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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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Updating .gitignore
#1509
lbergelson
closed
4 years ago
1
Add a getIDs method to VariantContext
#1508
lbergelson
opened
4 years ago
4
Exception is thrown when loading the BAM from a URL
#1507
SergejN
closed
2 years ago
18
VCF file ID field separated by semi-colon
#1506
BoscoSuen
opened
4 years ago
1
Change try-finally to try-with-resources in MetricsFile.write
#1505
lbergelson
closed
4 years ago
2
Rename HtsjdkPath to HtsPath.
#1504
cmnbroad
closed
4 years ago
1
Bug in .gitignore?
#1503
dariober
closed
4 years ago
2
Extended Attributes in Genotype not parsed
#1502
BoscoSuen
opened
4 years ago
1
Support very large sequence dictionaries/headers
#1501
nh13
closed
3 years ago
5
No longer require external call to `initializeAnyploidPLIndexToAlleleIndices`
#1500
kachulis
closed
4 years ago
5
Fix genotype validation error message
#1499
ldgauthier
closed
4 years ago
1
Unnecessary IllegalStateException "no sequences were added to the reference" in FastaReferenceWriter
#1498
d-cameron
opened
4 years ago
1
BasicFastqWriter: no longer flushing on every write
#1497
d-cameron
closed
4 years ago
6
IOPath interface and IOPathSpec implementation
#1496
cmnbroad
closed
4 years ago
6
Extend set of valid FASTA format file extensions
#1495
sjaenick
closed
4 years ago
1
Add HtsgetBAMFileReader
#1494
andersleung
closed
4 years ago
2
Include Mjson as a dependency
#1493
lbergelson
closed
4 years ago
4
only set wrapper version when htsjdk is root project
#1492
ssadedin
closed
4 years ago
1
Remove inaccurate downstream status badges
#1491
lbergelson
closed
4 years ago
3
AbstractLocusIterator uses a ArrayList but uses it like a queue
#1490
yfarjoun
opened
4 years ago
0
Fixed a bug in the locus accumulator where the accumulator didn't add…
#1489
yfarjoun
closed
4 years ago
1
BAMFileReader constructors not public; not accessible from library import
#1488
paulameena
closed
4 years ago
4
Handle spaces in input strings in Tabix and SeekableStreamFactory.
#1487
cmnbroad
closed
4 years ago
1
Gff3 Writer
#1486
kachulis
closed
4 years ago
2
some UTF-8 characters aren't being rendered properly on parse
#1485
nathandunn
closed
4 years ago
9
Improve error message in AbstractRecordAndOffset
#1484
lbergelson
closed
4 years ago
3
Extend SamLocusAndReferenceIterator to work with CRAMFileReader
#1483
jkaczynski1
closed
3 years ago
9
We got a grant to improve Htsjdk!
#1482
lbergelson
opened
4 years ago
5
SamLocusAndReferenceIterator fails with leading indels at the start of the reference
#1481
nh13
closed
4 years ago
9
Gff3BaseData precompute hash and Gff3Codec decodeShallow method
#1480
kachulis
closed
4 years ago
4
Adding a PEDIGREE header only works if no PEDIGREE headers are present
#1479
bartcharbon
closed
4 years ago
2
should `U` be considered a "valid read base"?
#1478
yfarjoun
closed
4 years ago
3
HTSJDK should not accept non-two-character header tags
#1477
jmarshall
closed
3 years ago
3
Switch to Java 11, Add GA4GH Crypt4H SeekableStream [WIP]
#1476
AlexanderSenf
opened
4 years ago
1
Mf get read position from ref
#1475
fleharty
closed
4 years ago
4
Add support for SQ-AN in SAMSequenceDictionary #956
#1474
yfarjoun
closed
4 years ago
2
new interface VCFReader (+ VCFFIleReader implements VCFReader)
#1473
lindenb
closed
4 years ago
6
- Make get/set attributes methods take a SAMTag input
#1472
yfarjoun
closed
4 years ago
7
htsjdk.samtools.SAMException sequence name doesn't match regex
#1471
kviljoen
opened
4 years ago
7
Expose option for memory mapping with private MEMORY
#1470
lbergelson
opened
4 years ago
7
Add VCFHeader javadoc
#1469
bbimber
closed
4 years ago
2
in VCFFileTest make sure that files are iterated through
#1468
yfarjoun
closed
4 years ago
0
Add another improvement to tribble error code
#1467
yfarjoun
closed
4 years ago
1
- fix a vcfFileReaderTest
#1466
yfarjoun
closed
4 years ago
0
CRAM huffman codeword is limited to 32 bits
#1465
cmnbroad
opened
4 years ago
0
Remove unecessary Array copy during VCF write
#1464
lbergelson
closed
4 years ago
1
Better tribble error message
#1463
yfarjoun
closed
4 years ago
1
Tribble parsing error message
#1462
jrobinso
closed
4 years ago
3
Add option to hard clip read in CigarUtils (replacement for #1453)
#1461
kachulis
closed
4 years ago
3
SamSort async for BlockCompressedOutputStream
#1460
Sergei-Poliakov
closed
4 years ago
0
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