David Roazen 932cd3ada7 Fix 3rd-party library dependency issues in the HC/PairHMM tests ... In general, test classes cannot use 3rd-party libraries that are not also dependencies of the GATK proper without causing problems when, at release time, we test that the GATK jar has been packaged correctly with all required dependencies. If a test class needs to use a 3rd-party library that is not a GATK dependency, write wrapper methods in the GATK utils/* classes, and invoke those wrapper methods from the test class.		2013-12-06 13:16:55 -05:00
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collections	Adding Graph-based likelihood ratio calculation to HC	2013-12-02 19:37:19 -05:00
genotyper	Relaxing the constraints on the readIsPoorlyModelled function.	2013-06-13 11:06:23 -04:00
gvcf	Bugfix for hom ref records that aren't GVCF blocks.	2013-09-29 19:19:26 -04:00
haplotype	Better caching for the HaplotypeCaller	2013-08-02 01:27:29 -04:00
haplotypeBAMWriter	Working version of HaplotypeCaller ReferenceConfidenceModel that accounts for indels as well as SNP confidences	2013-07-02 15:46:38 -04:00
nanoScheduler	A whole slew of improvements to the Haplotype Caller and related code.	2013-07-12 10:09:10 -04:00
pairhmm	Fix 3rd-party library dependency issues in the HC/PairHMM tests	2013-12-06 13:16:55 -05:00
recalibration	Added hidden mode for BQSR to force all read groups to be the same one.	2013-05-06 19:09:10 -04:00
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
ContigComparatorUnitTest.java	Generalize and fixup ContigComparator	2013-02-09 09:52:13 -05:00
RandomDNA.java	Adding Graph-based likelihood ratio calculation to HC	2013-12-02 19:37:19 -05:00