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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Valentin Ruano-Rubio 9e7bf75e89 Fix for the PairHMM transition probability miscalculation. 
Problem:

matchToMatch transition calculation was wrong resulting in transition probabilites coming out of the Match state that added more than 1.

Reports:

https://www.pivotaltracker.com/s/projects/793457/stories/62471780
https://www.pivotaltracker.com/s/projects/793457/stories/61082450

Changes:

The transition matrix update code has been moved to a common place in PairHMMModel to dry out its multiple copies.

MatchToMatch transtion calculation has been fixed and implemented in PairHMMModel.

Affected integration test md5 have been updated, there were no differences in GT fields and example differences always implied
small changes in likelihoods that is what is expected.
 		2014-01-26 16:30:36 -05:00
..
annotator Fix for the PairHMM transition probability miscalculation. 2014-01-26 16:30:36 -05:00
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 Fix for the PairHMM transition probability miscalculation. 2014-01-26 16:30:36 -05:00
haplotypecaller Fix for the PairHMM transition probability miscalculation. 2014-01-26 16:30:36 -05:00
indels Added in a check for what would be an empty allele after trimming. 2014-01-15 11:04:19 -05:00
phasing Add documentation for RBP, and also update the MD5 for the tests now that the output uses HP tags instead of '|', which is now reserved for trio-based phasing 2014-01-03 12:04:47 -05:00
rnaseq Write a new tool for spliting reads that have N cigar string. 2014-01-01 22:21:36 -05:00
simulatereads Fixed up and refactored what seems to be a useful private tool to create simulated reads around a VCF. 2014-01-15 13:49:31 -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 Allow for additional input data to be used in the VQSR for clustering but don't carry it forward into the output VCF file. 2014-01-02 14:46:04 -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
WalkerTestIntegrationTest.java Moving this test up one level to where it actually belongs. 2014-01-19 02:33:11 -05:00