{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.vNBeAiMR/b1/htsjdk_3.0.4+dfsg-2_amd64.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.vNBeAiMR/b2/htsjdk_3.0.4+dfsg-2_amd64.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,3 +1,3 @@\n \n- ade76d3e47ac7c87ff978658c9a13b8a 1039096 doc optional libhtsjdk-java-doc_3.0.4+dfsg-2_all.deb\n+ 96b25c388cdab2d1f1d20ddaf510edab 1039072 doc optional libhtsjdk-java-doc_3.0.4+dfsg-2_all.deb\n 3375151baf60e103b9d2d83d44ecd7ab 1813244 java optional libhtsjdk-java_3.0.4+dfsg-2_all.deb\n"}, {"source1": "libhtsjdk-java-doc_3.0.4+dfsg-2_all.deb", "source2": "libhtsjdk-java-doc_3.0.4+dfsg-2_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 2023-01-24 03:16:14.000000 debian-binary\n -rw-r--r-- 0 0 0 26364 2023-01-24 03:16:14.000000 control.tar.xz\n--rw-r--r-- 0 0 0 1012540 2023-01-24 03:16:14.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 1012516 2023-01-24 03:16:14.000000 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: 3.0.4+dfsg-2\n Architecture: all\n Maintainer: Debian Med Packaging Team \n-Installed-Size: 25095\n+Installed-Size: 25093\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": "@@ -1079,22 +1079,22 @@\n -rw-r--r-- 0 root (0) root (0) 10867 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html\n -rw-r--r-- 0 root (0) root (0) 32388 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html\n -rw-r--r-- 0 root (0) root (0) 29765 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html\n -rw-r--r-- 0 root (0) root (0) 9958 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFTextTransformer.html\n -rw-r--r-- 0 root (0) root (0) 28441 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFUtils.html\n -rw-r--r-- 0 root (0) root (0) 14736 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-summary.html\n -rw-r--r-- 0 root (0) root (0) 13991 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-tree.html\n--rw-r--r-- 0 root (0) root (0) 3125889 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/index-all.html\n+-rw-r--r-- 0 root (0) root (0) 3125124 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/index-all.html\n -rw-r--r-- 0 root (0) root (0) 25187 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/index.html\n -rw-r--r-- 0 root (0) root (0) 1498 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/jquery-ui.overrides.css\n drwxr-xr-x 0 root (0) root (0) 0 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/legal/\n -rw-r--r-- 0 root (0) root (0) 1522 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/legal/ASSEMBLY_EXCEPTION\n -rw-r--r-- 0 root (0) root (0) 2936 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/legal/jquery.md\n -rw-r--r-- 0 root (0) root (0) 1870 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/legal/jqueryUI.md\n--rw-r--r-- 0 root (0) root (0) 801891 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/member-search-index.js\n+-rw-r--r-- 0 root (0) root (0) 801636 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/member-search-index.js\n -rw-r--r-- 0 root (0) root (0) 45 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/module-search-index.js\n -rw-r--r-- 0 root (0) root (0) 826 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/overview-summary.html\n -rw-r--r-- 0 root (0) root (0) 237418 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/overview-tree.html\n -rw-r--r-- 0 root (0) root (0) 3152 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/package-search-index.js\n drwxr-xr-x 0 root (0) root (0) 0 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/resources/\n -rw-r--r-- 0 root (0) root (0) 499 2023-01-24 03:16:14.000000 ./usr/share/doc/libhtsjdk-java/api/resources/glass.png\n -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\n"}, {"source1": "./usr/share/doc/libhtsjdk-java/api/index-all.html", "source2": "./usr/share/doc/libhtsjdk-java/api/index-all.html", "unified_diff": "@@ -6640,25 +6640,25 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
findAndLoadSequenceDictionary(Path) - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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.BlockCompressedIndexedFastaSequenceFile
\n+
findFastaIndex(Path) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -6670,23 +6670,23 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
findRequiredFastaIndexFile(Path) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n
 
\n-
findSequenceDictionary(File) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n+
findSequenceDictionary(File) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\n
\n
Deprecated.\n
use findSequenceDictionary(Path) instead.
\n
\n
\n-
findSequenceDictionary(Path) - Static method in class htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
\n+
findSequenceDictionary(Path) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -7377,15 +7377,15 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
getAbsolutePath() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -9343,15 +9343,15 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
getIndex() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -10247,15 +10247,15 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
getPath() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -11086,15 +11086,15 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
getSequence(String) - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -11102,15 +11102,15 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
getSequenceDictionary() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -11352,15 +11352,15 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
getSource() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -11527,15 +11527,15 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
getSubsequenceAt(String, long, long) - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -14625,15 +14625,15 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
isIndexed() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -16769,15 +16769,15 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
nextSequence() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -19541,15 +19541,15 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
reset() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -20516,15 +20516,15 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
sanityCheckDictionaryAgainstIndex(String, SAMSequenceDictionary, FastaSequenceIndex) - Static method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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@@ -23599,15 +23599,15 @@\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.BlockCompressedIndexedFastaSequenceFile
\n+
toString() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile
\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": "@@ -5328,22 +5328,22 @@\n find(String,_Class) - Method in class htsjdk.utils.ClassFinder\n Scans the classpath for classes within the specified package and sub-\n packages that extend the parentType.\n find(List,_int,_int,_int) - Static method in class\n htsjdk.samtools.cram.CRAIIndex\n Currently unused, but retained for the native rai query implementation\n findAndLoadSequenceDictionary(Path) - Method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n Attempts to find and load the sequence dictionary if present.\n findByIndex(int) - Method in class htsjdk.samtools.util.IntervalTree\n Find the nth interval in the tree.\n findByName(String) - Static method in enum class htsjdk.samtools.SAMFlag\n \u00a0\n findFastaIndex(Path) - Static method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n \u00a0\n findIndex(File) - Static method in class htsjdk.samtools.SamFiles\n Finds the index file associated with the provided SAM file.\n findIndex(Path) - Static method in class htsjdk.samtools.SamFiles\n Finds the index file associated with the provided SAM file.\n findLastAlignedEntry(List) - Static method in class\n htsjdk.samtools.cram.CRAIIndex\n@@ -5351,22 +5351,22 @@\n findOverlapping(Interval) - Method in class\n htsjdk.tribble.index.interval.IntervalTree\n \u00a0\n findQualityTrimPoint(byte[],_int) - Static method in class\n htsjdk.samtools.util.TrimmingUtil\n Implements phred-style quality trimming.\n findRequiredFastaIndexFile(Path) - Static method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n \u00a0\n findSequenceDictionary(File) - Static method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n Deprecated.\n use findSequenceDictionary(Path) instead.\n findSequenceDictionary(Path) - Static method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n Attempts to locate the sequence dictionary file adjacent to the reference\n fasta file.\n findVirtualOffsetOfFirstRecordInBam(SeekableStream) - Static method in class\n htsjdk.samtools.SAMUtils\n Returns the virtual file offset of the first record in a BAM file - i.e.\n findVirtualOffsetOfFirstRecordInBam(File) - Static method in class\n htsjdk.samtools.SAMUtils\n@@ -5945,15 +5945,15 @@\n get(String) - Method in class htsjdk.variant.variantcontext.GenotypesContext\n Gets sample associated with this sampleName, or null if none is found\n get(K) - Method in class htsjdk.samtools.util.Histogram\n Retrieves the bin associated with the given key.\n get(Key) - Method in class htsjdk.samtools.util.ResourceLimitedMap\n Return an existing value, or create a new one if necessary.\n getAbsolutePath() - Method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n Returns the full path to the reference file.\n getAcceptedCount() - Method in class htsjdk.samtools.DownsamplingIterator\n Returns the number of records returned since creation of the last call to\n resetStatistics.\n getAcceptedFraction() - Method in class htsjdk.samtools.DownsamplingIterator\n Gets the fraction of records accepted since creation or the last call to\n resetStatistics().\n@@ -7725,15 +7725,15 @@\n getIndex() - Method in class htsjdk.samtools.cram.structure.ReadTag\n \u00a0\n getIndex() - Method in class htsjdk.samtools.CRAMFileReader\n \u00a0\n getIndex() - Method in class htsjdk.samtools.HtsgetBAMFileReader\n Always null as htsget sources do not have indices\n getIndex() - Method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n \u00a0\n getIndex() - Method in interface htsjdk.samtools.SamReader.Indexing\n Retrieves the index for the given file type.\n getIndex() - Method in interface htsjdk.samtools.SamReader.PrimitiveSamReader\n \u00a0\n getIndex() - Method in class\n htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter\n@@ -8493,15 +8493,15 @@\n \u00a0\n getPassword() - Method in interface\n htsjdk.samtools.seekablestream.UserPasswordInput\n \u00a0\n getPatchVersion() - Method in class htsjdk.beta.plugin.HtsVersion\n Get the patch version integer for this version.\n getPath() - Method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n Returns the path to the reference file.\n getPath(String) - Static method in class htsjdk.samtools.util.IOUtil\n Converts the given URI to a Path object.\n getPaths(List) - Static method in class htsjdk.samtools.util.IOUtil\n \u00a0\n getPathToDataFile(String) - Method in interface htsjdk.tribble.FeatureCodec\n Codecs may override this method if the file that they recognize with\n@@ -9219,28 +9219,28 @@\n Look up a sequence record by index.\n getSequence(int) - Method in class htsjdk.samtools.SAMSequenceDictionary\n \u00a0\n getSequence(String) - Method in class\n htsjdk.samtools.reference.FastaSequenceFile\n default implementation -- override if index is supported\n getSequence(String) - Method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n Retrieves the complete sequence described by this contig.\n getSequence(String) - Method in interface\n htsjdk.samtools.reference.ReferenceSequenceFile\n Retrieves the complete sequence described by this contig.\n getSequence(String) - Method in class htsjdk.samtools.SAMFileHeader\n Look up sequence record by name.\n getSequence(String) - Method in class htsjdk.samtools.SAMSequenceDictionary\n \u00a0\n getSequence(String) - Method in class\n htsjdk.samtools.sra.SRAIndexedSequenceFile\n \u00a0\n getSequenceDictionary() - Method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n Returns the list of sequence records associated with the reference\n sequence if found otherwise null.\n getSequenceDictionary() - Method in interface\n htsjdk.samtools.reference.ReferenceSequenceFile\n Must return a sequence dictionary with at least the following fields\n completed for each sequence: name, length.\n getSequenceDictionary() - Method in class\n@@ -9478,15 +9478,15 @@\n getSortOrder() - Method in class htsjdk.samtools.SAMFileHeader\n \u00a0\n getSortOrder() - Method in class htsjdk.samtools.SAMFileWriterImpl\n Must be called after calling setHeader().\n getSortOrder() - Method in class htsjdk.samtools.SAMSortOrderChecker\n \u00a0\n getSource() - Method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n Returns the named source of the reference file.\n getSource() - Method in class htsjdk.samtools.SAMValidationError\n \u00a0\n getSource() - Method in class\n htsjdk.samtools.seekablestream.ByteArraySeekableStream\n \u00a0\n getSource() - Method in class\n@@ -9637,15 +9637,15 @@\n getStructuralVariantType() - Method in class\n htsjdk.variant.variantcontext.VariantContext\n Search for the INFO=SVTYPE and return the type of Structural Variant\n getSubsequenceAt(String,_long,_long) - Method in class\n htsjdk.samtools.reference.FastaSequenceFile\n default implementation -- override if index is supported\n getSubsequenceAt(String,_long,_long) - Method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n Gets the subsequence of the contig in the range [start,stop]\n getSubsequenceAt(String,_long,_long) - Method in interface\n htsjdk.samtools.reference.ReferenceSequenceFile\n Gets the subsequence of the contig in the range [start,stop]\n getSubsequenceAt(String,_long,_long) - Method in class\n htsjdk.samtools.sra.SRAIndexedSequenceFile\n \u00a0\n@@ -12507,15 +12507,15 @@\n convenience method for indels\n isIndelOrSkippedRegion() - Method in enum class htsjdk.samtools.CigarOperator\n Returns true if the operator is a Skipped Region Insertion or Deletion\n operator\n isIndexed() - Method in class htsjdk.samtools.reference.FastaSequenceFile\n default implementation -- override if index is supported\n isIndexed() - Method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n \u00a0\n isIndexed() - Method in interface\n htsjdk.samtools.reference.ReferenceSequenceFile\n \u00a0\n isIndexed() - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile\n \u00a0\n isInitialized() - Method in class htsjdk.samtools.util.Lazy\n@@ -14357,15 +14357,15 @@\n htsjdk.samtools.util.ReferenceSequenceMask\n It is required that sequenceIndex is >= any previous sequenceIndex passed\n to this class.\n nextPosition(int,_int) - Method in class\n htsjdk.samtools.util.WholeGenomeReferenceSequenceMask\n \u00a0\n nextSequence() - Method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n Gets the next sequence if available, or null if not present.\n nextSequence() - Method in class htsjdk.samtools.reference.FastaSequenceFile\n \u00a0\n nextSequence() - Method in interface\n htsjdk.samtools.reference.ReferenceSequenceFile\n Retrieves the next whole sequences from the file.\n nextSequence() - Method in class htsjdk.samtools.sra.SRAIndexedSequenceFile\n@@ -16793,16 +16793,15 @@\n \u00a0\n reset() - Method in class htsjdk.samtools.cram.io.CountingInputStream\n \u00a0\n reset() - Method in class htsjdk.samtools.cram.io.CRC32InputStream\n \u00a0\n reset() - Method in class htsjdk.samtools.cram.io.DefaultBitInputStream\n \u00a0\n- reset() - Method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ reset() - Method in class htsjdk.samtools.reference.IndexedFastaSequenceFile\n Reset the iterator over the index.\n reset() - Method in class htsjdk.samtools.reference.FastaSequenceFile\n \u00a0\n reset() - Method in interface htsjdk.samtools.reference.ReferenceSequenceFile\n Resets the ReferenceSequenceFile so that the next call to nextSequence()\n will return the first sequence in the file.\n reset() - Method in class htsjdk.samtools.seekablestream.SeekableStream\n@@ -17603,15 +17602,15 @@\n Construct a SAMValidationError with possibly-known record number.\n SAMValidationError.Severity - Enum Class in htsjdk.samtools\n \u00a0\n SAMValidationError.Type - Enum Class in htsjdk.samtools\n \u00a0\n sanityCheckDictionaryAgainstIndex(String,_SAMSequenceDictionary,\n FastaSequenceIndex) - Static method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n Do some basic checking to make sure the dictionary and the index match.\n SanityCheckFailedException(String) - Constructor for exception\n htsjdk.samtools.SAMTestUtil.SanityCheckFailedException\n \u00a0\n SBI - Static variable in class htsjdk.samtools.util.FileExtensions\n \u00a0\n SBIIndex - Class in htsjdk.samtools\n@@ -20415,15 +20414,15 @@\n toString() - Method in class htsjdk.samtools.metrics.StringHeader\n \u00a0\n toString() - Method in class htsjdk.samtools.metrics.VersionHeader\n \u00a0\n toString() - Method in class htsjdk.samtools.QueryInterval\n \u00a0\n toString() - Method in class\n- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile\n+ htsjdk.samtools.reference.IndexedFastaSequenceFile\n Returns the full path to the reference file, or the source if no path was\n specified.\n toString() - Method in class\n htsjdk.samtools.reference.FastaSequenceIndexEntry\n For debugging.\n toString() - Method in class htsjdk.samtools.reference.ReferenceSequence\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": "@@ -8131,29 +8131,29 @@\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\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\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\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\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@@ -8175,25 +8175,25 @@\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\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\n \"l\": \"findRequiredFastaIndexFile(Path)\",\n \"u\": \"findRequiredFastaIndexFile(java.nio.file.Path)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\n \"l\": \"findSequenceDictionary(File)\",\n \"u\": \"findSequenceDictionary(java.io.File)\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\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@@ -9020,15 +9020,15 @@\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\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\n \"l\": \"getAbsolutePath()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"DownsamplingIterator\",\n \"l\": \"getAcceptedCount()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n@@ -11937,15 +11937,15 @@\n \"l\": \"getIndex()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"HtsgetBAMFileReader\",\n \"l\": \"getIndex()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\n \"l\": \"getIndex()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"SamReader.Indexing\",\n \"l\": \"getIndex()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n@@ -13222,15 +13222,15 @@\n \"l\": \"getPassword()\"\n }, {\n \"p\": \"htsjdk.beta.plugin\",\n \"c\": \"HtsVersion\",\n \"l\": \"getPatchVersion()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\n \"l\": \"getPath()\"\n }, {\n \"p\": \"htsjdk.samtools.util\",\n \"c\": \"IOUtil\",\n \"l\": \"getPath(String)\",\n \"u\": \"getPath(java.lang.String)\"\n }, {\n@@ -14349,15 +14349,15 @@\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\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\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@@ -14374,15 +14374,15 @@\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\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\n \"l\": \"getSequenceDictionary()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"ReferenceSequenceFile\",\n \"l\": \"getSequenceDictionary()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n@@ -14769,15 +14769,15 @@\n \"l\": \"getSortOrder()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"SAMSortOrderChecker\",\n \"l\": \"getSortOrder()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\n \"l\": \"getSource()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"SAMValidationError\",\n \"l\": \"getSource()\"\n }, {\n \"p\": \"htsjdk.samtools.seekablestream\",\n@@ -15054,15 +15054,15 @@\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\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\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@@ -18815,15 +18815,15 @@\n \"l\": \"isIndelOrSkippedRegion()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"FastaSequenceFile\",\n \"l\": \"isIndexed()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\n \"l\": \"isIndexed()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"ReferenceSequenceFile\",\n \"l\": \"isIndexed()\"\n }, {\n \"p\": \"htsjdk.samtools.sra\",\n@@ -21493,15 +21493,15 @@\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\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\n \"l\": \"nextSequence()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"FastaSequenceFile\",\n \"l\": \"nextSequence()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n@@ -25182,15 +25182,15 @@\n \"l\": \"reset()\"\n }, {\n \"p\": \"htsjdk.samtools.cram.io\",\n \"c\": \"DefaultBitInputStream\",\n \"l\": \"reset()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\n \"l\": \"reset()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"FastaSequenceFile\",\n \"l\": \"reset()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n@@ -26130,15 +26130,15 @@\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\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\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@@ -30221,15 +30221,15 @@\n \"l\": \"toString()\"\n }, {\n \"p\": \"htsjdk.samtools\",\n \"c\": \"QueryInterval\",\n \"l\": \"toString()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n- \"c\": \"BlockCompressedIndexedFastaSequenceFile\",\n+ \"c\": \"IndexedFastaSequenceFile\",\n \"l\": \"toString()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n \"c\": \"FastaSequenceIndexEntry\",\n \"l\": \"toString()\"\n }, {\n \"p\": \"htsjdk.samtools.reference\",\n"}]}]}]}]}]}