Mark DePristo 2ebdff074c Update MD5s for SOLiD recalibration ... -- MD5 db had spelling error; fixed -- Bug in AlignmentUtils resulted in some bases not being color space corrected. The integration test caught the change, and it's clear that the new version is correct, as the prev. version was not considering the last the N qualities for reads with a ND operation.		2011-10-13 18:01:51 -04:00
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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	Bugfix for file that must not exist on disk	2011-08-29 17:00:10 -04:00
gatk	Update MD5s for SOLiD recalibration	2011-10-13 18:01:51 -04:00
jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	Abandoning classfileset/rootfileset approach due to difficulting managing	2011-10-06 12:49:51 -04:00
BaseTest.java	Fixing syntax of BQSR and UG performance tests.	2011-08-11 17:04:09 -04:00
MD5DB.java	Update MD5s for SOLiD recalibration	2011-10-13 18:01:51 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.	2011-07-18 10:46:01 -04:00