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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/sam
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Mark DePristo 41aba491c0 Critical bugfix for adapter clipping in HaplotypeCaller 
-- The previous code would adapter clip before reverting soft clips, so because we only clip the adapter when it's actually aligned (i.e., not in the soft clips) we were actually not removing bases in the adapter unless at least 1 bp of the adapter was aligned to the reference.  Terrible.
-- Removed the broken logic of determining whether a read adaptor is too long.
-- Doesn't require isProperPairFlag to be set for a read to be adapter clipped
-- Update integration tests for new adapter clipping code
 		2013-07-02 15:46:36 -04:00
..
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 Critical bugfix for adapter clipping in HaplotypeCaller 2013-07-02 15:46:36 -04:00