htslib
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samtools
C library for high-throughput sequencing data formats
We have a variant with more than 50 alleles for almost 500000 samples. The line in question is over 3 gb in size. bcftools and our own program that uses...
Somehow this issue https://github.com/samtools/htslib/issues/842 has not been fully addressed. The following code shows the problem: ``` $ echo '#include int main() { htsFile *in = hts_open("-", "r"); bcf_hdr_t *hdr =...
-d, --delim .. add support for other delimiters, not just tab -h, --headers .. allow header lines in different formats. This is motivated by the common use of files with...
The bgzf_read function is long and not something that's likely to get inlined even if it was in the header. However most of the time our calls request a small...
See https://github.com/samtools/htslib/pull/1677 for prior discussion. I made the PR such that nibble2base is dynamically dispatched on x86-64 cpus with SSSE3 instructions. No build options need to be changed and nibble2base...
The VCF parser silently drops FORMAT fields when FORMAT column is ".". Perhaps it should complain when the corresponding sample fields are something else than "." in such case. See...
Building htslib 1.20 on OS X 10.11.6 with the version of clang included in Xcode 8.2.1 (`Apple LLVM version 8.0.0 (clang-800.0.42.1)`) configure says: ``` checking C compiler flags needed for...
Hi, I stumbled across an issue when testing multiple versions of htslib/bgzip. With release of a blasting fast decompression algorithm in 2023 [https://github.com/mxmlnkn/rapidgzip](https://github.com/mxmlnkn/rapidgzip), which achives a throughput of 1.5GB/s on...
Commit e495718 changed bgzip from unix raw POSIX read() calls to hread(). Unfortunately hread gets its buffer size from stat of the input file descriptor, which can be 4kb for...
Issue Summary: Inconsistency in formatting a floating-point tag value when using sam_parse1 function from htslib. Description: I encountered an inconsistency while using the sam_parse1 function from htslib to convert a...
