Christopher Hartl 92c7cfa1c8 BWA bindings and tests moved to public (was required for ValidationAmplicons) ... Integration tests for ValidationAmplicons. New argument to disable BWA, lowercase letters only for repetitiveness instead.		2011-07-19 20:11:31 -04:00
..
alignment	BWA bindings and tests moved to public (was required for ValidationAmplicons)	2011-07-19 20:11:31 -04:00
commandline	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
gatk	BWA bindings and tests moved to public (was required for ValidationAmplicons)	2011-07-19 20:11:31 -04:00
jna	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.	2011-07-12 14:11:53 -04:00
BaseTest.java	DiffEngine utility function simpleDiffFiles	2011-07-11 23:10:27 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00