-- Fixes monster bug in the way that traversal engines interacted with the NanoScheduler via the output tracker.
-- ThreadLocalOutputTracker is now a ThreadBasedOutputTracker that associates via a map from a master thread -> the storage map. Lookups occur by walking through threads in the same thread group, not just the thread itself (TBD -- should have a map from ThreadGroup instead)
-- Removed unnecessary debug statement in GenomeLocParser
-- nt and nct officially work together now
-- GenomeLocParser cache was a major performance bottleneck in parallel GATK performance. With 10 thread > 50% of each thread's time was spent blocking on the MasterSequencingDictionary object. Made this a thread local variable.
-- Now we can run the GATK with 48 threads efficiently on GSA4!
-- Running -nt 1 => 75 minutes (didn't let is run all of the way through so likely would take longer)
-- Running -nt 24 => 3.81 minutes
The primary use of this stratification is to provide a mechanism to divide asssessment of a call set up by whether a variant overlaps an interval or not. I use this to differentiate between variants occurring in CCDS exons vs. those in non-coding regions, in the 1000G call set, using a command line that looks like:
-T VariantEval -R human_g1k_v37.fasta -eval 1000G.vcf -stratIntervals:BED ccds.bed -ST IntervalStratification
Note that the overlap algorithm properly handles symbolic alleles with an INFO field END value. In order to safely use this module you should provide entire contigs worth of variants, and let the interval strat decide overlap, as opposed to using -L which will not properly work with symbolic variants.
Minor improvements to create() interval in GenomeLocParser.
Mark DePristo
Eric Banks
Guillermo del Angel
Khalid Shakir
David Roazen