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gatk-3.8/java/src/org/broadinstitute/sting
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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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alignment BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils. 2010-05-20 14:05:13 +00:00
analyzecovariates The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
commandline The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
gatk 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
oneoffprojects Read error rate is now parallelizable 2010-05-27 19:00:09 +00:00
playground Better Exception message when can't find annotation value in variant recalibrator. 2010-05-25 21:15:50 +00:00
utils 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