gatk-3.8

Author	SHA1	Message	Date
hanna	ccdb4a0313	General-purpose management of output streams. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1454 348d0f76-0448-11de-a6fe-93d51630548a	2009-08-23 00:56:02 +00:00
hanna	7a13647c35	Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. Very rough initial implementation, but should provide enough support so that people can stop creating SAMFileWriters in reduceInit. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a	2009-07-29 16:11:45 +00:00
hanna	2db86b7829	Move the cleaned read injector test from playground to core. Remove CovariateCounterTest's dependency on the CleanedReadInjector. Start doing a bit of cleanup on the CLP's FieldParsers. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1312 348d0f76-0448-11de-a6fe-93d51630548a	2009-07-24 19:44:04 +00:00