5 Commits (a63bbb2fecaed5db01e229a5f2e6d18439478c3e)

Author	SHA1	Message	Date
depristo	a63bbb2fec	Optimized BAQ implementation. No longer does excessive amounts of copying of arrays. At this point I'm not 100% certain where additional performance improvements would come from ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4808 348d0f76-0448-11de-a6fe-93d51630548a	2010-12-08 21:26:30 +00:00
depristo	db55b2b0c6	Better testing of BAQ. Now really handles soft clipped reads properly by doing an expensive copy operation :-( will need to be transformed to a ByteBuffer in the near future. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4807 348d0f76-0448-11de-a6fe-93d51630548a	2010-12-08 17:37:00 +00:00
depristo	16e1bbd380	Hidden command line option to control BAQ gap open penalty for testing by me and eric. ValidateBAQWalker has misc. useful improvements. PrintReads now adds BAQ tags on output, if requested. ... BAQ has generally useful improvements. Refactor code to make it easier for BAQUnitTest to run. minBaseQuality enforced on output, as well as input now. Added BAQUnitTest that checks that the BAQ calculation is performing as expected. Still needs to be expanded significantly. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4804 348d0f76-0448-11de-a6fe-93d51630548a	2010-12-08 01:01:39 +00:00
depristo	c91712bd59	BAQ calculation refactoring in the GATK. Single -baq argument can be NONE, CALCULATE_AS_NECESSARY, and RECALCULATE. Walkers can control bia the @BAQMode annotation how the BAQ calculation is applied. Can either be as a tag, by overwriting the qualities scores, or by only returning the baq-capped qualities scores. Additionally, walkers can be set up to have the BAQ applied to the incoming reads (ON_INPUT, the default), to output reads (ON_OUTPUT), or HANDLED_BY_WALKER, which means that calling into the BAQ system is the responsibility of the individual walker. ... SAMFileWriterStub now supports BAQ writing as an internal feature. Several walkers have the @BAQMode applied to this, with parameters that I think are reasonable. Please look if you own these walkers, though git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4798 348d0f76-0448-11de-a6fe-93d51630548a	2010-12-06 20:55:52 +00:00
depristo	5d2c2bd280	Just refactoring into utils/baq directory ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4795 348d0f76-0448-11de-a6fe-93d51630548a	2010-12-06 17:43:43 +00:00