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samtools
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htslib
C library for high-throughput sequencing data formats
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Preprocessor definitions with quotation marks
#1527
lczech
closed
1 year ago
4
How to get reads depth by sam.h
#1526
leon945945
closed
1 year ago
4
Install the shared library .so file as executable
#1525
StephDC
closed
1 year ago
7
Fix build on ancient versions of gcc
#1524
daviesrob
closed
1 year ago
0
std=c99 required by gcc 4.8.5
#1523
lmjakt
closed
1 year ago
2
Add CRAM SQ/M5 header checking when specifying a fasta file.
#1522
jkbonfield
closed
1 year ago
4
Fix ref fix from c91804c
#1521
jkbonfield
closed
1 year ago
0
Fix buffer read-overrun in bam_plp_insertion_mod.
#1520
jkbonfield
closed
1 year ago
0
Add faidx_seq_len64(), fai_adjust_region() interfaces and faidx tests
#1519
daviesrob
closed
1 year ago
0
Check for invalid BC tags in fastq output.
#1518
jkbonfield
closed
1 year ago
2
Warn if ref file is given but it doesn't contain the refs we need.
#1517
jkbonfield
closed
1 year ago
0
Add an fai_line_length function.
#1516
jkbonfield
closed
1 year ago
1
Trouble converting .cram to .fq
#1515
0106WeiWeiDeng
closed
1 year ago
10
Are `bam_aux_first` and `bam_aux_next` available from the shared library?
#1514
kojix2
closed
1 year ago
2
A minor speed improvement to VCF parsing by 5-9%
#1513
jkbonfield
closed
1 year ago
3
Fix a typo in sam.h documentation
#1512
kojix2
closed
1 year ago
1
Switch to building libdeflate with cmake
#1511
daviesrob
closed
1 year ago
0
bcf_strerror method to get description of error code
#1510
vasudeva8
closed
1 year ago
2
Use POSIX `grep`
#1509
SoapGentoo
closed
1 year ago
1
tok3_decode_names() in cram/cram_io.c is undefined.
#1508
wangyugui
closed
1 year ago
2
Prevent crash when only FASTA entry has no sequence.
#1507
jkbonfield
closed
1 year ago
1
Make tabix support CSI indices with large positions.
#1506
jkbonfield
closed
1 year ago
4
Use a more conservative approach for SOVERSION
#1505
StefanBruens
closed
1 year ago
27
Fix error code 0 returned by bcftools after error
#1504
janinl
closed
2 years ago
2
Fix n-squared complexity in sample line with many adjacent tabs
#1503
daviesrob
closed
2 years ago
0
Update man SEE ALSO sections from .BR to .IR so the website uses URLs
#1502
jkbonfield
closed
2 years ago
1
Add some more NEWS updates.
#1501
daviesrob
closed
2 years ago
0
Fix problems found attempting to build on i686
#1500
daviesrob
closed
2 years ago
0
Fix newer clang warning of unused variable.
#1499
jkbonfield
closed
2 years ago
0
Make ksort.h use hts_defs.h instead of hts.h for HTSLIB_EXPORT
#1498
jkbonfield
closed
2 years ago
0
Fix clang builds on Windows/mingw.
#1497
jkbonfield
closed
2 years ago
1
Fix "make check" on MinGW.
#1496
jkbonfield
closed
2 years ago
5
Fix a remaining endianness bug in bcf_format_gt()
#1495
jmarshall
closed
2 years ago
1
Add trivial le_to_u8() endianness routine
#1494
jmarshall
closed
2 years ago
0
Bgzip text mode (try 2)
#1493
jkbonfield
closed
2 years ago
0
Fix SEGV when handling errors from sam_read1_sam without headers
#1492
jkbonfield
closed
2 years ago
0
Recognise FASTA/Q even if the file has a very long header file
#1491
jmarshall
closed
2 years ago
1
Fastaq switch
#1490
jkbonfield
closed
2 years ago
0
Update to htscodecs 1.3.0
#1489
daviesrob
closed
2 years ago
0
Add a mapping of Zlib to Libdeflate compression levels for BGZF.
#1488
jkbonfield
closed
2 years ago
1
Warn if bgzf_getline() returned apparently UTF-16-encoded text
#1487
jmarshall
closed
3 months ago
8
Catch arrays of BCF_BT_NULL in bcf_record_check()
#1486
daviesrob
closed
2 years ago
0
Report HTS_CFLAGS_AVX2 et al in `make print-config`
#1485
jmarshall
closed
2 years ago
1
Fix (un)lock bug and memory leak introdued in commit 9562aeba
#1484
daviesrob
closed
2 years ago
0
Summer 2022 Copyright Corrections.
#1483
whitwham
closed
2 years ago
0
Binning index virtual file offsets
#1482
mmalenic
closed
2 years ago
3
Fail to generate a beagle file
#1481
cnxiaobo94
closed
2 years ago
4
Minimal support for CRAM files with missing @RG headers.
#1480
jkbonfield
closed
2 years ago
2
RG tag gets lost in cram format
#1479
ASLeonard
closed
2 years ago
11
Improve filter expression language consistency
#1478
jkbonfield
closed
2 years ago
3
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