Story:
https://www.pivotaltracker.com/story/show/77250524
Changes:
- Remove the annotating code in GeneralPloidyExactAFCalc (GPEAFC) class.
- Added the asAlleleList to GenotypeAlleleCounts class and get (GPEAFC) to use that instead of implementing its own (nicer and more reusable code).
- Removed the explicit addition of AlleleCountBySample fields to the VCF header by the walker initialize
- Added utility methods in Utils to wrap and int[] array into a List<Integer>, and double[] array into a List<Double> efficiently.
Test:
- Added unit-testing for asAlleleList in GenotypeAlleleCountsUnitTest (within testFirst and testNext).
- Added unit-testing for new methods in Utils : asList(int[]) and asList(double[])
- Changed UG General Ploidy test to add explicitly those annotations.
- Non-trivial changes in integration tests involving non-diploid runs (namelly haploid and tetraploid) as they are not showing
those annotations anylonger, so the MD5s have been changed accordingly.
Changes in several walker to use new sample, allele closed lists and new GenotypingEngine constructors signatures
Rebase adoption of new calculation system in walkers
If any pair of variants occurs on all used haplotypes together, then we propagate that information into the gVCF.
Can be enabled with the --tryPhysicalPhasing argument.
- Read groups that are excluded by sample_name, platform, or read_group arguments no longer appear in the header
- The performance penalty associated with filtering by read group has been essentially eliminated
- Partial fulfillment of PT 73075482
Stories:
https://www.pivotaltracker.com/story/show/70222086https://www.pivotaltracker.com/story/show/67961652
Changes:
Done some changes that I missed in relation with making sure that all PairHMM implentations use the same interface; as a consequence we were running always the standard PairHMM.
Fixed some additional bugs detected when running it on full wgs single sample and exom multi sample data set.
Updated some integration test md5s.
Fixing GraphBased bugs with new master code
Fixed ReadLikelihoods.changeReads difficult to spot bug.
Changed PairHMM interface to fix a bug
Fixed missing changes for various PairHMM implementations to get them to use the new structure.
Fixed various bugs only detectable when running with full sample(s).
Believe to have fixed the lack of annotations in UG runs
Fixed integrationt test MD5s
Updating some md5s
Fixed yet another md5 probably left out by mistake
The array structure should be faster to populate and query (no properly benchmarked) and reduce memory footprint considerably.
Nevertheless removing PairHMM factor (using likelihoodEngine Random) it only achieves a speed up of 15% in some example WGS dataset
i.e. there are other bigger bottle necks in the system. Bamboo tests also seem to run significantly faster with this change.
Stories:
https://www.pivotaltracker.com/story/show/70222086https://www.pivotaltracker.com/story/show/67961652
Changes:
- ReadLikelihoods added to substitute Map<String,PerSampleReadLikelihoods>
- Operation that involve changes in full sets of ReadLikelihoods have been moved into that class.
- Simplified a bit the code that handles the downsampling of reads based on contamination
Caveats:
- Still we keep Map<String,PerReadAlleleLikelihoodsMap> around to pass to annotators..., didn't feel like change the interface of so many public classes in this pull-request.
In particular, it was possible to specify arguments for Files or Compound types without values
Added a special "none" value for annotations, since a bare "-A" is no longer allowed
Delivers PT 71792842 and 59360374
ValidationStringency was moved from htsjdk.samtools.SAMFileReader to htsjdk.samtools
samtools find BAM index file method was also moved (and made public!)
- Edited intervals merging docs for correctness & clarity
- Edited VQSR arg docs and made mode required (+added -mode SNP to VQSR tests)
- Moved PaperGenotyper to Toy Walkers to declutter the actually useful docs
- Moved GenotypeGVCFs to Variant Discovery category and clarified a few points
- Clarified that the -resource argument depends on using the -V:tag format
- Clarified how the pcr indel model works
- Added caveat for -U ALLOW_N_CIGAR_READS
- Added MathJax support for displaying equations in GATKDocs
- Updated HC example commands and caveats
In these cases, where the alignment contains multiple indels, we output a single complex
variant instead of the multiple partial indels.
We also re-enable dangling tail recovery by default.
-- AD,DP will now correspond directly to the reads that were used to construct the PLs
-- RankSumTests, etc. will use the bases from the realigned reads instead of the original alignments
-- There is now no additional runtime cost to realign the reads when using bamout or GVCF mode
-- bamout mode no longer sets the mapping quality to zero for uninformative reads, instead the read will not be given an HC tag
Valentin Ruano-Rubio
Eric Banks
Ryan Poplin
Geraldine Van der Auwera
jmthibault79
Phillip Dexheimer
Laura Gauthier
David Roazen
Khalid Shakir
kshakir
Nigel Delaney