1. Add the symbolic 'current' link for the new bundle dir
2. Don't gzip and copy .out files
3. Don't call chr20 SNPs on the example BAM because it's now just a few reads on chr1
-- Don't just read all inputs into a list, and then provide an iterator to that list, actually make a real iterator so NanoScheduler input thread can contribute meaningfully to the work load
-- Use NanoScheduler progress function, instead of home-grown updater
-- Refactor calculation so that upfront constant values are pre-computed, and cached, and their values just looked up during application
-- Trivial comment on how we might use BAQ better in BaseRecalibrator
-- Cleaned up code in updateDataForRead so that constant values where not computed in inner loops
-- BaseRecalibrator doesn't create it's own fasta index reader, it just piggy backs on the GATK one
-- ReadCovariates <init> now uses a thread local cache for it's int[][][] keys member variable. This stops us from recreating an expensive array over and over. In order to make this really work had to update recordValues in ContextCovariate so it writes 0s over base values its skipping because of low quality base clipping. Previously the values in the ReadCovariates keys were 0 because they were never modified by ContextCovariates. Now these values are actually zero'd out explicitly by the covariates.
-- No longer computes at each update the overall read group table. Now computes this derived table only at the end of the computation, using the ByQual table as input. Reduces BQSR runtime by 1/3 in my test
The indels are still annotated as before, but now all other variant types are annotated too.
I'm doing this because of requests on the forum but am not making it standard. If we find it to be useful we can turn it on by default later.
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.
Yossi Farjoun
eitanbanks
Mark DePristo
Ryan Poplin
Jacob Silterra
Mauricio Carneiro
Guillermo del Angel
Kristian Cibulskis
Ami Levy-Moonshine
David Roazen