htsjdk
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samtools
A Java API for high-throughput sequencing data (HTS) formats.
https://github.com/samtools/htsjdk/blob/222d10b4e7be763453e2a0a1886cbec99e15e886/build.gradle#L220 lists MIT as the only license applying to this package. This is inconsistent with the actual licensing as described in the README; additional entries should be included listing the...
When using `IntervalMergerIterator` to merge many small intervals over a whole contig it can take quite a bit of memory to store each interval. This can happen when trying to...
The main feature implemented here is that a bundle can be used in place of a reference, without executing any code paths that assume that the individual resources are located...
Is there any desire to make the HTSJDK a modernised modular Java library? It would be useful for people trying to build and distribute applications as it can be used...
PR to test setting up carrot. @KevinCLydon I took your branch and added some stuff on it 1. A dockerfile that just includes the htsjdk source so we can run...
### Description of the issue: When reading a VCF with HTSJDK it causes an exception when there is a duplicate ALT allele. I believe duplicate ALT alleles are allowed in...
This is a squashed and rebased branch containing all of the changes from Yash's CRAM 3.1 codec branches. Draft until I get all of the issues resolved. Replacement for [#1618](https://github.com/samtools/htsjdk/pull/1618),...