Chris Norman
Chris Norman
Reflect the changes from https://github.com/broadinstitute/picard/pull/1782 in the GATK doc build. Note that this requires a new version of Picard that is not yet released. Also, I suppressed deprecation warnings caused...
Update cromwell and womtool. See if I feel lucky.
Fix for https://github.com/broadinstitute/gatk/issues/7401. Draft mode for now until I do more verification.
Fixes NPE reported in https://github.com/broadinstitute/gatk/issues/7811.
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...
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...