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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 an NPE in CRAMRecordReadFeatures.restoreReadBases
#1655
lbergelson
closed
1 year ago
0
docs: fix typo in README
#1654
Manice18
closed
1 year ago
3
Question: Tabix index to find min(POS) and max(POS) in each contig
#1652
lindenb
opened
1 year ago
0
Add a better error message when the reference is too long for indexing
#1651
lbergelson
opened
1 year ago
5
Updating gradle to 7.6
#1650
lbergelson
closed
1 year ago
0
Migrate to Java 17
#1649
lbergelson
closed
1 year ago
0
Expose the ability to encode a Genotoype into a GT field
#1648
lbergelson
closed
1 year ago
0
Adding Cigar.fromCigarString()
#1647
lbergelson
closed
1 year ago
0
Removed 'backed' last cache hit hard references; it seems that that i…
#1645
vruano
opened
1 year ago
5
Add Range codec (Update CRAM Codecs to CRAM 3.1)
#1644
yash-puligundla
opened
1 year ago
2
Race conditions accessing CRAM's reference data through ReferenceSource
#1643
vruano
opened
1 year ago
0
Feature/earthly
#1642
genestack-okunitsyn
closed
1 year ago
2
Test case helper and fix EOF detection
#1641
lbergelson
opened
1 year ago
0
Removing scala test infrastructure
#1640
lbergelson
closed
1 year ago
3
Update commons-compress to close vulnerabilities
#1639
lbergelson
closed
1 year ago
0
VCF sorting change breaks existing VCFs
#1637
lbergelson
opened
1 year ago
1
Make AbstractVCFCodec thread-safe, allowing for multi-threaded VariantContext genotype decoding
#1636
rcoleb
opened
1 year ago
3
add SINGULAR platform to read group
#1635
omicsorama
closed
11 months ago
4
Allow the BAM index to be up to 5 seconds older than the BAM before e…
#1634
tfenne
closed
1 year ago
0
CRAM files have zero-length blocks with a compression method associated with them (so cannot be decompressed).
#1633
jkbonfield
opened
1 year ago
1
Fix HtsCRAMCodec test data provider.
#1632
cmnbroad
closed
1 year ago
0
The last-but-one argument of test testQueryAlignmentStart in HtsCRAMCodec30And21QueryTest.java is long
#1631
pgrt
closed
1 year ago
1
Our FastaSequenceIndex too large to fit in memory
#1630
wbazant
closed
1 year ago
4
Refactoring VariantContextComparator
#1629
lbergelson
opened
1 year ago
2
Remove deprecation from Allele.acceptableAlleleBases
#1625
lbergelson
closed
1 year ago
0
Minor improvements to AbstractLocusIterator
#1624
lbergelson
closed
1 year ago
0
What is the non-deprecated replacement for acceptableAlleleBases?
#1623
danking
closed
1 year ago
4
removing codecov from github actions until we can migrate to the new uploader
#1622
lbergelson
closed
1 year ago
0
Fix temporary directory hijacking or temporary directory information disclosure
#1621
lbergelson
closed
1 year ago
0
IntervalTree.Node's methods have package visibility only
#1620
holtgrewe
closed
1 year ago
1
Added ULTIMA and ELEMENT as valid value for RG-PL according to SAM spec.
#1619
rickymagner
closed
1 year ago
0
Add RANS Nx16 codec (Update CRAM Codecs to CRAM 3.1)
#1618
yash-puligundla
opened
1 year ago
3
[SECURITY] Fix Temporary Directory Hijacking or Information Disclosure Vulnerability
#1617
JLLeitschuh
closed
1 year ago
5
Fix EdgeReadIterator
#1616
michaelgatzen
closed
1 year ago
2
EdgeReadIterator (used in Picard's CollectWgsMetrics) doesn't handle intervals correctly
#1615
michaelgatzen
closed
1 year ago
2
LittleEndianInputStream EOF test is incorrect
#1614
cmnbroad
opened
2 years ago
9
Question: how to code a GTFCodec beside of the existing GFF3Codec
#1613
lindenb
closed
1 year ago
1
Require sequence dictionary MD5s when writing CRAM.
#1612
cmnbroad
opened
2 years ago
0
Nashorn engine removed from OpenJDK 17 causes htsjdk to throw exceptions
#1611
pgrt
closed
1 year ago
2
Remove validation of VCF Header line field order?
#1610
tfenne
opened
2 years ago
1
Add support for re-serializing (sharding and reassembling) CRAM containers.
#1609
cmnbroad
opened
2 years ago
1
Would it be OK to remove the Travis app from the Samtools organisation?
#1608
daviesrob
closed
1 year ago
3
Make the CRAM MD5 failure message more user friendly.
#1607
cmnbroad
closed
2 years ago
0
Add support for reserializing CRAM containers
#1606
cmnbroad
opened
2 years ago
0
Support CRAM reference regions.
#1605
cmnbroad
closed
2 years ago
2
Question: Gettting SAMFileHeader from partial files or byte chunks.
#1604
gariem
closed
9 months ago
3
Remove validateArg call with a high invocation count when writing CRAM.
#1603
cmnbroad
closed
8 months ago
2
Remove unncessary println.
#1602
cmnbroad
closed
2 years ago
1
Change queryname sort to match samtools
#1601
nh13
opened
2 years ago
1
Implementation of a SAMRecord comparator that matches samtools' queryname sort order.
#1600
tfenne
opened
2 years ago
9
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