gatk-3.8

Author	SHA1	Message	Date
hanna	8d2c14b29c	Update Picard / sam-jdk at Tim's request. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4925 348d0f76-0448-11de-a6fe-93d51630548a	2011-01-03 02:17:25 +00:00
depristo	974aaa134d	Trival fix to broken build git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4820 348d0f76-0448-11de-a6fe-93d51630548a	2010-12-11 13:56:03 +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