Mauricio Carneiro 5bba44d693 Added hardClipByReferenceCoordinates UnitTest for the ReadClipper ... * fixed edge case when requested to hard clip beginning of a read that had hanging soft clipped bases on the left tail. * fixed edge case when requested to hard clip end of a read that had hanging soft clipped bases on the right tail. * fixed AlignmentStart of a clipped read that results in only hard clips and soft clips note: added tests to all these beautiful cases...		2011-12-16 18:01:33 -05:00
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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Updating busted integration tests	2011-12-14 16:24:43 -05:00
jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00
utils	Added hardClipByReferenceCoordinates UnitTest for the ReadClipper	2011-12-16 18:01:33 -05:00
BaseTest.java	Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-12-07 09:03:17 -05:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00