depristo f2e7582cfc Reorganization of SW code for clarity. Totally failure at raw optimization. Discovered that ~50% of reads being cleaned were perfect reference matches. New code comes with flag to look at NM field and not clean perfect matches. Can we turned off with command line option (needed for 1KG bams with bad NM fields). Going to rerun cleaning jobs due to accidentally rebuilding of stable codebase and loss of 2 days of runtime. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3452 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-27 23:16:00 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Reorganization of SW code for clarity. Totally failure at raw optimization. Discovered that ~50% of reads being cleaned were perfect reference matches. New code comes with flag to look at NM field and not clean perfect matches. Can we turned off with command line option (needed for 1KG bams with bad NM fields). Going to rerun cleaning jobs due to accidentally rebuilding of stable codebase and loss of 2 days of runtime.	2010-05-27 23:16:00 +00:00
test/org/broadinstitute/sting	Reorganization of SW code for clarity. Totally failure at raw optimization. Discovered that ~50% of reads being cleaned were perfect reference matches. New code comes with flag to look at NM field and not clean perfect matches. Can we turned off with command line option (needed for 1KG bams with bad NM fields). Going to rerun cleaning jobs due to accidentally rebuilding of stable codebase and loss of 2 days of runtime.	2010-05-27 23:16:00 +00:00