Commit Graph

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