htslib
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samtools
C library for high-throughput sequencing data formats
This affects `hts_expr` and causes `test/test_expr` failures (e.g., for `16==0x10`) as that uses `hts_str2dbl()` to parse integer hex constants. This is because `hts_str2dbl()` uses `strtod()` to parse hex constants like...
The version I use is 1.11 The command I ran is `bcftools view -R .tsv -Oz -o .vcf.gz .vcf.gz` The vcf file is from simulation data, the golden vcf file....
I'm running into problems trying to build `htslib-1.11.tar.bz2`: ``` $ wget https://github.com/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2 $ tar -xf htslib-1.11.tar.bz2 $ cd htslib-1.11 $ ./configure PREFIX=/project/M-mtgraovac182840/tools/htslib-1.11 checking for gcc... gcc checking whether the C...
I've been using bgzf methods for processing some BGZ files and I found some issues with them that could be adresses with not too much effort. My needs were to...
PR #201 (“allow underscore and dot in keys for structured header lines”) changed some parsing in `bcf_hdr_parse_line()` to also allow underscore and fullstop. The PR description and the `^[A-Za-z_][0-9A-Za-z_.]*$` comment...
Current header files of htslib cannot be included in c++ code without correction. Function declarations in macro function are put out of "extern C" in c++ code, and they trigger...
A reminder to my future self, or to inspire others with time on their hands. :-) An htslib built without finding xz-utils / lzma library is possible, with appropriate configure...
Is there a user guide / documentation for htslib?
I have some code that looks something like: ```bcftools view foo.bcf -R
We have the BCF synched reader code which can on-the-fly merge (and dedup / intersect) multiple BCF files. I'm thinking there is room for a similar action in the SAM...