-- The previous version of TribbleIndexedFeatureReader.query() would open a RandomAccessFile each time the GATK crossed a shard boundary. When running with -L wex.intervals (or any time there were lots of intervals) we'd be opening and closing enormous numbers of files, radically slowing down the GATK. With these patched versions of Tribble we see something like the following performance improvements:
SelectVariants with -L wex.intervals on my local machine against non-local file
pre-patch => 3 hours
post-patch => 30 seconds
* As reported here: http://gatkforums.broadinstitute.org/discussion/comment/4270#Comment_4270
* This was a commit into the variant.jar; the changes here are a rev of that jar and handling of errors in VF
* Added integration test to confirm failure with User Error
* Removed illegal header line in KB test VCF that was causing related tests to fail.
These 2 changes improve runtime performance almost as much as Ryan's previous attempt (with ID-based comparisons):
* Don't unnecessarily overload Allele.getBases() in the Haplotype class.
* Haplotype.getBases() was calling clone() on the byte array.
* Added a constructor to Allele (and Haplotype) that takes in an Allele as input.
* It makes a copy of he given allele without having to go through the validation of the bases (since the Allele has already been validated).
* Rev'ed the variant jar accordingly.
For the reviewer: all tests passed before rebasing, so this should be good to go as far as correctness.
The migration of org.broadinstitute.variant into the Picard repo is
complete. This commit deletes the org.broadinstitute.variant sources
from our repo and replaces it with a jar built from a checkout of the
latest Picard-public svn revision.
Ami Levy-Moonshine
Eric Banks
Mark DePristo
David Roazen
Guillermo del Angel