Class org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMergerUnitTest

35

tests

0

failures

0

ignored

0.119s

duration

100%

successful

Tests

Test Duration Result
testBadAlleleRemap 0.003s passed
testGenerateADWithNewAlleles 0.001s passed
testGetBestDepthValue[0]([sample C/G], 0) 0.001s passed
testGetBestDepthValue[1]([sample C/G DP 10 {MIN_DP=5}], 5) 0s passed
testGetBestDepthValue[2]([sample C/G DP 10 {MIN_DP=5}], 5) 0s passed
testGetBestDepthValue[3]([sample C/G DP 10], 10) 0s passed
testMedianCalculationOnMixedSerializedTypes 0.050s passed
testReferenceConfidenceMerge[0](test00, [[VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C] attr={} GT=[[A_C ./. PL 30,20,10,71,72,73]] filters=], 20:10-10, false, false, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[[A_C ./. PL 30,20,10]] filters=) 0.008s passed
testReferenceConfidenceMerge[10](test10, [[VC test2 @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C] attr={} GT=[[A_C ./. PL 30,20,10]] filters=, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C] attr={} GT=[[A_C ./. PL 30,20,10,71,72,73]] filters=], 20:10-10, false, true, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[[A_C.test ./. PL 30,20,10],[A_C.test2 ./. PL 30,20,10]] filters=) 0.002s passed
testReferenceConfidenceMerge[11](test11, [[VC test2 @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C, G] attr={} GT=[[A_C_G ./. PL 40,20,30,20,10,30]] filters=, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C, G] attr={} GT=[[A_C_G ./. PL 40,20,30,20,10,30,71,72,73,74]] filters=], 20:10-10, false, true, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[A_C_G.test ./. PL 40,20,30,20,10,30],[A_C_G.test2 ./. PL 40,20,30,20,10,30]] filters=) 0.003s passed
testReferenceConfidenceMerge[12](test12, [[VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, ATC] attr={} GT=[[A_ATC ./. AD 20,10 PL 30,20,10,71,72,73]] filters=, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C, G] attr={} GT=[[A_C_G ./. AD 30,0,8 PL 40,20,30,20,10,30,71,72,73,74]] filters=], 20:10-10, false, false, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, ATC, C, G] attr={} GT=[[A_ATC ./. AD 20,10,0,0 PL 30,20,10,71,72,73,71,72,73,73],[A_C_G ./. AD 30,0,0,8 PL 40,71,74,20,72,30,20,73,10,30]] filters=) 0.003s passed
testReferenceConfidenceMerge[13](test13, [[VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C, G] attr={} GT=[[A_C_G ./. AD 60,9,20]] filters=, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C, G] attr={} GT=[[A_C_G ./. AD 60,9,20]] filters=], 20:10-10, false, false, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[A_C_G ./. AD 60,9,20],[A_C_G ./. AD 60,9,20]] filters=) 0.003s passed
testReferenceConfidenceMerge[14](test14, [[VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C, G] attr={} GT=[[A_C_G ./. AD 60,9,20]] filters=, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, AA, ATC] attr={} GT=[[A_ATC_AA ./. AD 30,8,40]] filters=], 20:10-10, false, false, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, AA, ATC, C, G] attr={} GT=[[A_ATC_AA ./. AD 30,0,0,8,40],[A_C_G ./. AD 60,9,20,0,0]] filters=) 0.010s passed
testReferenceConfidenceMerge[1](test01, [[VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C] attr={} GT=[[A_C ./. PL 30,20,10,71,72,73]] filters=, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, G] attr={} GT=[[A_G ./. PL 30,20,10,71,72,73]] filters=], 20:10-10, false, false, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[A_C ./. PL 30,20,10,71,72,73],[A_G ./. PL 30,71,73,20,72,10]] filters=) 0.004s passed
testReferenceConfidenceMerge[2](test02, [[VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C] attr={} GT=[[A_C ./. PL 30,20,10,71,72,73]] filters=, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, ATC] attr={} GT=[[A_ATC ./. PL 30,20,10,71,72,73]] filters=], 20:10-10, false, false, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, ATC, C] attr={} GT=[[A_ATC ./. PL 30,71,73,20,72,10],[A_C ./. PL 30,20,10,71,72,73]] filters=) 0.004s passed
testReferenceConfidenceMerge[3](test03, [[VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C] attr={} GT=[[A_C ./. PL 30,20,10,71,72,73]] filters=, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C, G] attr={} GT=[[A_C_G ./. PL 40,20,30,20,10,30,71,72,73,74]] filters=], 20:10-10, false, false, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[A_C ./. PL 30,20,10,71,72,73],[A_C_G ./. PL 40,20,30,20,10,30]] filters=) 0.004s passed
testReferenceConfidenceMerge[4](test04, [[VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C] attr={} GT=[[A_C ./. PL 30,20,10,71,72,73]] filters=, [VC test @ 20:10 Q. of type=SYMBOLIC alleles=[A*, <NON_REF>] attr={} GT=[[A ./. PL 0,100,1000]] filters=], 20:10-10, false, false, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[[A ./. PL 0,100,1000],[A_C ./. PL 30,20,10]] filters=) 0.004s passed
testReferenceConfidenceMerge[5](test05, [[VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C] attr={} GT=[[A_C ./. PL 30,20,10,71,72,73]] filters=, [VC test @ 20:9 Q. of type=SYMBOLIC alleles=[AA*, <NON_REF>] attr={} GT=[[AA ./. PL 0,80,800]] filters=], 20:10-10, false, false, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[[AA ./. PL 0,80,800],[A_C ./. PL 30,20,10]] filters=) 0.004s passed
testReferenceConfidenceMerge[6](test06, [[VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C] attr={} GT=[[A_C ./. PL 30,20,10,71,72,73]] filters=, [VC test @ 20:9 Q. of type=MIXED alleles=[AA*, <NON_REF>, A] attr={} GT=[[AA_A ./. PL 30,20,10,71,72,73]] filters=], 20:10-10, false, false, [VC test @ 20:10 Q. of type=SNP alleles=[A*, *, C] attr={} GT=[[AA_A ./. PL 30,71,73,20,72,10],[A_C ./. PL 30,20,10,71,72,73]] filters=) 0.003s passed
testReferenceConfidenceMerge[7](test07, [[VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C] attr={} GT=[[A_C ./. PL 30,20,10,71,72,73]] filters=, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, G] attr={} GT=[[A_G ./. PL 30,20,10,71,72,73]] filters=, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, ATC] attr={} GT=[[A_ATC ./. PL 30,20,10,71,72,73]] filters=, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, <NON_REF>, C, G] attr={} GT=[[A_C_G ./. PL 40,20,30,20,10,30,71,72,73,74]] filters=, [VC test @ 20:10 Q. of type=SYMBOLIC alleles=[A*, <NON_REF>] attr={} GT=[[A ./. PL 0,100,1000]] filters=, [VC test @ 20:9 Q. of type=SYMBOLIC alleles=[AA*, <NON_REF>] attr={} GT=[[AA ./. PL 0,80,800]] filters=, [VC test @ 20:9 Q. of type=MIXED alleles=[AA*, <NON_REF>, A] attr={} GT=[[AA_A ./. PL 30,20,10,71,72,73]] filters=], 20:10-10, false, false, [VC test @ 20:10 Q. of type=MIXED alleles=[A*, *, ATC, C, G] attr={} GT=[[A ./. PL 0,100,1000,100,1000,1000,100,1000,1000,1000,100,1000,1000,1000,1000],[AA ./. PL 0,80,800,80,800,800,80,800,800,800,80,800,800,800,800],[AA_A ./. PL 30,71,73,71,73,73,71,73,73,73,20,72,72,72,10],[A_ATC ./. PL 30,71,73,71,73,73,20,72,72,10,71,73,73,72,73],[A_C ./. PL 30,20,10,71,72,73,71,72,73,73,71,72,73,73,73],[A_C_G ./. PL 40,20,30,20,10,30,71,72,73,74,71,72,73,74,74],[A_G ./. PL 30,71,73,20,72,10,71,73,72,73,71,73,72,73,73]] filters=) 0.006s passed
testReferenceConfidenceMerge[8](test08, [[VC test @ 20:9 Q. of type=SYMBOLIC alleles=[AA*, <NON_REF>] attr={} GT=[[AA ./. PL 0,80,800]] filters=], 20:10-10, false, false, null) 0.003s passed
testReferenceConfidenceMerge[9](test09, [[VC test @ 20:9 Q. of type=SYMBOLIC alleles=[AA*, <NON_REF>] attr={} GT=[[AA ./. PL 0,80,800]] filters=], 20:10-10, true, false, [VC test @ 20:10 Q. of type=NO_VARIATION alleles=[A*] attr={} GT=[[AA ./. PL 0]] filters=) 0.002s passed
testRemapAlleles[0]([VC null @ 1:1 Q. of type=MIXED alleles=[A*, <NON_REF>, C] attr={} GT=[] filters=, A*, [A*, C, <NON_REF>]) 0.001s passed
testRemapAlleles[1]([VC null @ 1:1 Q. of type=SNP alleles=[A*, C] attr={} GT=[] filters=, ATC*, [ATC*, CTC]) 0s passed
testRemapAlleles[2]([VC null @ 1:1 Q. of type=SNP alleles=[A*, *, C] attr={} GT=[] filters=, A*, [A*, C, *]) 0s passed
testRemapAlleles[3]([VC null @ 1:1 Q. of type=SNP alleles=[A*, *] attr={} GT=[] filters=, A*, [A*, *]) 0s passed
testVCWithNewAllelesIsSpanningDeletion[0](org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger$VCWithNewAlleles@1a5b8f77, true) 0s passed
testVCWithNewAllelesIsSpanningDeletion[1](org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger$VCWithNewAlleles@42ff5c92, false) 0s passed
testVCWithNewAllelesIsSpanningDeletion[2](org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger$VCWithNewAlleles@4afad6bd, false) 0s passed
testVCWithNewAllelesIsSpanningDeletion[3](org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger$VCWithNewAlleles@35c344ce, false) 0s passed
testVCWithNewAllelesIsSpanningDeletion[4](org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger$VCWithNewAlleles@43e587cd, true) 0s passed
testVCWithNewAllelesIsSpanningDeletion[5](org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger$VCWithNewAlleles@6557d4c6, true) 0s passed
testVCWithNewAllelesIsSpanningDeletion[6](org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger$VCWithNewAlleles@62509b77, true) 0s passed
testVCWithNewAllelesIsSpanningDeletion[7](org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger$VCWithNewAlleles@1b261005, true) 0s passed
testVCWithNewAllelesIsSpanningDeletion[8](org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger$VCWithNewAlleles@55704859, true) 0s passed

Standard error

20:41:55.744 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
20:41:55.744 DEBUG GenomeLocParser -  1 (16000 bp)
20:41:55.744 DEBUG GenomeLocParser -  2 (16000 bp)
20:41:55.744 DEBUG GenomeLocParser -  3 (16000 bp)
20:41:55.744 DEBUG GenomeLocParser -  4 (16000 bp)