Guillermo del Angel 901f47d8af Final step (for now) in VA refactoring: update MD5's because, a) since it's not guaranteed that we'll iterate through reads/pileups in the same order, the rank sum dithering will change annotations, b) FS uses new generic threshold to distinguish uninformative reads (it used to use ad-hoc thresholds), c) AD definition changed and throws away uninformative reads, d) shortened general ploidy integration tests for quicker debugging. May have missed some MD5's in the update so there may be lingering test failures still		2012-08-22 11:38:51 -04:00
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datasources	Adding support of X and = CIGAR operators to the GATK	2012-08-10 14:54:07 -04:00
downsampling	Make downsampler classes themselves generic (instead of just the Downsampler interface)	2012-06-13 16:43:39 -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	WTF - why is support for whole-read insertions all messed up in LIBS? I've pushed a temporary patch for now (the right solution should certainly not be implemented in stable; LIBS needs to be better thought out). Added another unit test.	2012-08-22 00:24:01 -04:00
refdata	RMDTrackBuilderUnitTest now uses private/testdata file to avoid filesystem race conditions	2012-07-25 22:05:04 -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	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
walkers	Final step (for now) in VA refactoring: update MD5's because, a) since it's not guaranteed that we'll iterate through reads/pileups in the same order, the rank sum dithering will change annotations, b) FS uses new generic threshold to distinguish uninformative reads (it used to use ad-hoc thresholds), c) AD definition changed and throws away uninformative reads, d) shortened general ploidy integration tests for quicker debugging. May have missed some MD5's in the update so there may be lingering test failures still	2012-08-22 11:38:51 -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	Sorting out HMS error handling (fingers crossed)	2012-07-25 23:13:12 -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