David Roazen 133085469f Experimental, downsampler-friendly read shard balancer ... -Only used when experimental downsampling is enabled -Persists read iterators across shards, creating a new set only when we've exhausted the current BAM file region(s). This prevents the engine from revisiting regions discarded by the downsamplers / filters, as could happen in the old implementation. -SAMDataSource no longer tracks low-level file positions in experimental mode. Can strip out all related code when the engine fork is collapsed. -Defensive implementation that assumes BAM file regions coming out of the BAM Schedule can overlap; should be able to improve performance if we can prove they cannot possibly overlap. -Tests a bit on the extreme side (~8 minute runtime) for now; will scale these back once confidence in the code is gained		2012-09-21 22:17:58 -04:00
..
datasources	Experimental, downsampler-friendly read shard balancer	2012-09-21 22:17:58 -04:00
downsampling	Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"	2012-09-10 15:52:39 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Updated and more thorough version of the BadCigar read filter	2012-08-17 17:05:27 -04:00
iterators	Experimental, downsampler-friendly read shard balancer	2012-09-21 22:17:58 -04:00
refdata	Part I of GSA-462: Consistent RODBinding access across Ref and Read trackers	2012-08-30 10:15:10 -04:00
report	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
samples	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
traversals	Refactor TraversalEngine to extract the progress meter functions	2012-09-10 20:14:13 -04:00
walkers	Bad news folks: BQSR scatter-gather was totally busted; you absolutely cannot trust any BQSR table that was a product of SG (for any version of BQSR). I fixed BQSR-gathering, rewrote (and enabled) the unit test, and confirmed that outputs are now identical whether or not SG is used to create the table.	2012-09-20 14:14:34 -04:00
CommandLineGATKUnitTest.java	Adding Unit Tests to cover the exception catching for Picard errors: because we are using String matching, we want to ensure that we know if/when the exception text changes underneath us.	2012-07-18 21:48:58 -04:00
EngineFeaturesIntegrationTest.java	Proper error handling in NanoScheduler	2012-09-19 17:03:13 -04:00
GenomeAnalysisEngineUnitTest.java	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
WalkerManagerUnitTest.java	Fixing walker unit test with the new naming convention	2012-07-20 17:50:29 -04:00