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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/sam
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Mark DePristo 4d0e7b50ec ArtificialBAMBuilder utility class for creating streams of GATKSAMRecords with a variety of properties 
--  Allows us to make a stream of reads or an index BAM file with read having the following properties (coming from n samples, of fixed read length and aligned to the genome with M operator, having N reads per alignment start, skipping N bases between each alignment start, starting at a given alignment start)
-- This stream can be handed back to the caller immediately, or written to an indexed BAM file
-- Update LocusIteratorByStateUnitTest to use this functionality (which was refactored from LIBS unit tests and ArtificialSAMUtils)
 		2013-01-16 15:29:59 -05:00
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AlignmentUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArtificialBAMBuilderUnitTest.java ArtificialBAMBuilder utility class for creating streams of GATKSAMRecords with a variety of properties 2013-01-16 15:29:59 -05:00
ArtificialPatternedSAMIteratorUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArtificialSAMFileWriterUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -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 PileupElement and LIBS cleanup 2013-01-11 15:17:17 -05:00
MisencodedBaseQualityUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ReadUtilsUnitTest.java getAdaptorBoundary returns an int, not an Integer, as this was taking 30% of the allocation effort for LIBS 2013-01-14 16:30:15 -05:00