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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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CRAM: Refactor AlignmentSpan
#1260
jmthibault79
closed
5 years ago
2
Load BlockCompressedIndexedFastaSequenceFile and GZIIndex from streams
#1259
tomwhite
closed
5 years ago
2
Only compute BIN on BAM write and on index building
#1258
tfenne
closed
5 years ago
4
Remove indexingBin from SAMRecord and only compute it when writing BA…
#1257
tfenne
closed
5 years ago
1
Immutable CRAIEntry
#1256
jmthibault79
closed
5 years ago
2
Fix to ensure that SeekableStream#available() never returns a negative value
#1255
tomwhite
closed
5 years ago
3
Fix nitpick in IntervalKeepPairFilterTest
#1254
lbergelson
closed
5 years ago
0
Misc CRAM cleanup
#1253
jmthibault79
closed
5 years ago
3
Makes IntervalKeepPairFilter filter out single ended reads
#1252
meganshand
closed
5 years ago
4
BlockCompressedInputStream.readFully seems likely to be buggy
#1251
lbergelson
closed
5 years ago
0
Deprecated htsjdk.samtools.apps package.
#1250
lbergelson
closed
5 years ago
1
Async BAM performance improvements
#1249
d-cameron
opened
5 years ago
18
Parse valid VCF 4.2 with ##INFO containing Source + Version
#1248
romanzenka
closed
5 years ago
22
Yf add getters to vcb
#1247
yfarjoun
closed
5 years ago
2
resolving some nitpicks from pr #1245
#1246
lbergelson
closed
5 years ago
3
new Interface VCFIterator extends CloseableIterator<VariantContext> (continued)
#1245
romanzenka
closed
5 years ago
3
CRAM should validate the SAM header against the reference being used
#1244
cmnbroad
opened
5 years ago
0
VCFFileReader that can read from InputStream
#1243
romanzenka
closed
5 years ago
2
CRAM: Refactor and Test Slice
#1242
jmthibault79
closed
5 years ago
2
Adding some constants due to additions to hts-spec
#1241
yfarjoun
closed
5 years ago
3
Add finals for issues raised during review of PR 1091.
#1240
cmnbroad
closed
5 years ago
2
allow SBI indexing on the fly within BamWriter
#1239
yfarjoun
opened
5 years ago
0
- implementing the spec change in
#1238
yfarjoun
closed
5 years ago
5
Broken index with igvtools (?)
#1237
jean-philippe-martin
closed
5 years ago
6
CRAM: better testing of unmapped reads
#1236
jmthibault79
opened
5 years ago
0
Likely bug with VariantContext.getType and phased variants
#1235
lbergelson
closed
5 years ago
2
Replaced several for-each loops in VariantContext.Make() based on HaplotypeCaller profiling
#1234
jamesemery
closed
5 years ago
2
Relax Beta Encoding requirement to allow 0 bits
#1233
jmthibault79
closed
5 years ago
1
Enforcing CRAM spec compliance (must have nonzero External Content ID) causes test failures
#1232
jmthibault79
opened
5 years ago
4
CRAM: Immutable Block
#1231
jmthibault79
closed
5 years ago
5
Adding some sanity checking to IntervalList reading.
#1230
yfarjoun
closed
5 years ago
6
There should be a constants class for file extensions
#1229
jamesemery
closed
5 years ago
1
parsing missing values in VCF info field doesn't work
#1228
davidbenjamin
opened
5 years ago
1
more changes to SAMTagUtil
#1227
lbergelson
closed
5 years ago
3
Allele should contain a `MASKED_ANY_BASE` constant corresponding to `N`.
#1226
jonn-smith
opened
5 years ago
0
Update the README with working test examples
#1225
lbergelson
closed
5 years ago
3
CRAM: Refactor Encodings and Codecs
#1224
jmthibault79
closed
5 years ago
2
Adding getPathToDataFile default method to FeatureCodec
#1223
lbergelson
closed
5 years ago
3
Add hashCode() to classes with equals() and clean up equals()
#1222
jmthibault79
closed
5 years ago
3
CRAM: Be explicit about spec IDs instead of using ordinal()
#1221
jmthibault79
closed
5 years ago
2
CramCompressionRecord defines equals but not hashCode
#1220
lbergelson
closed
5 years ago
2
CRAM DataSeries/DataReader/DataWriter refactor
#1219
jmthibault79
closed
5 years ago
5
CRAM: Interaction between APDelta and Multi-Reference Slices
#1218
jmthibault79
opened
5 years ago
1
Allow space to separate date from time in Iso8601Date
#1217
dariober
opened
5 years ago
1
htsjdk doesn't seem to honour CRAM "RR" (reference required) header.
#1216
jkbonfield
closed
2 years ago
3
Add isRefOnlyBlock function...
#1215
jsotobroad
closed
5 years ago
5
Deprecate SQTagUtil
#1214
magicDGS
closed
5 years ago
3
Delete long-term deprecated code
#1213
magicDGS
closed
5 years ago
1
Getter for generic fields in VCFSimpleHeaderLine
#1212
Wathis
closed
5 years ago
4
Changing htsjdk to produce sam version 1.6
#1211
lbergelson
closed
5 years ago
2
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