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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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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
..
R Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
activeregion Adaptations to accomodate Tribble API changes, comprising mostly of the following. 2013-08-19 15:52:47 -04:00
baq Fixing BQSR/BAQ bug: 2013-01-31 11:03:17 -05:00
classloader Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements 2013-05-10 19:00:33 -04:00
clipping Write a new tool for spliting reads that have N cigar string. 2014-01-01 22:21:36 -05:00
codecs/hapmap Adaptations to accomodate Tribble API changes, comprising mostly of the following. 2013-08-19 15:52:47 -04:00
collections Fixing license on Yossi's file 2013-02-05 11:14:43 -05:00
crypt Update expected test output for Java 7 2013-05-01 16:18:01 -04:00
fasta Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
file Detect stuck lock-acquisition calls, and disable file locking for tests 2013-04-24 22:49:02 -04:00
fragments A whole slew of improvements to the Haplotype Caller and related code. 2013-07-12 10:09:10 -04:00
haplotype Major improvements to HC that trims down active regions before genotyping 2013-04-08 12:47:49 -04:00
interval Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists 2013-04-02 14:01:52 -04:00
io Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
locusiterator Working version of HaplotypeCaller ReferenceConfidenceModel that accounts for indels as well as SNP confidences 2013-07-02 15:46:38 -04:00
nanoScheduler Further tweaking of test timeouts 2013-03-15 14:49:21 -04:00
pileup Fixing ReadBackedPileup to represent mapping qualities as ints, not (signed) bytes. 2013-07-23 23:47:15 -04:00
progressmeter Subshard timeouts in the GATK 2013-05-15 07:00:39 -04:00
recalibration Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
report Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
runtime Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
sam Write a new tool for spliting reads that have N cigar string. 2014-01-01 22:21:36 -05:00
smithwaterman New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points. 2013-05-13 09:36:39 -04:00
text Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
threading Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variant Added some bug fixes to the gVCF merging code after finally getting some real data to play with. 2014-01-08 08:34:35 -05:00
AutoFormattingTimeUnitTest.java AutoFormattingTimeUnitTest should be in utils 2013-01-30 09:47:47 -05:00
BaseUtilsUnitTest.java More aggressive checking of AWS key quality upon startup in the GATK 2013-01-31 09:08:38 -05:00
BitSetUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLocParserBenchmark.java Optimize GenomeLocParser.createGenomeLoc 2013-01-30 09:47:47 -05:00
GenomeLocParserUnitTest.java Adding Graph-based likelihood ratio calculation to HC 2013-12-02 19:37:19 -05:00
GenomeLocSortedSetUnitTest.java Fixed the add functionality of GenomeLocSortedSet. 2013-02-28 23:31:00 -05:00
GenomeLocUnitTest.java Added distance across contigs calculation to GenomeLocs 2013-02-07 16:31:41 -05:00
MRUCachingSAMSequencingDictionaryUnitTest.java Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -05:00
MWUnitTest.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
MathUtilsUnitTest.java Introducing the latest-and-greatest in genotyping: CalculatePosteriors. 2013-11-27 13:00:45 -05:00
MedianUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
NGSPlatformUnitTest.java Expand NGSPlatform to meet SAM 1.4 spec, with full unit tests 2013-02-09 11:16:21 -05:00
PathUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
QualityUtilsUnitTest.java Fix for the PairHMM transition probability miscalculation. 2014-01-26 16:30:36 -05:00
SequenceDictionaryUtilsUnitTest.java Sequence dictionary validation: detect problematic contig indexing differences 2013-02-25 11:14:22 -05:00
SimpleTimerUnitTest.java Fix tests that were consistently or intermittently failing when run in parallel on the farm 2013-03-06 13:56:54 -05:00
UtilsUnitTest.java New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points. 2013-05-13 09:36:39 -04:00