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samtools
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htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Fix bug in BlockCompressedInputStream.checkTermination()
#1310
lbergelson
closed
5 years ago
1
making changes to reduce size of giant interval lists
#1309
lbergelson
closed
5 years ago
6
Simplify CRAM sequence dictionary extractor to not require a fake reference.
#1308
cmnbroad
closed
5 years ago
1
CramHeader ID does not clear its buffer on set or construction
#1307
jmthibault79
closed
2 years ago
5
DO NOT MERGE: CRAM improve test coverage and fix a few bugs
#1306
jmthibault79
closed
4 years ago
4
SamSequenceDictionaryExtractor for cram
#1305
lindenb
closed
5 years ago
1
CRAM: Only calculate alignmentDelta as needed for records
#1304
jmthibault79
closed
5 years ago
1
Spotbugs remaining fixes
#1303
tomwhite
closed
5 years ago
2
Proposed replacement for progress PR
#1302
yfarjoun
closed
5 years ago
2
*CramCompressionRecord getAlignmentSpan() and getAlignmentEnd() don't reflect changed state
#1301
jmthibault79
closed
4 years ago
2
Changing the team name/url in the maven pom
#1300
lbergelson
closed
5 years ago
2
Update java version information in the README
#1299
lbergelson
closed
5 years ago
2
fix toFile call
#1298
lbergelson
closed
5 years ago
2
Remove Path.toFile in IntervalListWriter
#1297
lbergelson
closed
5 years ago
0
adding new overloads to IOUtils with Path for some file only methods
#1296
lbergelson
closed
5 years ago
2
Ensembl fasta files no long usable as references
#1295
bwlang
opened
5 years ago
9
Add Path versions of IOUtil openGzipFileForWriting
#1294
lbergelson
closed
5 years ago
0
CRAMFileReader enableFileSource is not propagated to SAMRecords consistently
#1293
cmnbroad
closed
2 years ago
3
Remove redundant and unused BAM_FLAGS from CRAM code.
#1292
cmnbroad
closed
5 years ago
1
Build and test on java 11
#1291
lbergelson
closed
5 years ago
2
BlockCompressedIndexedFastaSequenceFile checks for a gzi even if an index is passed in.
#1290
lbergelson
closed
5 years ago
0
moving HttpUtilsTest to externalApi test task
#1289
lbergelson
closed
5 years ago
4
Add an IntervalCodec that use useful for sorting large sets of
#1288
nh13
closed
5 years ago
3
Standard test set failed due to http test failure
#1287
lbergelson
closed
5 years ago
2
Yf add get reference to sam set builder
#1286
yfarjoun
closed
5 years ago
5
Changes to FastaReferenceWriter
#1285
lbergelson
closed
5 years ago
1
update CramCompressionRecord.isPlaced() to make it APDelta-aware
#1284
jmthibault79
closed
5 years ago
1
Fixes for issues found by SpotBugs
#1283
jmthibault79
closed
5 years ago
1
remove caching of alleles in AbstractVCFCodec
#1282
lbergelson
closed
5 years ago
2
[SpotBugs] htsjdk.samtools.cram.structure.CramHeader defines clone() but doesn't implement Cloneable
#1281
tomwhite
closed
5 years ago
0
[SpotBugs] Field only ever set to null: htsjdk.samtools.CRAMIterator.nextRecord
#1280
tomwhite
closed
5 years ago
0
[SpotBugs] contentId isn't initialized in htsjdk.samtools.cram.structure.block.ExternalBlock.getContentId() when invoked from constructor for superclass
#1279
tomwhite
closed
5 years ago
0
A few fixes for issues found by spotbugs
#1278
tomwhite
closed
5 years ago
4
Fix spotbugs issues in tests.
#1277
tomwhite
closed
5 years ago
5
CRAM indexing tests and associated fixes and updates
#1276
jmthibault79
closed
5 years ago
2
Use Integer.parseInt over Integer.valueOf to avoid unnecessary boxing…
#1275
tomwhite
closed
5 years ago
4
CRAM: formalize Slice Type with an enum
#1274
jmthibault79
closed
5 years ago
1
Changed IntervalList fromFiles() so that it doesn't call .unique() on…
#1273
yfarjoun
closed
5 years ago
1
Moving the SRA tests to a separate env
#1272
yfarjoun
closed
5 years ago
2
References in different order to headers
#1271
jkbonfield
opened
5 years ago
8
changing WARNING to WARN and deprecating WARN
#1270
lbergelson
closed
5 years ago
9
Test on Java 11
#1269
tomwhite
closed
5 years ago
8
Fix fields that should be final, as reported by SpotBugs
#1268
tomwhite
closed
5 years ago
1
Address issues found by SpotBugs
#1267
tomwhite
closed
5 years ago
4
CRAM: Container and Slice states
#1266
jmthibault79
closed
5 years ago
1
- Make Unique intervals keep both interval names even when intervals …
#1265
yfarjoun
closed
5 years ago
1
Fixed memory leak in VCFCodec
#1264
d-cameron
closed
5 years ago
8
Index merging
#1263
tomwhite
closed
4 years ago
10
Rename LogLevel.WARNING to LogLevel.WARN.
#1262
heuermh
closed
5 years ago
6
Non-standard logging level WARNING prevents downstream configuration
#1261
heuermh
opened
5 years ago
0
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