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
-- More meaningful histogram axes
-- Counts of multi-allelic variants
-- Removed from stratified plots that didn't mean anything (SNP : indel ratio, for example)
-- 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
Guillermo del Angel
Ryan Poplin
Menachem Fromer
Eric Banks
Mauricio Carneiro
Khalid Shakir
Mark DePristo