htsjdk
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samtools
A Java API for high-throughput sequencing data (HTS) formats.
### Verify Can you see anything in the logs? Make sure your issue is not already in the [htsjdk issue tracker](https://github.com/samtools/htsjdk/issues?q=) ### Subject of the issue In htsjdk 2.1.0, the...
The proposed VCF 4.3 spec (https://github.com/samtools/hts-specs/pull/88) adds some clarifications regarding uniqueness of header lines. Specifically, "structured" lines that have their value enclosed with "" must have an ID attribute that...
Currently `VCFHeader` strips out version line(s) at construction, and then SOME of the accessor methods add a VCF 4.1 header line back in on-demand. This is incredibly poor design --...
The current version of the `VCFHeader` class maintains a master list of header lines (`mMetaData`) plus type-specific lookup tables for each kind of header line. This design is unsafe and...
### Description The existing aysnc read code performs read-ahead and decompression on a seperate thread. Combining with AsyncBufferedIterator and we can get ~3x performance increase when doing light processing (eg....
### Description of the issue: Using picard `SamFormatConverter` to turn a long-read CRAM to BAM with more than 65536 cigar ops generates a `CG:B:i,` tag. The SAM specification dictates this...
### Subject of the issue Question regarding String fields in VCFs/BCFs Allele specific annotations fields such as AS_RAW_ReadPosRankSum are coded as Strings in VCFs. The header specifies the field as:...
… runtime) In the cram code the code throws an IllegalArgumentException when asked about the bases when a reference was not provided. This PR changes it to a CRAMException to...
### Description As described in #701, it will be nice to have a simple mechanism to write features in tribble not only for `VariantContext`. This is a port from one...
### Description of the issue: While implementing support for [htsget in IGV-desktop](https://github.com/igvteam/igv/pull/850), we (@reisingerf and @brainstorm) noticed that there's no `htsgetVariantsReader` or any [similar reader akin to htsgetbamreader](https://github.com/samtools/htsjdk/pull/1494). In other...
