htslib
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samtools
C library for high-throughput sequencing data formats
Hi, In Debian we recently had the problem, that a tool had a [function called `json` clashing with a value from an enum defined in `hts.h`](https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=866646). Already, most functions are...
Hello htslib devs, I'm starting to work on a htsget-server implementation that relies on htslib, based on preliminary work on https://github.com/samtools/hts-specs/pull/385. The first issue I've found is finding public getters...
If we don't do a "make all all-htslib" first and let the install build do the compilation first, then this trips up when using the joint samtools+htslib tarballs. The samtools...
This is obviously only partial because we need CRAM4 for long reads, but it's now better at reporting errors and also now copes correctly with the cases inbetween 28-bit and...
A quick benchmark of current htslib vs manual replacement (just copied over) rANS_static.c and rANS_byte.h from https://github.com/jkbonfield/htscodecs shows decoding a NovaSeq CRAM v3.0 file is 20% faster. That's quite a...
Perhaps this is just a documentation issue, but I am having problems (memory issues) with `hts_idx_set_meta`. Here is the source: ```C int hts_idx_set_meta(hts_idx_t *idx, uint32_t l_meta, uint8_t *meta, int is_copy)...
Would make it very clear what type of file is being dealth with. Additionally, can avoid issues with things like vim being able to read bgziped files saved with .gz...
See samtools/bcftools#1045 At least it should print a better error message, but ideally it should be able to complete somehow.
I was wondering if htslib/samtools support extraction of blocks of unaligned reads similar to what a bgzipped FASTQ file that has been indexed with grabix currently allows. This is relevant...
Hi, thanks for htslib and how responsive developers have always been. Apologies in advance for the long text below. While exploring potential speedups setting `bcf1_t.max_unpack` as documented in vcf.h: ```...
