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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Valentin Ruano-Rubio 89c4e57478 gVCF <NON_REF> in all vcf lines including variant ones when –ERC gVCF is requested. 
Changes:
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  <NON_REF> likelihood in variant sites is calculated as the maximum possible likelihood for an unseen alternative allele: for reach read is calculated as the second best likelihood amongst the reported alleles.

  When –ERC gVCF, stand_conf_emit and stand_conf_call are forcefully set to 0. Also dontGenotype is set to false for consistency sake.

  Integration test MD5 have been changed accordingly.

Additional fix:
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  Specially after adding the <NON_REF> allele, but also happened without that, QUAL values tend to go to 0 (very large integer number in log 10) due to underflow when combining GLs (GenotypingEngine.combineGLs). To fix that combineGLs has been substituted by combineGLsPrecise that uses the log-sum-exp trick.

  In just a few cases this change results in genotype changes in integration tests but after double-checking using unit-test and difference between combineGLs and combineGLsPrecise in the affected integration test, the previous GT calls were either border-line cases and or due to the underflow.
 		2014-01-30 11:23:33 -05:00
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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 gVCF <NON_REF> in all vcf lines including variant ones when –ERC gVCF is requested. 2014-01-30 11:23:33 -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 gVCF <NON_REF> in all vcf lines including variant ones when –ERC gVCF is requested. 2014-01-30 11:23:33 -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