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
..
net/sf	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
org/broadinstitute/sting	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