Nils Homer
Nils Homer
Fixes a long standing bug, but made more apparent in https://github.com/lh3/bwa/pull/336. Thank @jmarshall for pointing this out. I tested this by on my local machine three ways. 1. Not specifying...
I am confused as to why after increasing the `5'` clipping penalty, I do not see an alignment with no `5'` clipping promoted to be the primary, and in fact,...
Output reads may have zero length after adapter or quality trimming, and for paired FASTQs, one end may be trimmed more than the other. I'd like the zero length reads...
This is a slight optimization when we only care if there exists an overlap, not which overlaps.
@lh3 I would like to use `cgranges` via a conda install, but to [add the recipe to bioconda](https://github.com/bioconda/bioconda-recipes/pull/34812) a release is needed (see [this link for why](https://bioconda.github.io/contributor/linting.html#uses-vcs-url )). This can...
This PR is meant to start a discussion to standardize the queryname sort order between samtools and htsjdk. It is a constant source of confusion, and sometimes problems, especially when...
I was wondering if other folks (@tfenne @lbergelson @yfarjoun) are seeing frequent core dumps using the latest Picard/fgbio, which rely upon htsjdk. I have exactly five users over here compiling...
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...
@tfenne a rough implementation of https://github.com/samtools/htsjdk/issues/793. I can probably make the function itself faster. Related to https://github.com/samtools/htsjdk/issues/793
See https://github.com/samtools/hts-specs/pull/405