Mauricio Carneiro c85100ce9c Fix ClippingOp bug when performing multiple hardclip ops ... bug: When performing multiple hard clip operations in a read that has indels, if the N+1 hardclip requests to clip inside an indel that has been removed by one of the (1..N) previous hardclips, the hard clipper would go out of bounds. fix: dynamically adjust the boundaries according to the new hardclipped read length. (this maintains the current contract that hardclipping will never return a read starting or ending in indels).		2011-12-14 16:57:47 -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jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00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	Fix ClippingOp bug when performing multiple hardclip ops	2011-12-14 16:57:47 -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