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
* 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)
* 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
-- 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
-- Now calculates the number of Indels overlapping gold standard sites, as well as the percent of indels overlapping gold standard sites
-- Removed insertion : deletion ratio for 1 bp event, replaced it with 1 + 2 : 3 bp ratio for insertions and deletions separately. This is based on an old email from Mark Daly:
// - Since 1 & 2 bp insertions and 1 & 2 bp deletions are equally likely to cause a
// downstream frameshift, if we make the simplifying assumptions that 3 bp ins
// and 3bp del (adding/subtracting 1 AA in general) are roughly comparably
// selected against, we should see a consistent 1+2 : 3 bp ratio for insertions
// as for deletions, and certainly would expect consistency between in/dels that
// multiple methods find and in/dels that are unique to one method (since deletions
// are more common and the artifacts differ, it is probably worth looking at the totals,
// overlaps and ratios for insertions and deletions separately in the methods
// comparison and in this case don't even need to make the simplifying in = del functional assumption
-- Added a new VEW argument to bind a gold standard track
-- Added two new stratifications: OneBPIndel and TandemRepeat which do exactly what you imagine they do
-- Deleted random unused functions in IndelUtils
* fixed bug where some keys were using the same recal datum objects
* fixed quantization qual calculations when combining multiple reports
* fixed rounding error with empirical quality reported when combining reports
* fixed combine routine in the gatk reports due to the primary keys being out of order
* added auto-recalibration option to BQSR scala script
* reduced the size of the recalibration report by ~15%
* updated md5's
-- Molten now supports variableName and valueName so you don't have to use variable and value if you don't want to.
-- Cleanup code, reorganize a bit more.
-- Fix for broken integrationtests
*** WAY FASTER ***
-- 3x performance for multiple sample analysis with 1000 samples
-- Analyzing 1MB of the ESP call set (3100 samples) takes 40 secs, compared to several minutes in the previous version
-- According to JProfiler all of the runtime is now spent decoding genotypes, which will only get better when we move to BCF2
-- Remove the TableType system, as this was way too complex. No longer possible to embed what were effectively multiple tables in a single Evaluator. You now have to have 1 table per eval
-- Replaced it with @Molten, which allows an evaluator to provide a single Map from variable -> value for analysis. IndelLengthHistogram is now a @Molten data type. GenotypeConcordance is also.
-- No longer allow Evaluators to use private and protected variables at @DataPoints. You get an error if you do.
-- Simplified entire IO system of VE. Refactored into VariantEvalReportWriter.
-- Commented out GenotypePhasingEvaluator, as it uses the retired TableType
-- Stratifications are all fully typed, so it's easy for GATKReports to format them.
-- Removed old VE work around from GATKReportColumn
-- General code cleanup throughout
-- Updated integration tests
-- Added memory and safety optimizations to StratNode and StratificationManager. Fresh, immutable Hashmaps are allocated for final data structures, so they exactly the correct size and cannot be changed by users.
-- Added ability of a stratification to specify incompatible evaluation. The two strats using this are AC and Sample with VariantSummary, as this computes per-sample averages and so combining these results in an O(n^2) memory requirement. Added integration test to cover incompatible strats and evals
-- Renamed and reorganized infrastructure
-- StratificationManager now a Map from List<Object> -> V. All key functions are implemented. Less commonly used TODO
-- Ready for hookup to VE
-- Created a unit tested tree mapping from a List<String> -> integer (StratificationStates). This class is the key infrastructure necessary to create a complete static mapping from all stratification combinations to an offset in a vector of EvalutionContexts for update in map.
-- Minor code cleanup throughout VE (removing unused headers, for example)
Khalid Shakir
Guillermo del Angel
Laurent Francioli
Mauricio Carneiro
Eric Banks
Ryan Poplin
Mark DePristo