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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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SamSort async for BlockCompressedOutputStream
#1460
Sergei-Poliakov
closed
4 years ago
0
SamSequenceRecord implements Locatable
#1459
lindenb
closed
4 years ago
0
interval_list with gz compression
#1458
lindenb
closed
4 years ago
0
TabixReader implements Autoclose
#1457
lindenb
closed
4 years ago
0
javadoc oops
#1456
yfarjoun
closed
4 years ago
2
Made toIntervalList an iterator as well ...
#1455
yfarjoun
closed
4 years ago
2
Extract Allele into a interface with only one implementation as is currently the case.
#1454
vruano
closed
3 years ago
6
Add option to hard clip reads in CigarUtils
#1453
fleharty
closed
4 years ago
5
CRAM 2.1 test files have incorrect container block byte sizes
#1452
cmnbroad
opened
4 years ago
0
fix resource leak in VCFFileReader.getSequenceDictionary
#1451
lindenb
closed
4 years ago
1
Test Ticket GitZen
#1450
GATKSupportTeam
closed
4 years ago
0
Fix IndexFactory on non-default file system.
#1449
cmnbroad
closed
4 years ago
2
Some improvements on CigarOperator enum.
#1448
vruano
opened
4 years ago
2
Modified numLikelihoods calculation for performance
#1447
KevinCLydon
closed
4 years ago
7
GenotypeLikelihoods.calcNumLikelihoods() should not be recursive
#1446
droazen
closed
4 years ago
1
Question using BlockCompressedInputStream + random access bam
#1445
lindenb
closed
4 years ago
6
SAMFileWriter does not do proper cleanup on IOException
#1444
duffrohde
closed
4 years ago
1
Upgrade to samtools 1.10.
#1443
cmnbroad
closed
4 years ago
1
Getting java.lang.InternalError while querying a VCFFileReader
#1442
Habush
closed
4 years ago
2
Reduce test output from BlockCompressedInputStreamTest test method args.
#1441
cmnbroad
closed
4 years ago
2
Refactor CRAM package code
#1440
cmnbroad
closed
4 years ago
1
Gff3 Tribble Codec
#1439
kachulis
closed
4 years ago
3
MarkDuplicates will prefer a longer read over a proper read in some cases
#1438
RyanBio
opened
4 years ago
7
Improve calculation of available memory when sizing buffers in SortingCollection
#1437
tfenne
closed
4 years ago
2
Updating versions of commons-compress and xz library
#1436
lbergelson
closed
4 years ago
1
Update snappy version to 1.1.7.3
#1435
lbergelson
closed
4 years ago
1
Install samtools and add SamtoolsUtils class.
#1434
cmnbroad
closed
4 years ago
1
add method we killed accidentally
#1433
lbergelson
closed
4 years ago
3
Improve TextualBAMIndexWriter text output.
#1432
cmnbroad
closed
4 years ago
2
Replace IndexFactory reflection.
#1431
lbergelson
closed
4 years ago
2
Path-enable IndexFactory.
#1430
cmnbroad
closed
4 years ago
5
Fixes broken XSV Indexing
#1429
jonn-smith
closed
4 years ago
3
Tribble indexing complex files fails
#1428
jonn-smith
closed
4 years ago
0
Yf add platforms
#1427
yfarjoun
closed
4 years ago
2
Slice MD5 check allows accepts an MD5 match for a partial slice span
#1426
cmnbroad
closed
2 years ago
3
SamIndexes methods present CSIs as BAIs
#1425
cmnbroad
opened
5 years ago
0
Inefficient random access patterns
#1424
jkbonfield
opened
5 years ago
3
Need to support complex rearrangements in SV (VCF)
#1423
yfarjoun
opened
5 years ago
5
CRAM writer doesn't gzip the SAMFileHeader block in the first container
#1422
cmnbroad
closed
4 years ago
2
Add a URLHelper factory API to ParsingUtils
#1421
jrobinso
closed
5 years ago
9
Possible core dumps due to Intel's gkl
#1420
nh13
opened
5 years ago
10
Add a method to conditionally apply a Consumer on a nullable input
#1419
yfarjoun
closed
5 years ago
1
Make VCFHeader not throw exception if contig header lines lack length field
#1418
cwhelan
closed
5 years ago
4
Proposal: handling UCSC 2bit sequences as ReferenceFile
#1417
lindenb
opened
5 years ago
3
Fixing bad behavior in IOUtil.deletePaths
#1416
lbergelson
closed
5 years ago
1
Fix issue 1414- add proper behavior of clear() to DiskBackedQueue
#1415
biotinker
closed
5 years ago
3
DiskBackedQueue closeIOResources is broken
#1414
biotinker
opened
5 years ago
4
Allow partially spanned alleles.
#1413
tfenne
opened
5 years ago
11
Add LiftOver constructor that takes an input stream
#1412
kevinpetersavage
closed
5 years ago
2
Added alignment type to RecordAndOffset class
#1411
michaelgatzen
closed
5 years ago
2
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