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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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Mauricio Carneiro d16cb68539 Updated and more thorough version of the BadCigar read filter 
* No reads with Hard/Soft clips in the middle of the cigar
   * No reads starting with deletions (with or without preceding clips)
   * No reads ending in deletions (with or without follow-up clips)
   * No reads that are fully hard or soft clipped
   * No reads that have consecutive indels in the cigar (II, DD, ID or DI)

 Also added systematic test for good cigars and iterative test for bad cigars.
 		2012-08-17 17:05:27 -04:00
..
datasources Adding support of X and = CIGAR operators to the GATK 2012-08-10 14:54:07 -04:00
downsampling Make downsampler classes themselves generic (instead of just the Downsampler interface) 2012-06-13 16:43:39 -04:00
executive
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filters Updated and more thorough version of the BadCigar read filter 2012-08-17 17:05:27 -04:00
iterators Adding support of X and = CIGAR operators to the GATK 2012-08-10 14:54:07 -04:00
refdata RMDTrackBuilderUnitTest now uses private/testdata file to avoid filesystem race conditions 2012-07-25 22:05:04 -04:00
report Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
samples Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
traversals Removed the "Walker" suffix from all walkers that had it. 2012-07-20 17:27:11 -04:00
walkers Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2012-08-16 13:05:36 -04:00
CommandLineGATKUnitTest.java Adding Unit Tests to cover the exception catching for Picard errors: because we are using String matching, we want to ensure that we know if/when the exception text changes underneath us. 2012-07-18 21:48:58 -04:00
EngineFeaturesIntegrationTest.java Sorting out HMS error handling (fingers crossed) 2012-07-25 23:13:12 -04:00
GenomeAnalysisEngineUnitTest.java Removed the "Walker" suffix from all walkers that had it. 2012-07-20 17:27:11 -04:00
WalkerManagerUnitTest.java Fixing walker unit test with the new naming convention 2012-07-20 17:50:29 -04:00