htslib
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samtools
C library for high-throughput sequencing data formats
Hi, First, thank you all for htslib. This is an amazing resource and incredibly useful library. I have a project that includes uses both libbwa and libhts. However both of...
I have a custom hFILE backend over C++ streams that I have written for vg: https://github.com/vgteam/vg/blob/39ac300bb735abf8350e3d2a7ec0356a0742fd56/src/stream/hfile_cppstream.cpp It has built just fine up until now, since vg ships htslib as a...
The public _htslib/cram.h_ declares typedef struct refs_t refs_t; This type name is not particularly unique to HTSlib. It should be renamed to `cram_refs_t`— or `hts_refs_t` if it's not inherently CRAM-specific...
zlib can spot truncated files, as can bgzf, but the code for bcf_read glosses over all such things and treats any error as EOF. Note this isn't the same issues...
I'm forwarding Debian bug 865012 (https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=865012), which mentions failing tests on i386. I can reproduce these on a plain Debian stretch i386 install with the most recent htslib release 1.5:...
I’m currently using the GCS_OAUTH_TOKEN environment variable method to provide an OAuth access token to samtools in order to access GCS stored objects (see #390). Obtaining an access token is...
Would it be possible to add the configure option to only build htslib as a shared or static library? Currently, both are built always. The tools provided by htslib (e.g....
When including htslib as a Git submodule and building it from the parent project's build system via `autoreconf && configure && make`, the htslib version is not correctly detected. The...
This came up in issue #795, opening it here to keep it documented beyond the closing of that issue: It is confusing when reading the code, that the mapping quality...
The error message printed when tabix fails to parse the input when there is no preset `-p` option given is of the form: ``` [E::get_intv] failed to parse TBX_GENERIC, was...
