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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Eric Banks 165b936fcd Fixing the 'header is negative' problem in Reduce Reads... again. 
Previous fixes and tests only covered trailing soft-clips.  Now that up front
hard-clipping is working properly though, we were failing on those in the tool.

Added a patch for this as well as a separate test independent of the soft-clips
to make sure that it's working properly.
 		2013-06-24 14:06:21 -04:00
..
annotator Fixes to several of the annotations for reduced reads (and other issues). 2013-06-16 01:18:20 -04:00
beagle Simpler FILTER and info field encoding for BeagleOutputToVCF 2013-06-14 15:56:13 -04:00
bqsr Removed plots generation from the BaseRecalibration software 2013-06-19 14:47:56 -04:00
compression/reducereads Fixing the 'header is negative' problem in Reduce Reads... again. 2013-06-24 14:06:21 -04:00
diagnostics Update MD5s and the Diagnose Target scala script 2013-05-13 12:06:17 -04:00
diffengine Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
fasta Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec). 2013-04-05 00:52:32 -04:00
genotyper Better GATK version and command line output 2013-06-20 11:19:13 -04:00
haplotypecaller Adding new pruning parameter to ReadThreadingAssembler 2013-06-17 16:46:40 -04:00
indels Another fix for the Indel Realigner that arises because of secondary alignments. 2013-06-21 16:59:22 -04:00
phasing Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
validation MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods 2013-03-29 14:52:10 -04:00
varianteval Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
variantrecalibration Update MD5s for VQSR header change 2013-04-16 11:45:45 -04:00
variantutils CombineVariants no longer adds PASS to unfiltered records 2013-05-20 16:53:51 -04:00