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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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amilev f81a38f596 Merge pull request #446 from broadinstitute/ami-RNAseq-tools 
Write a new tool for spliting reads that have N cigar string.
 		2014-01-01 21:06:25 -08:00
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annotator Improvements to the reference model pipeline. 2013-11-01 17:58:25 -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 Bug fix for RR: stop (incorrectly) pulling the MQ out of the SAMRecord as a byte instead of an int. 2013-11-27 18:55:03 -05:00
diagnostics Add GC Content to DiagnoseTargets 2013-12-03 23:04:40 -05:00
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 Fixed up edge condition for clipping long reads in the HMM. 2014-01-01 19:05:09 -05:00
haplotypecaller Fixed issue > 0 log likelihoods using GraphBased likelihood engine reported by Mauricio 2013-12-13 11:19:57 -05:00
indels Fixed up edge condition for clipping long reads in the HMM. 2014-01-01 19:05:09 -05:00
phasing Fixed bug in PhaseByTransmission where it was completely dropping multi-allelic records. 2013-08-21 15:46:57 -04:00
rnaseq Write a new tool for spliting reads that have N cigar string. 2014-01-01 22:21:36 -05:00
validation MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods 2013-03-29 14:52:10 -04:00
varianteval adding a check for the UNAVAILABLE case of GenotypeType in CountVariants 2013-08-29 17:27:00 -04:00
variantrecalibration Various VQSR optimizations in both runtime and accuracy. 2013-11-29 13:04:46 -05:00
variantutils Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline. 2013-12-31 12:07:56 -05:00