Eric Banks 1c387848de No more use of -D in the integration tests but instead stick with VCFs only. Since all of these tests were duplicated (one each for dbSNP format and for VCF), we don't actually lose coverage in the integration tests.		2011-08-02 10:39:50 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	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
test	No more use of -D in the integration tests but instead stick with VCFs only. Since all of these tests were duplicated (one each for dbSNP format and for VCF), we don't actually lose coverage in the integration tests.	2011-08-02 10:39:50 -04:00