d363725b4b
Same changes fixed the problem for GenotypeGVCFs and CombineGVCFs. Stories: - https://www.pivotaltracker.com/story/show/77626044 - https://www.pivotaltracker.com/story/show/77626854 Changes: - Generalized the code for the merging in GATKVariantContextUtils to cope with ploidy != 2. - GenotypeGVCFs now check that the input's ploidy conform to the '-ploidy' argument. - Moved out Refernce Confidence VC merging code from GATKVariantContextUtils so that we can keep new code in protected. Caveats: - GenotypeGVCFs only can deal with input files that have the same ploidy in all positions; the one that the user MUST indicate in the -ploidy argument (if different to the default 2). - CombineGVCFs won't necessarely complain if its passed mixed ploidy inputs but you won't be able to genotype it with GenotypeGVCFs. Test: - Removed deprecated unit tests for GATKVariantContextUtils. - Moved unit-tests regarding GVCF merging from GATKVariantContextUtilsUnitTest to ReferenceConfidenceVariantContextUtilsUnitTest. - Added unit test for new code for mapping genotype indices between allele index encoding in GenotypeLikelihoodCalculator. - GenotypeGVCFs and CombineGVCFs original integration test are unaffected by the change. - Added tetraploid run integration tests to check on non-diploid execution of GenotypeGVCFs and CombineGVCFs. |
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| gatk-package-distribution | ||
| gatk-queue-extensions-distribution | ||
| gatk-queue-package-distribution | ||
| gatk-tools-protected | ||
| pom.xml | ||