)\",\n \"u\": \"findSequenceDictionary(java.io.File)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"findSequenceDictionary(Path)\",\n \"u\": \"findSequenceDictionary(java.nio.file.Path)\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"SAMUtils\",\n \"l\": \"findVirtualOffsetOfFirstRecordInBam(File)\",\n \"u\": \"findVirtualOffsetOfFirstRecordInBam(java.io.File)\"\n@@ -9064,15 +9064,15 @@\n }, {\n \"p\": \"htsjdk.variant.variantcontext\",\n \"c\": \"GenotypesContext\",\n \"l\": \"get(String)\",\n \"u\": \"get(java.lang.String)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"getAbsolutePath()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"DownsamplingIterator\",\n \"l\": \"getAcceptedCount()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n@@ -11981,15 +11981,15 @@\n \"l\": \"getIndex()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"HtsgetBAMFileReader\",\n \"l\": \"getIndex()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"getIndex()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"SamReader.Indexing\",\n \"l\": \"getIndex()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n@@ -13266,15 +13266,15 @@\n \"l\": \"getPassword()\"\n }, {\n \"p\": \"htsjdk.beta.plugin\",\n \"c\": \"HtsVersion\",\n \"l\": \"getPatchVersion()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"getPath()\"\n }, {\n \"p\": \"htsjdk.samtools.util\",\n \"c\": \"IOUtil\",\n \"l\": \"getPath(String)\",\n \"u\": \"getPath(java.lang.String)\"\n }, {\n@@ -14393,15 +14393,15 @@\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"FastaSequenceFile\",\n \"l\": \"getSequence(String)\",\n \"u\": \"getSequence(java.lang.String)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"getSequence(String)\",\n \"u\": \"getSequence(java.lang.String)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"ReferenceSequenceFile\",\n \"l\": \"getSequence(String)\",\n \"u\": \"getSequence(java.lang.String)\"\n@@ -14418,15 +14418,15 @@\n }, {\n \"p\": \"htsjdk.samtools.sra\",\n \"c\": \"SRAIndexedSequenceFile\",\n \"l\": \"getSequence(String)\",\n \"u\": \"getSequence(java.lang.String)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"getSequenceDictionary()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"ReferenceSequenceFile\",\n \"l\": \"getSequenceDictionary()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n@@ -14813,15 +14813,15 @@\n \"l\": \"getSortOrder()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"SAMSortOrderChecker\",\n \"l\": \"getSortOrder()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"getSource()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"SAMValidationError\",\n \"l\": \"getSource()\"\n }, {\n \"p\": \"htsjdk.samtools.seekablestream\",\n@@ -15098,15 +15098,15 @@\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"FastaSequenceFile\",\n \"l\": \"getSubsequenceAt(String, long, long)\",\n \"u\": \"getSubsequenceAt(java.lang.String,long,long)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"getSubsequenceAt(String, long, long)\",\n \"u\": \"getSubsequenceAt(java.lang.String,long,long)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"ReferenceSequenceFile\",\n \"l\": \"getSubsequenceAt(String, long, long)\",\n \"u\": \"getSubsequenceAt(java.lang.String,long,long)\"\n@@ -18872,15 +18872,15 @@\n \"l\": \"isIndelOrSkippedRegion()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"FastaSequenceFile\",\n \"l\": \"isIndexed()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"isIndexed()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"ReferenceSequenceFile\",\n \"l\": \"isIndexed()\"\n }, {\n \"p\": \"htsjdk.samtools.sra\",\n@@ -21554,15 +21554,15 @@\n }, {\n \"p\": \"htsjdk.samtools.util\",\n \"c\": \"WholeGenomeReferenceSequenceMask\",\n \"l\": \"nextPosition(int, int)\",\n \"u\": \"nextPosition(int,int)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"nextSequence()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"FastaSequenceFile\",\n \"l\": \"nextSequence()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n@@ -25256,15 +25256,15 @@\n \"l\": \"reset()\"\n }, {\n \"p\": \"htsjdk.samtools.cram.io\",\n \"c\": \"DefaultBitInputStream\",\n \"l\": \"reset()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"reset()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"FastaSequenceFile\",\n \"l\": \"reset()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n@@ -26204,15 +26204,15 @@\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"SAMValidationError\",\n \"l\": \"SAMValidationError(SAMValidationError.Type, String, String, long)\",\n \"u\": \"%3Cinit%3E(htsjdk.samtools.SAMValidationError.Type,java.lang.String,java.lang.String,long)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"sanityCheckDictionaryAgainstIndex(String, SAMSequenceDictionary, FastaSequenceIndex)\",\n \"u\": \"sanityCheckDictionaryAgainstIndex(java.lang.String,htsjdk.samtools.SAMSequenceDictionary,htsjdk.samtools.reference.FastaSequenceIndex)\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"SAMTestUtil.SanityCheckFailedException\",\n \"l\": \"SanityCheckFailedException(String)\",\n \"u\": \"%3Cinit%3E(java.lang.String)\"\n@@ -30294,15 +30294,15 @@\n \"l\": \"toString()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"QueryInterval\",\n \"l\": \"toString()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"IndexedFastaSequenceFile\",\n+ \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n \"l\": \"toString()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"FastaSequenceIndexEntry\",\n \"l\": \"toString()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n"}]}]}]}]}]}