Eric Banks 2c5e526eb7 Don't use the mismatch fraction by default in the RealignerTargetCreator (since it's only useful when using SW in the indel realigner). Also, no more use of -D but instead move over to using VCFs. One integration test is temporarily commented out while I wait for a VCF file to get fixed.		2011-08-02 10:34:46 -04:00
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arguments	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
datasources	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
iterators	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
refdata	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
report	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
traversals	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
walkers	Don't use the mismatch fraction by default in the RealignerTargetCreator (since it's only useful when using SW in the indel realigner). Also, no more use of -D but instead move over to using VCFs. One integration test is temporarily commented out while I wait for a VCF file to get fixed.	2011-08-02 10:34:46 -04:00
GenomeAnalysisEngineUnitTest.java	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
WalkerManagerUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00