3 Commits (c08936d6f47894f4073c9e4d2678a05fa6798c55)

Author	SHA1	Message	Date
ebanks	79ab7affda	- Change sortOnDisk option to sortInMemory ... - Fix horrible cleaner bug - Trivial optimizations to cleaner code - more significant ones coming soon. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2850 348d0f76-0448-11de-a6fe-93d51630548a	2010-02-17 20:52:57 +00:00
ebanks	fddca032bb	Initial commit of v2.0 of the cleaner. DO NOT USE. (this means you, Chris) ... Cleaned up SW code and started moving over everything to use byte[] instead of String or char[]. Added a wrapper class for SAMFileWriter that allows for adding reads out of order. Not even close to done, but I need to commit now to sync up with Andrey. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2712 348d0f76-0448-11de-a6fe-93d51630548a	2010-01-27 21:36:42 +00:00
ebanks	59f0c00d77	-set indel cleaning walkers to be in core package ... -move Andrey's alignment utility classes to core git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1307 348d0f76-0448-11de-a6fe-93d51630548a	2009-07-24 05:23:29 +00:00