htsjdk
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samtools
A Java API for high-throughput sequencing data (HTS) formats.
### Description Removed 'backed' last cache hit hard references; it seems that that it might be trying to solve an non-existent issue. Changed WeakReference to SoftReference to make cache more...
### Description of the issue: Problem spotted in GATK due to smelly use and no use of synchronized in CRAM ReferenceSource: https://github.com/broadinstitute/gatk/issues/8139 .../cram/.../ReferenceSource.java has a mixture of synchronized and non-synchronzed...
* Responding to my own pr comments on #1593 * doing some refactoring to use the Comparator.comparing API * adding a few more tests @clintval I might have gone a...
This started as me fixing the minor bug in https://github.com/samtools/htsjdk/issues/1614. I got annoyed with something that I am regularly annoyed with, needing different data providers for the severals sets of...
I failed to consider the effect of changing the VCF sort order on processing existing VCFs when merging https://github.com/samtools/htsjdk/pull/1593. This breaks many things. I think this is still a good...
### Description of the issue: htsjdk produces CRAM files with zero length blocks that have a compression codec listed. An empty block post-compression is valid. An empty-block in RAW (uncompressed)...
htsjdk can neither read nor write BCFs that are block gzipped, even though that seems to be the recommended state based on the BCF spec. It mostly describes BCF as...
Fix for https://github.com/broadinstitute/gatk/issues/8768.
### Description For now HTSJDK does not support **BCF2.2** but sometimes you just want to only get the VCF header in a **BCF** file while you don't care about the...
- Improved documentation to clarify that PairOrientation (in SamUtils) pertains only to reads on the same contig. - Now getPairOrientation will throw an exception if thrown when the two reads...
