-- Other tribble contributors did major refactoring / simplification of tribble, which required some changes to GATK code
-- Integrationtests pass without modification, though some very old index files (callable loci beds) were apparently corrupt and no longer tolerated by the newer tribble codebase
Updated ReadFilter abstract class to implement (via UnsupportedOperationException) the new SamRecordFilter.filterOut().
In IndelRealignerIntegrationTest updates for Picard fixes to SAMRecord.getInferredInsertSize() in svn r1115 & r1124.
- Ran FixMates to create new input BAM since running IR with variable maxReadsInMemory means all reads weren't realigned leading to different outputs.
- Updated md5s to match new expectations after looking at TLEN diff engine output.
* Not working yet, still very much a work-in-progress with lots of placeholders
* Needed to check this in to enable possible collaboration, since it's
going slower than anticipated and the conference deadline looms.
a) Add ability for ErrorModel to be specified by external log-probability vector for testing.
b) For a given depth and ploidy(=2*samples/pool), create artificial high quality pileup testing from AC=0 to AC=ploidy, and test that pool GL's have expected content.Misc. refactorings and cleanups
c) Misc. cleanups and beautification.
a) Utility class called Probability Vector that holds a log-probability vector and has the ability to clip ends that deviate largely from max value.
b) Used this class to hold site error model, since likelihoods of error model away from peak are so far down that it's not worth computing with them and just wastes time.
c) Expand unit tests and add an exhaustive test for ErrorModel class.
d) Corrected major math bug in ErrorModel uncovered by exhaustive test: log(e^x) is NOT x if log's base = 10.
e) Refactored utility functions that created artificial pileups for testing into separate class ArtificialPileupTestProvider. Right now functionality is limited (one artificial contig of 10 bp), can only specify pileups in one position with a given number of matches and mismatches to ref) but functionality will be expanded in future to cover more test cases.
f) Use this utility class for IndelGenotypeLikelihoods unit test and for PoolGenotypeLikelihoods unit test (the latter testing functionality still not done).
g) Linearized implementation of biallelic exact model (very simple approach, similar to diploid exact model, just abort if we're past the max value of AC distribution and below a threshold). Still need to add unit tests for this and to expand to multiallelic model.
h) Update integration test md5's due to minor differences stemming from linearized exact model and better error model math
The GATK -L unmapped is for GenomeLocs with SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, not SAMRecord.getReadUnmappedFlag()
Previously unmapped flag reads in the last bin were being printed while also seeking for the reads without a reference contig.
* fixed queue script plot file names
* updated the ReadGroupCovariate to use the platform unit instead of sample + lane.
* fixed plotting of marginalized reported qualities
* updated BQSR queue script for faster turnaround
* implemented plot generation for scatter/gatherered runs
* adjusted output file names to be cooperative with the queue script
* added the recalibration report file to the argument table in the report
* added ReadCovariates unit test -- guarantees that all the covariates are being generated for every base in the read
* added RecalibrationReport unit test -- guarantees the integrity of the delta tables
* fixed context covariate famous "off by one" error
* reduced maximum quality score to Q50 (following Eric/Ryan's suggestion)
* remove context downsampling in BQSR R script
This test brings together the old and the new BQSR, building a recalibration table using the two separate frameworks and performing the recalibration calculation using the two different frameworks for 10,000+ bases and asserting that the calculations match in every case.
* Refactored CycleCovariate to be a fragment covariate instead of a per read covariate
* Refactored the CycleCovariateUnitTest to test the pairing information
* Updated BQSR Integration tests accordingly
* Made quantization levels parameter not hidden anymore
* Added hidden option to keep intermediate plotting files for debug purposes (they're automatically deleted)
* Added hidden option not to generate the plots automatically (important for scatter/gathering)
The most important reason for this change is that we no longer need to read the entire recal file into memory up front in ApplyRecalibration. For 1000G calling this was prohibitive in terms of memory requirements. Now we go through the rod system and pull in just the records we need at a given position.
As an added bonus, once BCF2 is live we can drastically cut down the sizes of these recal files (which can grow large for whole genome calling).
* removed low quality bases from the recalibration report.
* refactored the Datum (Recal and Accuracy) class structure
* created a new plotting csv table for optimized performance with the R script
* added a datum object that carries the accuracy information (AccuracyDatum) for plotting
* added mean reported quality score to all covariates
* added QualityScore as a covariate for plotting purposes
* added unit test to the key manager to operate with one required covariate and multiple optional covariates
* integrated the plotting into BQSR (automatically generates the pdf with the recalibration tearsheet)
- By porting from jython to java now accessible to Queue via automatic extension generation.
- Better handling for problematic sample names by using PicardAggregationUtils.
GATKReportTable looks up keys using arrays instead of dot-separated strings, which is useful when a sample has a period in the name.
CombineVariants has option to suppress the header with the command line, which is now invoked during VCF gathering.
Added SelectHeaders walker for filtering headers for dbGAP submission.
Generated command line for read filters now correctly prefixes the argument name as --read_filter instead of -read_filter.
Latest WholeGenomePipeline.
Other minor cleanup to utility methods.
-- Not hooked up yet, so the output of VariantEval should be the same as before
-- Implemented a VariantEvalUnitTest that tests the low level strat / eval combinatorics and counting routines
-- Better docs throughout
-- Now properly includes both bi and multi-allelic variants. These are actually counted as well, and emitted as counts and % of sites with multiple alleles
-- Bug fix for gold standard rate
-- HMS no longer tries to grab and throw all exceptions. Exceptions are just thrown directly now.
-- Proper error handling is handled by functions in HMS, which are used by ShardTraverser and TreeReducer
-- Better printing of stack traces in WalkerTest
-- Unfortunately the result of the multi-threaded test is non-deterministic so run the test 10x times to see if the right expection is always thrown
-- Now prints the stack trace and exception message of the caught exception of the wrong type, if this occurs
Adding support for active-region-based annotation for most standard annotations. I need to discuss with Ryan what to do about tests that require offsets into the reads (since I don't have access to the offsets) like e.g. the ReadPosRankSumTest.
IMPORTANT NOTE: this is still very much a dev effort and can only be accessed through private walkers (i.e. the HaplotypeCaller). The interface is in flux and so we are making no attempt at all to make it clean or to merge this with the Locus-Traversal-based annotation system. When we are satisfied that it's working properly and have settled on the proper interface, we will clean it up then.
* Fixed output format to get a valid vcf
* Optimzed the per sample pileup routine O(n^2) => O(n) pileup for samples
* Added support to overlapping intervals
* Removed expand target functionality (for now)
* Removed total depth (pointless metric)
-- SamFileReader.java:525
-- BlockCompressedInputStream:376
These were both instances were we weren't catching and rethrowing picard exceptions as UserExceptions.
- refactored the statistics classes
- concurrent callable statuses by sample are now available.
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
Mark DePristo
Eric Banks
Khalid Shakir
Mauricio Carneiro
Guillermo del Angel
Joel Thibault
Ryan Poplin
David Roazen
Christopher Hartl
Laurent Francioli
Roger Zurawicki