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samtools
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htslib
C library for high-throughput sequencing data formats
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Support building with htscodecs not in a submodule.
#1750
teo-tsirpanis
closed
4 months ago
2
Base mod tweaks to improve validity checking.
#1749
jkbonfield
closed
4 months ago
6
wishlist s3 cache
#1748
cariaso
closed
4 months ago
6
Allow a specified output name in bgzip
#1747
whitwham
closed
4 months ago
2
todo: Improve `--regions-overlap variant`
#1746
pd3
opened
4 months ago
0
Add check for .gzi when determining whether to rebuild the fai index.
#1745
jkbonfield
closed
4 months ago
0
Make faidx error messages slightly more enlightening
#1743
nickzoic
closed
4 months ago
0
Fix indexing bug by flushing BCF bgzf stream after header write
#1742
daviesrob
closed
4 months ago
0
Speed up sam_parse_B_vals
#1741
jkbonfield
closed
4 months ago
5
Using POSIX and htslib to create x compressed vcf files using x threads
#1739
Npaffen
closed
3 months ago
2
Fix arithmetic overflow in load_ref_portion() on very long refs
#1738
daviesrob
closed
4 months ago
2
Samtools view fails on CRAM and compressed reference if .gzi file is missing
#1744
TheodoreSpeaks
closed
4 months ago
1
Fix possible heap overflow in cram_encode_aux() on bad RG:Z tags
#1737
daviesrob
closed
5 months ago
5
Drop duplicate FORMAT tags and fix an error with dropping large tags
#1736
pd3
closed
4 months ago
3
bcftools-1.19: Invalid index is produced by --write-index and --threads on my bcf.gz files
#1740
graphenn
closed
4 months ago
4
feature request: parallelize tabix
#1735
dbolser
closed
3 months ago
5
CRAM load_ref_portion() fails on some Mistletoe references
#1734
daviesrob
closed
4 months ago
0
bcftools --write-index creates sometimes indexes older than the data file.
#1732
ghuls
closed
3 months ago
1
bcftools corrupts duplicate GT format fields
#1733
anthakki
closed
3 months ago
1
NEWS and copyright date updates
#1731
daviesrob
closed
5 months ago
0
Update copyright date in LICENSE file and version messages
#1730
daviesrob
closed
5 months ago
0
Revert a bug from c1f4b7c where CRAM aux tags were not compressed.
#1729
jkbonfield
closed
5 months ago
0
Fix over-lenient check in bam_aux_first() / bam_aux_next()
#1728
daviesrob
closed
5 months ago
0
bgzip - modified and access time as in source file
#1727
vasudeva8
closed
4 months ago
2
bgzip: allow specification of output name.
#1726
ghuls
closed
4 months ago
0
Fix B aux tag length check in cram_encode_aux
#1725
daviesrob
closed
6 months ago
0
fix for incorrect failure message with invalid reference file and crash fix
#1724
vasudeva8
closed
5 months ago
0
Passing missing --reference incorrectly reports cram file missing as well
#1723
ASLeonard
closed
5 months ago
1
formerly caught bgzf_idx_amend_last symbol
#1722
emollier
closed
6 months ago
3
Unable to install the HTSlib on Ubuntu 20.04
#1721
LEGMCGILL
closed
6 months ago
2
Annottsv1
#1720
vasudeva8
closed
6 months ago
0
Update htscodecs to v1.6.0
#1719
daviesrob
closed
6 months ago
0
bgzip: keep original modification time when compressing a file.
#1718
ghuls
closed
4 months ago
0
Update to latest htscodecs
#1717
daviesrob
closed
6 months ago
0
man update for -a option
#1716
vasudeva8
closed
6 months ago
1
Reading BCFtools FORMAT/BCSQ field
#1715
barneyhill
closed
6 months ago
2
Annottsv
#1714
vasudeva8
closed
6 months ago
1
More CRAM fuzz fixes (integer overflows)
#1713
jkbonfield
closed
7 months ago
0
Move typecast to the right place
#1712
daviesrob
closed
7 months ago
0
configure.ac: Define _DEFAULT_SOURCE along with _XOPEN_SOURCE
#1711
fweimer-rh
closed
6 months ago
5
Ensure no-stored-sequence reads are counted in container size
#1710
daviesrob
closed
7 months ago
0
Allow renaming of the default -a annotations
#1709
pd3
closed
6 months ago
0
Segmentation fault of htslib c program written myself
#1708
leon945945
closed
7 months ago
3
Fix possible shift of negative value in cram_encode_aux()
#1707
daviesrob
closed
7 months ago
0
`annot-tsv --version` does not follow conventions
#1706
jmarshall
closed
6 months ago
1
Miscellaneous trivia and minor fixes
#1705
jmarshall
closed
7 months ago
1
Disable hts_set_fai_filename call in hts_open_fuzzer.
#1704
jkbonfield
closed
7 months ago
0
Winter News 2023
#1703
whitwham
closed
6 months ago
1
Fix `@PG` linking when records make a loop
#1702
daviesrob
closed
7 months ago
0
Cram fuzzing improvements.
#1701
jkbonfield
closed
7 months ago
3
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