htsjdk
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samtools
A Java API for high-throughput sequencing data (HTS) formats.
### Description This PR adds a file VCFReaderFactory that open a **VCFReader** using a few methods. ``` VCFReader open(final File vcfFile,boolean requiredIndex); VCFReader open(final Path vcfFile,boolean requiredIndex); VCFReader open(final String...
For example, `varlociraptor` currently outputs the `FORMAT/DP` field as a [per-alternate-allele set of values](https://github.com/varlociraptor/varlociraptor/issues/160), whereas the spec defines it as only one value (total read depth for the sample). The...
### Description of the issue: An issue started from [an error](https://github.com/igvteam/igv/issues/927) in IGV, but we traced back to htjdk. In short, htsjdk thinks IUPAC code for [ambiguous bases](https://www.bioinformatics.org/sms/iupac.html) are not...
### Description Closes #277 Closes #500 Currently, it is not possible to add multiple `VCFSimpleHeaderLine`s to a VCFHeader if they are of the same type (see issues linked above). A...
`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...
Fixes #1535 - Adding enum BaseComparisonMode to toggle different modes of comparing bases - MatchExact: bases match when they are equal - MatchAmbiguity: bases match when they are equal or...
Dear, Firstly thanks for your amazing work on this library. I try to read a bcffile through `VCFFileReader` but I have this error: ``` Unable to parse header with error:...
The NM tag describes the number of mismatches between the read and the reference. According to the spec, this is defined as: > Number of differences (mismatches plus inserted and...
… runtime) (sorry again about the push to master) ### Description Please explain the changes you made here. Explain the **motivation** for making this change. What existing problem does the...
… examples to more accurately show where the jar will be after compiling.