Reads that are soft-clipped off the contig (before the beginning of the contig) were being soft-clipped to position 0 instead of 1 because of an off-by-one issue. Fixed and included in the integration test.
-- Uses high-performance local writer backed by byte array that writes the entire VCF line in some write operation to the underlying output stream.
-- Fixes problems with indexing of unflushed writes while still allowing efficient block zipping
-- Same (or better) IO performance as previous implementation
-- IndexingVariantContextWriter now properly closes the underlying output stream when it's closed
-- Updated compressed VCF output file
this introduced a bug in reduce reads by de-activating it's hard clipping of the out of bounds soft-clips (specially in the MT).
DEV-322 #resolve #time 4m
This reverts commit 42acfd9d0bccfc0411944c342a5b889f5feae736.
-Switch back to the old implementation, if needed, with --use_legacy_downsampler
-LocusIteratorByStateExperimental becomes the new LocusIteratorByState, and
the original LocusIteratorByState becomes LegacyLocusIteratorByState
-Similarly, the ExperimentalReadShardBalancer becomes the new ReadShardBalancer,
with the old one renamed to LegacyReadShardBalancer
-Performance improvements: locus traversals used to be 20% slower in the new
downsampling implementation, now they are roughly the same speed.
-Tests show a very high level of concordance with UG calls from the previous
implementation, with some new calls and edge cases that still require more examination.
-With the new implementation, can now use -dcov with ReadWalkers to set a limit
on the max # of reads per alignment start position per sample. Appropriate value
for ReadWalker dcov may be in the single digits for some tools, but this too
requires more investigation.
-- Was screwing up mixed reviewed / non-reviewed sites. Now only considered reviewed calls, if any are present, or all calls if no reviewed sites are found
-- Was just taking the first genotype, now it properly looks at all of the genotype calls and makes a reasonable guess what the answer should be
-- Added unit tests for the consensus creation algorithm
-- The current implementation of AFCalcResult contains a map from allele -> log10pNonRef. The only use of this field is to support the isPolymorphic function per allele. The call to this function looks like isPolymorphic(allele, QUAL). The QUAL is a phred-scaled threshold where you want to include alleles where the log10pNonRef >= QUAL (appropriately transformed). The problem is that when log10pNonRef is large, it quickly gets set to 0, while it's complementary log10pRef value has a meaningful log10 value. For example, if log10pRef = -100 (not an uncommonly large value), log10pNonRef = 0.0.
-- In order to preserve precision and allow us to more finally differentiate high QUAL from low QUAL (but still poly) sites we should store log10pRef values instead, and test that log10pRef <= threshold.
-- See https://jira.broadinstitute.org/browse/GSA-671 for more information.
-- The previous approach tried to remove the entire MongoVariantContext but when it was malformed was prone to error. Now just grabs the _id and uses it to remove the bad record.
depristo
Eric Banks
Yossi Farjoun
Jacob Silterra
Mauricio Carneiro
Guillermo del Angel
Chris Hartl
Ryan Poplin
Kristian Cibulskis
Ami Levy-Moonshine
David Roazen
Joel Thibault