-- Invert logic in GATKArgumentCollection to disable monitoring, not enable. That means monitoring is on by default
-- Fix testing error in unit tests
-- Rename variables in ThreadAllocation to be clearer
-- Old version StateMonitoringThreadFactory refactored into base class ThreadEfficiencyMonitor and subclass EfficiencyMonitoringThreadFactory.
-- Base class is used by LinearMicroScheduler to monitor performance of GATK in single threaded mode
-- MicroScheduler now handles management of the efficiency monitor. Includes master thread in monitor, meaning that reduce is now included for both schedulers
-- Allows us to ID (by proxy) time spent doing IO
-- Refactor StateMonitoryingThreadFactory to use it's own enum, not Thread.State
-- Reliable unit tests across mac and unix
-- See https://jira.broadinstitute.org/browse/GSA-502
-- New command line argument -mt enables thread monitoring
-- If enabled, HMS uses StateMonitoringThreadFactory to create monitored threads, and prints out an efficiency report when HMS exits, telling the user information like:
for BQSR – known to be inefficient locking
INFO 17:10:33,195 StateMonitoringThreadFactory - Number of activeThreads used: 8
INFO 17:10:33,196 StateMonitoringThreadFactory - Total runtime 90.3 m
INFO 17:10:33,196 StateMonitoringThreadFactory - Fraction of time spent blocked is 0.72 ( 64.8 m)
INFO 17:10:33,197 StateMonitoringThreadFactory - Fraction of time spent running is 0.26 ( 23.7 m)
INFO 17:10:33,197 StateMonitoringThreadFactory - Fraction of time spent waiting is 0.02 ( 112.8 s)
INFO 17:10:33,197 StateMonitoringThreadFactory - Efficiency of multi-threading: 26.19% of time spent doing productive work
for CountLoci
INFO 17:06:12,777 StateMonitoringThreadFactory - Number of activeThreads used: 8
INFO 17:06:12,777 StateMonitoringThreadFactory - Total runtime 43.5 m
INFO 17:06:12,778 StateMonitoringThreadFactory - Fraction of time spent blocked is 0.00 ( 4.2 s)
INFO 17:06:12,778 StateMonitoringThreadFactory - Fraction of time spent running is 1.00 ( 43.3 m)
INFO 17:06:12,779 StateMonitoringThreadFactory - Fraction of time spent waiting is 0.00 ( 6.0 s)
INFO 17:06:12,779 StateMonitoringThreadFactory - Efficiency of multi-threading: 99.61% of time spent doing productive work
- Fix for M_Trieb's error report on the forum, and addition of integration tests to cover the walker.
- Addition of StructuralIndel as a class of variation within the VariantContext. These are for variants with a full alt allele that's >150bp in length.
- Adaptation of the MVLikelihoodRatio to work for a set of trios (takes the max over the trios of the MVLR)
- InsertSizeDistribution changed to use the new gatk report output (it was previously broken)
- RetrogeneDiscovery changed to be compatible with the new gatk report
- A maxIndelSize argument added to SelectVariants
- ByTranscriptEvaluator rewritten for cleanliness
- VariantRecalibrator modified to not exclude structural indels from recalibration if the mode is INDEL
- Documentation added to DepthOfCoverageIntegrationTest (no, don't yell at chartl ;_; )
Also sorry for the long commit history behind this that is the result of fixing merge conflicts. Because this *also* fixes a conflict (from git stash apply), for some reason I can't rebase all of them away. I'm pretty sure some of the commit notes say "this note isn't important because I'm going to rebase it anyway".
-- When merging multiple VCF records at a site, the combined VCF record has the QUAL of the first VCF record with a non-MISSING QUAL value. The previous behavior was to take the max QUAL, which resulted in sometime strange downstream confusion.
* No reads with Hard/Soft clips in the middle of the cigar
* No reads starting with deletions (with or without preceding clips)
* No reads ending in deletions (with or without follow-up clips)
* No reads that are fully hard or soft clipped
* No reads that have consecutive indels in the cigar (II, DD, ID or DI)
Also added systematic test for good cigars and iterative test for bad cigars.
-- Removed REFERENCE_BASES option. You only have REFERENCE now. There's no efficiency savings for the REFERENCE_BASES option any longer, since the reference bases are loaded lazy so if you don't use them there's effectively no cost to making the RefContext that could load them.
Mark DePristo
Eric Banks
Guillermo del Angel
Ryan Poplin
Christopher Hartl
Mauricio Carneiro