Note that this functionality will only work if the directory with the fasta is writeable. GATK will fail if directory is read only and and either the .fasta.fai or .dict files don't exist. In the future, we could have these references be created in memory, but we decided against it this time.
Locking was also added to ReferenceDataSource so no issues come up while running multiple GATKs on the same reference: we don't want one process to be half-finished and another try to read it. So, you could see error messages related to locking. See ReferenceDataSource.java for explanation of the locking strategy.
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will not be as fast as they could be because the workflow is currently merge sam records (sharding)
-> split sam records (LocusIteratorByState) -> merge records (LocusIteraotorByState) -> split
records (StratifiedAlignmentContext), but this will be fixed when StratifiedAlignmentContext
is updated to take advantage of the new functionality in ReadBackedPileup.
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issue building up pileups from pileups of individual sample data.
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Provides a cleaner interface with extended events inheriting all of the basic RBP
functionality. Implementation is still slightly messy, but should allow users to
provide separate implementations of methods for sample split pileups and unsplit
pileups for efficiency's sake.
Methods not covered by unit/integration tests have not been sufficiently tested yet.
Unit tests will follow this week.
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are gone where I could identify them, but hierarchies that split to support two sharding systems have
not yet been taken apart.
@Eric: ~4k lines.
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new implementation. Hard testing and performance enhancements are still
pending.
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b) Added back old Beagle ROD to maintain backward compatibility (does anyone even use this???)
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We can now run with a reduced memory footprint, and output VCF is exactly identical to previous version. Drawback is increased runtime because Tribble has to create an index for all the Beagle files when starting if the idx files are missing.
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independent while processing, and only merged back in a priority queue if necessary in a special
variant of the ReadBackedPileup. This code is not live yet except in the case of naive deduping.
Downsampling by sample temporarily disabled, and the ReadBackedPileup variant is sketchy and
not well integrated with StratifiedAlignmentContext or the walkers. Cleanup to follow.
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Updated dbsnp/hapmap membership info fields to be flags now instead of ints.
While I was there, I added the change in the Annotator for Jan to force reads to be from a specific sample.
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String.valueOf(byte[]) doesn't work. You must use new String(byte[]).
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Added an integration test for the read-less case.
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1. VA is now a ROD walker so it no longer requires reads (needs a little more testing)
2. Annotations can now represent multiple INFO fields (i.e. sets of key/value pairs)
3. The chromosome count annotations have been pulled out of UG and the VCF writer code and into VA where they belong. Fixed the headers too.
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not currently as flat as it could / should be, but it's already comparable
to the speed of the reference implementation.
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the LocusOverflowTracker into LocusIteratorByState. Note that the 'Matt Hanna exception', is still enabled
because I haven't yet validated the performance of the DownsamplingLocusIteratorByState when running
without downsampling.
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in preparation for merging the two into one.
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the imminent move of IlluminaUtil into picard public.
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bthomas
ebanks
hanna
depristo
kiran
rpoplin
aaron
kshakir
delangel
asivache
chartl