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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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Implementation of CRAM 3.1 codecs.
#1714
cmnbroad
opened
2 days ago
0
Support reference bundles.
#1713
cmnbroad
opened
1 month ago
0
reducing memory required in IntervalMergerIterator when not concatting names
#1711
meganshand
closed
2 months ago
1
Incomplete license metadata in build.gradle
#1710
tapdiego-amzn
opened
3 months ago
0
SamUtils PairOrientation is confusingly ambiguous about paired reads needing to map to the same contig
#1709
yfarjoun
opened
3 months ago
0
Fix CRAMReferenceRegion updating.
#1708
cmnbroad
closed
3 months ago
0
Ignore version validation for BCF in VCFHeaderReader because we only need the header
#1707
lindenb
opened
5 months ago
0
Upgrade to samtools 1.19.1 for interop testing.
#1706
cmnbroad
closed
6 months ago
2
Add FQZComp Codec (Update CRAM Codecs to CRAM 3.1)
#1704
yash-puligundla
opened
7 months ago
0
Implement VCF bundles.
#1703
cmnbroad
closed
3 days ago
0
Implements collections of bundles.
#1702
cmnbroad
closed
3 weeks ago
1
Iterator not working on vcffileReader
#1701
AlessandroBalestrucci
closed
7 months ago
3
Minor updates to MemoryMappedFileBuffer
#1700
lbergelson
opened
7 months ago
0
Updating our dependencies to the the newest version
#1699
lbergelson
closed
8 months ago
0
Update for to use Java 21
#1698
lbergelson
opened
8 months ago
0
Update to gradle 8.5
#1697
lbergelson
closed
8 months ago
0
Updating tests in SAMRecordUnitTest to remove ambiguity
#1696
lbergelson
closed
8 months ago
2
Ambiguous assertions in the tests
#1695
pgrt
closed
8 months ago
1
Improving the somewhat slipshod change I made to HtsPath
#1694
lbergelson
closed
8 months ago
0
Re-Ordering priority in SeekableStreamFactory
#1693
lbergelson
closed
8 months ago
1
Truncation issue with GZIPInputStream when reading bgzip-compressed streams
#1691
jkmatila
opened
10 months ago
2
Update test dependencies to newest versions
#1690
lbergelson
closed
10 months ago
0
Resolve issues around integrating HTTP NIO provider
#1689
lbergelson
opened
10 months ago
0
Fix IOUtil.unrollPaths for http paths with query parameters
#1688
lbergelson
closed
10 months ago
0
Update snappy-java
#1687
bbimber
closed
11 months ago
1
VariantContext has inconsistent behavior on getting allele type with spanning deletions
#1686
rickymagner
opened
11 months ago
0
support for Azure blob storage? (specifically access to BAM/CRAM files in Azure blob storage by IGV)
#1685
smrgit
opened
11 months ago
0
VCF_CSI_index_implementation
#1684
gokalpcelik
opened
11 months ago
1
VCF 4.4 optimistic read switch.
#1683
cmnbroad
closed
11 months ago
1
IOUtil.openFileForMd5CalculatingWriting() puts the md5 file in the wrong place.
#1682
lbergelson
opened
1 year ago
0
Update some methods to accept Path input
#1681
takutosato
closed
11 months ago
1
Add NamedFeature for common interface to name in bed or interval_list
#1680
rickymagner
closed
1 year ago
1
two methods for Genotype: HasRefAllele HasAltAllele
#1678
lindenb
closed
1 year ago
0
Update two remaining out of date dependencies
#1677
lbergelson
closed
1 year ago
0
Move the EnaRefServiceTest to the externalAPI test group
#1675
lbergelson
closed
1 year ago
0
Zero len array
#1674
gileshall
closed
1 year ago
0
Deleted Java developers team
#1673
lbergelson
opened
1 year ago
0
SAMFileWriterFactory creates .bai file when writing .cram file
#1672
rickymagner
opened
1 year ago
1
htsjdk.samtools.util.IOUtil.assertFileIsWritable on certain NFS environments fails to correctly assess permissions
#1671
jd-daniels
opened
1 year ago
4
Update snappy-java and migrate mjson to org.json to address CVEs
#1670
bbimber
closed
1 year ago
4
Remove remaining incorrect zero-length-B-array checks and exception throwing
#1669
jmarshall
closed
1 year ago
8
Error when reading a VCF 4.3 file with spaces in INFO field values
#1667
jkmatila
opened
1 year ago
1
SamReaderFactory should use current defaults when makeDefault() is called
#1666
lbergelson
opened
1 year ago
0
Question: How to generate FAI files and TBI files
#1665
Lys9527
opened
1 year ago
5
removed redundant code that sets the secondary alignment flag for a r…
#1664
KleinSamuel
closed
1 year ago
0
Add Name Tokenization Codec (Update CRAM Codecs to CRAM 3.1)
#1663
yash-puligundla
opened
1 year ago
0
proposal for a package htsjdk.tribble.gtf
#1662
lindenb
opened
1 year ago
0
Escaped doublequotes in INFO descriptions result in invalid VCF file
#1661
bartcharbon
opened
1 year ago
2
SamReader slower than expected on network drive
#1660
BeatWolf
opened
1 year ago
1
Remove low-value progress logging message
#1659
nh13
closed
1 year ago
0
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