Chris Norman
Chris Norman
Its been a while since I've looked at it, but my recollection is that support for reading was mostly there, with the exception of one remaining BCF2.2. feature (end-of-vector marker...
@agostof BCF2.2 is still not supported.
@fgvieira There is both good news and bad news on the status of this. We have a branch and PR with the 4.3 changes that is ready for review, and...
Holding off until samtools/hts-specs#405 is merged.
Fixed in refactoring branch.
@jkbonfield Thanks for the detailed analysis. Its certainly the case that htsjdk converts the crai to bai internally, and it does seem to result in lots of unnecessary I/O. I...
I suspect this is related to the jar configuration (3 separate uber- jars) that is unique to the docker CI tests. I'll debug and resolve this after #6351 is merged.
Closing in favor of https://github.com/broadinstitute/gatk/pull/8035.
@mcovarr Ouch. Well, thanks for the update - I guess we'll add that to the long list of reasons to move off of Java 8.
Closing in favor of https://github.com/broadinstitute/gatk/pull/8035.