Eric Banks 1afc49a297 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
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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	When using the BWA bindings, you have to explicitly call close() to get the	2011-07-21 12:13:29 -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