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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/sam
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Mark DePristo f42bb86bdd e# This is a combination of 2 commits. 
Only try to clip adaptors when both reads of the pair are on opposite strands

-- Read pairs that have unusual alignments, such as two reads both oriented like:

  <-----
     <-----

where previously having their adaptors clipped as though the standard calculation of the insert size was meaningful, which it is not for such oddly oriented pairs.  This caused us to clip extra good bases from reads.
-- Update MD5s due change in adaptor clipping, which add some coverage in some places
 		2013-05-03 11:19:14 -04:00
..
AlignmentUtilsUnitTest.java Bugfix for AlignmentUtils.trimCigarByBases 2013-05-03 09:32:05 -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