Eric Banks dadcfe296d Reworking of the dangling tails merging code. ... We now run Smith-Waterman on the dangling tail against the corresponding reference tail. If we can generate a reasonable, low entropy alignment then we trigger the merge to the reference path; otherwise we abort. Also, we put in a check for low-complexity of graphs and don't let those pass through. Added tests for this implementation that checks exact SW results and correct edges added.		2013-06-11 12:53:04 -04:00
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AlignmentUtilsUnitTest.java	Reworking of the dangling tails merging code.	2013-06-11 12:53:04 -04:00
ArtificialBAMBuilderUnitTest.java	Last manual license update (hopefully)	2013-01-18 16:13:07 -05:00
ArtificialPatternedSAMIteratorUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
ArtificialSAMFileWriterUnitTest.java	PrintReads writes a header when used with -BQSR	2013-02-14 22:19:14 -05:00
ArtificialSAMQueryIteratorUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
ArtificialSAMUtilsUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
ArtificialSingleSampleReadStreamUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
GATKSAMRecordUnitTest.java	Update expected test output for Java 7	2013-05-01 16:18:01 -04:00
MisencodedBaseQualityUnitTest.java	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00
ReadUtilsUnitTest.java	e# This is a combination of 2 commits.	2013-05-03 11:19:14 -04:00