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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo 6555361742 Fix error in merging code in HC 
-- Ultimately this was caused by an underlying bug in the reverting of soft clipped bases in the read clipper.  The read clipper would fail to properly set the alignment start for reads that were 100% clipped before reverting, such as 10H2S5H => 10H2M5H.  This has been fixed and unit tested.
-- Update 1 ReduceReads MD5, which was due to cases where we were clipping away all of the MATCH part of the read, leaving a cigar like 50H11S and the revert soft clips was failing to properly revert the bases.
-- delivers #50655421
 		2013-05-31 16:29:29 -04:00
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annotator Update expected test output for Java 7 2013-05-01 16:18:01 -04:00
beagle Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
bqsr Trivial BQSR bug fixes and improvement 2013-04-11 17:08:35 -04:00
compression/reducereads Fix error in merging code in HC 2013-05-31 16:29:29 -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 Bugfix for GGA mode in UG silently ignoring indels 2013-05-24 13:47:26 -04:00
haplotypecaller New implementation of the GGA mode in the HaplotypeCaller 2013-05-31 10:35:36 -04:00
indels Secondary alignments were not handled correctly in IndelRealigner 2013-05-06 19:09:10 -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