Chris Norman

Mirror of Picard metrics documentation generation changes.

2

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 from v51 to v59.

3

Update cromwell and womtool. See if I feel lucky.

Fix asynchronous Python exception propagation in StreamingPythonExecutor/CNNScoreVariants.

6

Fix for https://github.com/broadinstitute/gatk/issues/7401. Draft mode for now until I do more verification.

Test for presence of ack result message and simplify ProcessControllerAckResult API

1

Fixes NPE reported in https://github.com/broadinstitute/gatk/issues/7811.

VCFHeader and VCFHeaderLine rewrite/refactoring

6

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...

LittleEndianInputStream EOF test is incorrect

9

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...