Ryan Poplin 98a96f07c1 Updated standard deviation parameter in VQSR to our current recommended value		2011-08-04 14:06:26 -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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
gatk	Updated standard deviation parameter in VQSR to our current recommended value	2011-08-04 14:06:26 -04:00
jna	Memory limits changed from Int to Double.	2011-07-21 22:57:18 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	There are some really 'interesting' (but apparently valid) records in the Mus musculus dbSNP file. Generalized the handling of complex cases in the dbSNP adaptor to handle it all. I just grabbed the actual Mus musculus dbSNP file as a test, ran it whole genome, and confirmed that we finally produce a valid VCF on it. Should be the last commit needed on this adaptor.	2011-07-28 13:55:58 -04:00
BaseTest.java	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.	2011-07-18 10:46:01 -04:00
MD5DB.java	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.	2011-07-18 10:46:01 -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