htslib
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samtools
C library for high-throughput sequencing data formats
I am trying to convert a cram to a bam using the following samtools command set-up: samtools view -h -b -@ 16 file.cram -o file.bam -T reference.fa 2>&1 | tee...
The use case I am currently working on is use htslib with C++ istream. And this change makes htslib able to consume data from a set of consumized callback functions....
There have been several github issues related to the installation of samtools/htslib. This is mainly because samtools requires a few non-trivial dependencies for advanced features such as https/htsget and bzip2/xz...
Problem -------- Release 1.6 introduced checks on alignments, such as inconsistent CIGARs. This is great, but the current implementation causes iterators such as `sam_itr_next` to subsequently flag a premature EOF...
Since PR #600, hfile_libcurl uses the JSON tokeniser, which is private HTSlib functionality declared in _hts_internal.h_. This is a problem when hfile_libcurl is built as a plugin. Plugins should not...
It appears it's only possible to create a single working _stdout_ `htsFile` instance in a single execution, even if only one is actually open. Writing to a second instance results...
Per @tk2, EBI recently began switching all www connections, including to the CRAM Reference Registry, to HTTPS. This is good even though the references are public data, because it helps...
The following python code would call into htslib seek() and hts_iter_next() for reads. When libcurl_seek fails the following code still passes and leads to erronous output. I've noticed this happen...
See https://github.com/samtools/htslib/issues/593#issue-259627325 for context.
See https://github.com/samtools/htslib/issues/593#issue-259627325 for context.