droazen
droazen
GenomicsDBImport: add the ability to specify explicit index locations via the sample name map file
The sample name map file accepted by GenomicsDBImport can now optionally contain a third column giving an explicit path to an index for the corresponding GVCF. It is allowed to...
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?
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...
`BCF2Codec` has not been well-maintained over the years, and does not fully support the latest BCF 2.2 spec (see the BCF section in http://samtools.github.io/hts-specs/VCFv4.3.pdf). We now have at least one...
The pipelines team here at the Broad Institute has confirmed non-determinism in the DRAGMAP output -- here is their report on the issue: **Description** When the same unmapped bam is...
Minimal GATK port of nvscorevariants from https://github.com/NVIDIA-Genomics-Research/nvscorevariants The tool runs successfully in both 1D and 2D modes, and a strict integration test passes for the 1D model. However, this PR...
As reported recently by Eric Jones: "Many newer Linux distributions will mount /tmp with the noexec mount option. If /tmp is noexec, then any JNA code (Java code that extracts...