depristo 29f3ad72f3 SAMFileWriter that allows the user to move reads, but only a bit, in an incoming coordinated sorted BAM files. Does some local reordering and local mate fixing, under specified constrained. These constrains allow us to make a special -- under testing for Eric, who promised to try this out a bit, expand test cases and integration tests -- but soon to be the default and only model of the realigner that only moves reads with ISIZE < 3000 that directly emits a coordinate sorted, mate fixed validating BAM file without needing FixMates externally. Preliminary testing shows this runs in a totally fine amount of memory and produces equivalent results to the previous version. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5199 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-04 22:27:05 +00:00
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ArtificialPatternedSAMIteratorUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
ArtificialSAMFileWriterUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
ArtificialSAMQueryIteratorUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
ArtificialSAMUtilsUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
ConstrainedMateFixingSAMFileWriterUnitTest.java	SAMFileWriter that allows the user to move reads, but only a bit, in an incoming coordinated sorted BAM files. Does some local reordering and local mate fixing, under specified constrained. These constrains allow us to make a special -- under testing for Eric, who promised to try this out a bit, expand test cases and integration tests -- but soon to be the default and only model of the realigner that only moves reads with ISIZE < 3000 that directly emits a coordinate sorted, mate fixed validating BAM file without needing FixMates externally. Preliminary testing shows this runs in a totally fine amount of memory and produces equivalent results to the previous version.	2011-02-04 22:27:05 +00:00