htsjdk
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samtools
A Java API for high-throughput sequencing data (HTS) formats.
AFAICT, CRAM files created with htsjdk contain the samFileHeader that was passed in to the CRAM writer, whether or not it has the attributes required by the CRAM spec.The following...
Fixes https://github.com/samtools/htsjdk/issues/1606.
The containing method gets called frequently, and the validateArg call shows up as a hotspot (3-4%) when profiling writing CRAM .
TLDR: This PR will make coordinate VCF sorting in HTSJDK/Picard similar to bcftools. I tried to use Picard's [SortVcf](https://gatk.broadinstitute.org/hc/en-us/articles/360036858331-SortVcf-Picard) for a VCF comparison task, but I had difficulty because it's...
I'm not sure about the best venue for this discussion, but this seems as good as anywhere... Following the recent [OAUTH breach](https://github.blog/2022-04-15-security-alert-stolen-oauth-user-tokens/), it seems like a good idea to have...
There are cases where we want to be able to re-serialize CRAM containers into a new stream without fully decoding and then re-encoding them (and without the need for the...
Htsjdk does not currently support VCFv4.3 and BCFv2.2. Is there a volunteer in the community who is interested in taking on the task of adding support for the latest spec?
### Description of the issue: This is rather a request or a question about creating a file header from an arbitrary chuck of bytes (i.e. a partial file being downloaded...
@nh13, @lbergelson I put this together mostly for fun - it's a comparator that will sort read names the same way samtools does. I'm not really sure what the best...
This PR is meant to start a discussion to standardize the queryname sort order between samtools and htsjdk. It is a constant source of confusion, and sometimes problems, especially when...
