samtools htslib issues - Githubissues

samtools / htslib

C library for high-throughput sequencing data formats

Other

784 stars 447 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Cram fuzzing improvements.

#1701 jkbonfield closed 7 months ago
3
Heap overflow during hts_md5_update

#1700 OctavioGalland closed 7 months ago
0
Allocation size too big/invalid memory access during `extend_ref`/`cram_add_to_ref`

#1699 OctavioGalland closed 7 months ago
0
Use-after-free during `hts_md5_update`

#1698 OctavioGalland closed 7 months ago
0
Assertion violation during `cram_beta_encode_init`

#1697 OctavioGalland closed 7 months ago
0
Assertion violation during `cram_ref_decr_locked`

#1696 OctavioGalland closed 7 months ago
0
Loosing precision due to avoidable rounding of float annotations in VCF

#1695 vruano closed 5 months ago
2
Heap overflow during `sam_hdr_add_pg`

#1694 OctavioGalland closed 7 months ago
1
Heap overflow during `hts_md5_update`

#1693 OctavioGalland closed 7 months ago
1
segfault during `hts_md5_update`

#1692 OctavioGalland closed 7 months ago
0
segfault during `cram_generate_reference`

#1691 OctavioGalland closed 7 months ago
1
Temporary workaround when excessive memory is required by FORMAT fields

#1689 pd3 closed 7 months ago
0
Fix a couple of unused value warnings when built with NDEBUG

#1688 daviesrob closed 7 months ago
0
Make compiler flag detection work with zig cc

#1687 daviesrob closed 7 months ago
0
Bug in ks_expand?

#1686 rmhubley closed 7 months ago
1
Update htscodecs to v1.5.2 (2aca18b3)

#1685 daviesrob closed 9 months ago
0
Tabix failed on FTP file

#1684 stunme closed 8 months ago
1
Add C++ casts for external headers.

#1683 jkbonfield closed 9 months ago
0
Add test case compiling the public headers as C++

#1682 jmarshall closed 8 months ago
0
Always do the CRAM mutex lock/destroys.

#1681 jkbonfield closed 9 months ago
0
Fix a cram decode hang from block_resize.

#1680 jkbonfield closed 9 months ago
0
Enable optimisation level -O3 for SAM QUAL+33 formatting.

#1679 jkbonfield closed 8 months ago
4
Large memory leak involving libcurl when attempting to use htslib C library on remote BAM

#1678 rlorigro closed 9 months ago
6
Faster nibble parsing and a SSSE3 routine for even faster nibble parsing

#1677 rhpvorderman closed 5 months ago
15
Fix hfile_libcurl small seek bug

#1676 daviesrob closed 9 months ago
2
Fix crypt4gh redirection

#1675 daviesrob closed 9 months ago
0
Apply seqtk PR to improve kseq.h parsing performance

#1674 jmarshall closed 9 months ago
2
configure error on ubuntu lastest version

#1673 kemin711 closed 9 months ago
1
Fix multi-threaded on-the-fly indexing problems

#1672 daviesrob closed 9 months ago
0
Fix a minor memory leak in malformed CRAM EXTERNAL blocks.

#1671 jkbonfield closed 9 months ago
0
htslib in pysam.fetch on S3 Bucket

#1670 StephanHolgerD opened 10 months ago
4
Enable auto-vectorisation in CRAM 3.1 codecs.

#1669 jkbonfield closed 9 months ago
0
bgzf_useek fails when offset is above block limits

#1668 vasudeva8 closed 10 months ago
0
Apply the packed attribute to uint*_u types for Clang

#1667 MaskRay closed 10 months ago
2
Demo / sample code update

#1666 vasudeva8 opened 10 months ago
8
Avoid really closing stdin/stdout in hclose()/hts_close()/et al

#1665 jmarshall closed 10 months ago
7
Fuzz testing improvements

#1664 daviesrob closed 10 months ago
0
Vcf write speed

#1663 jkbonfield closed 9 months ago
7
Speed up removal of lines in large headers.

#1662 whitwham closed 10 months ago
0
Version 1.18 of tabix exhibits poorer performance in querying locus information compared to version 1.16.

#1661 TuBieJun closed 10 months ago
2
Add an hclen SAM filter function.

#1660 jkbonfield closed 10 months ago
0
changes to support multiple files

#1658 vasudeva8 closed 9 months ago
7
formatting update

#1657 vasudeva8 closed 11 months ago
0
Add "uncompressed" in hts_format_description() where appropriate

#1656 jmarshall closed 11 months ago
0
Switch to htscodecs 1.5.1

#1654 daviesrob closed 11 months ago
0
Add missing Makefile dependencies and other minor fixes

#1653 jmarshall closed 11 months ago
1
./configure with or without libcurl htslib-1.17

#1652 grenaud closed 10 months ago
17
Make bam_parse_cigar able to modify existing BAM records rather than partially parsed ones.

#1651 jkbonfield closed 11 months ago
0
`bam_parse_cigar` possibly adds data to a wrong place

#1650 oleksii-nikolaienko closed 11 months ago
6

Previous Next