htsjdk
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samtools
A Java API for high-throughput sequencing data (HTS) formats.
# Security Vulnerability Fix This pull request fixes either 1.) Temporary Directory Hijacking Vulnerability, or 2.) Temporary Directory Information Disclosure Vulnerability, which existed in this project. ## Preamble The system...
- Fixing #1615 - EdgeReadIterator was calling AbstractLocusIterator's `getCurrentInterval()` to determine the read overlaps. However, the `lastInterval` that it uses internally was never updated. This PR removes the method `getCurrentInterval()`...
When running Picard's CollectWgsMetrics with an IntervalList, only the start and end coordinates of the first interval in that list are considered. This can be traced back to a bug...
This PR is resurrected from the PR graveyard, updated and rebased. It contains: - significant updates to VCFHeader and VCFHeaderLine class hierarchy - significantly updated VCFHeader merging - prerequisites for...
As reported by @jrobinso: The test for EOF in `LittleEndianInputStream.readString` is wrong because in.read() is cast to a byte. The contract for read() returns an "int", and the signal for...
More a question than an issue. I would like htsjdk to support the **GTF** format. There was a previous discussion about this here https://github.com/samtools/htsjdk/issues/537 . But I think since this...
Hi there, I'd like to add another voice for providing support for longer reference sequences: it already seems useful for some genomes, and as better assembled and larger genomes come...
Fixes https://github.com/samtools/htsjdk/issues/506 (and by extension will also fix https://github.com/broadinstitute/gatk/issues/5195). If the SAM header used to create a CRAM doesn't have a sequence dictionary with MD5s, the code will attempt to...
@lbergelson, @droazen and anyone else who may be interested. Following the discussion in https://github.com/samtools/hts-specs/issues/642 would there be support for (or any objections to) a PR that eliminated the validation of...
Hello, I am working on the packaging of htsjdk in Debian. Soon OpenJDK 17 will become the standard in Debian, so I built htsjdk against OpenJDK 17 and got the...
