Class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkageTest

all > org.broadinstitute.hellbender.tools.sv.cluster > CanonicalSVLinkageTest

tests

failures

ignored

0.014s

duration

100%

successful

Tests
Standard error

Tests

Test	Duration	Result
testClusterTogether	0.001s	passed
testClusterTogetherCNVs	0.001s	passed
testClusterTogetherInsertedComplex[0](chr1, 1000, chr1, 1000, dDUP, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@ef27cf74], true)	0s	passed
testClusterTogetherInsertedComplex[1](chr1, 1010, chr1, 1010, dDUP, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@ef2abd06], true)	0s	passed
testClusterTogetherInsertedComplex[2](chr1, 2000, chr1, 3000, dDUP, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@ef2abd06], false)	0s	passed
testClusterTogetherInsertedComplex[3](chr1, 1000, chr1, 1000, dDUP_iDEL, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@ef27cf74], false)	0s	passed
testClusterTogetherInsertedComplex[4](chr1, 1000, chr1, 1000, dDUP, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@ef553874], false)	0s	passed
testClusterTogetherInsertedComplex[5](chr1, 1000, chr1, 1000, dDUP, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@9eff4adf], false)	0s	passed
testClusterTogetherIntervaledComplex[0](chr1, 1000, chr1, 2000, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@428fbb71, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@9ebbe303], true)	0s	passed
testClusterTogetherIntervaledComplex[1](chr1, 1100, chr1, 1900, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@42907d31, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@9ebc9299], true)	0s	passed
testClusterTogetherIntervaledComplex[2](chr2, 1000, chr2, 2000, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@428fbb71, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@9ebbe303], false)	0s	passed
testClusterTogetherIntervaledComplex[3](chr1, 1600, chr1, 2400, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@428fbb71, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@9ebbe303], false)	0s	passed
testClusterTogetherIntervaledComplex[4](chr1, 1000, chr1, 2000, delINVdel, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@428fbb71, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@9ebbe303], false)	0s	passed
testClusterTogetherIntervaledComplex[5](chr1, 1000, chr1, 2000, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@428fbb71], false)	0s	passed
testClusterTogetherIntervaledComplex[6](chr1, 1000, chr1, 2000, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@428b24d5, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@9ebbe303], false)	0s	passed
testClusterTogetherIntervaledComplex[7](chr1, 1000, chr1, 2000, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@428fbb71, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@eee46798], false)	0s	passed
testClusterTogetherInvalidInterval	0s	passed
testClusterTogetherVaryAlgorithms	0.001s	passed
testClusterTogetherVaryContigs	0.001s	passed
testClusterTogetherVaryParameters	0s	passed
testClusterTogetherVaryPositionsBND[0](chr1, 100, chr1, 100, chr1, 100, chr1, 100, 0.5, 0.5, 100, true, 1.0, 1.0, 0, 0)	0s	passed
testClusterTogetherVaryPositionsBND[1](chr1, 100, chr2, 100, chr1, 100, chr2, 100, 0.5, 0.5, 0, true, null, null, 0, 0)	0s	passed
testClusterTogetherVaryPositionsBND[2](chr1, 100, chr2, 101, chr1, 100, chr2, 100, 0.5, 0.5, 0, false, null, null, 0, 1)	0s	passed
testClusterTogetherVaryPositionsBND[3](chr1, 101, chr2, 100, chr1, 100, chr2, 100, 0.5, 0.5, 0, false, null, null, 1, 0)	0s	passed
testClusterTogetherVaryPositionsBND[4](chr1, 100, chr1, 200, chr1, 150, chr1, 250, 0.5, 0.5, 50, true, 0.5, 1.0, 50, 50)	0s	passed
testClusterTogetherVaryPositionsBND[5](chr1, 100, chr1, 200, chr1, 150, chr1, 250, 0.5, 0.5, 49, false, 0.5, 1.0, 50, 50)	0s	passed
testClusterTogetherVaryPositionsBND[6](chr1, 100, chr1, 200, chr1, 100, chr1, 250, 0.5, 0.5, 49, false, 0.6666666666666666, 0.6666666666666666, 0, 50)	0s	passed
testClusterTogetherVaryPositionsBND[7](chr1, 100, chr1, 200, chr1, 150, chr1, 200, 0.5, 0.5, 49, false, 0.5, 0.5, 50, 0)	0s	passed
testClusterTogetherVaryPositionsBND[8](chr1, 100, chr1, 200, chr1, 150, chr1, 250, 0.51, 0.5, 50, false, 0.5, 1.0, 50, 50)	0s	passed
testClusterTogetherVaryPositionsBND[9](chr1, 100, chr1, 200, chr1, 150, chr1, 200, 0.5, 0.51, 50, false, 0.5, 0.5, 50, 0)	0.001s	passed
testClusterTogetherVaryPositions[0](500, 1001, 1001, 1502, false, 0.00199203187250996, 1.0, 501, 501)	0s	passed
testClusterTogetherVaryPositions[10](1, 10001, 1, 10001, true, 1.0, 1.0, 0, 0)	0s	passed
testClusterTogetherVaryPositions[11](248946422, 248956422, 248946422, 248956422, true, 1.0, 1.0, 0, 0)	0s	passed
testClusterTogetherVaryPositions[12](100000, 200000, 101001, 201001, false, 0.989990100098999, 1.0, 1001, 1001)	0s	passed
testClusterTogetherVaryPositions[13](100000, 200000, 101000, 201000, true, 0.990000099999, 1.0, 1000, 1000)	0s	passed
testClusterTogetherVaryPositions[1](500, 1001, 500, 1001, true, 1.0, 1.0, 0, 0)	0s	passed
testClusterTogetherVaryPositions[2](500, 1001, 600, 1101, true, 0.8007968127490039, 1.0, 100, 100)	0s	passed
testClusterTogetherVaryPositions[3](500, 1001, 601, 1102, false, 0.798804780876494, 1.0, 101, 101)	0s	passed
testClusterTogetherVaryPositions[4](500, 1000, 600, 1101, false, 0.798804780876494, 0.99800796812749, 100, 101)	0.001s	passed
testClusterTogetherVaryPositions[5](500, 501, 500, 501, true, 1.0, 1.0, 0, 0)	0s	passed
testClusterTogetherVaryPositions[6](500, 501, 500, 502, false, 0.6666666666666666, 0.6666666666666666, 0, 1)	0s	passed
testClusterTogetherVaryPositions[7](500, 500, 500, 500, true, 1.0, 1.0, 0, 0)	0s	passed
testClusterTogetherVaryPositions[8](500, 500, 501, 501, false, 0.0, 1.0, 1, 1)	0s	passed
testClusterTogetherVaryPositions[9](1, 248956422, 1, 248956422, true, 1.0, 1.0, 0, 0)	0s	passed
testClusterTogetherVaryStrands	0s	passed
testClusterTogetherVaryTypes	0.001s	passed
testClusterTogetherWithSizeSimilarityInsertions[0](1000, 1000, 1000, 1000, true)	0s	passed
testClusterTogetherWithSizeSimilarityInsertions[1](1000, 1000, 1000, 500, true)	0s	passed
testClusterTogetherWithSizeSimilarityInsertions[2](1000, 1000, 1000, 2000, true)	0s	passed
testClusterTogetherWithSizeSimilarityInsertions[3](1000, 1000, 100, 1000, true)	0s	passed
testClusterTogetherWithSizeSimilarityInsertions[4](1000, 1000, 1900, 1000, true)	0s	passed
testClusterTogetherWithSizeSimilarityInsertions[5](1000, 1000, 99, 1000, false)	0s	passed
testClusterTogetherWithSizeSimilarityInsertions[6](1000, 1000, 1901, 1000, false)	0s	passed
testClusterTogetherWithSizeSimilarityInsertions[7](1000, 1000, 1000, 499, false)	0.001s	passed
testClusterTogetherWithSizeSimilarityInsertions[8](1000, 2001, 1000, 1000, false)	0s	passed
testClusterTogetherWithSizeSimilarity[0](1001, 2000, 1001, 2000, DEL, true)	0s	passed
testClusterTogetherWithSizeSimilarity[1](1001, 2000, 1501, 2000, DEL, true)	0s	passed
testClusterTogetherWithSizeSimilarity[2](1001, 2000, 1900, 2900, DEL, true)	0.001s	passed
testClusterTogetherWithSizeSimilarity[3](1001, 2000, 1502, 2000, DEL, false)	0s	passed
testClusterTogetherWithSizeSimilarity[4](1001, 2000, 1901, 2399, DEL, false)	0s	passed
testClusterTogetherWithSizeSimilarity[5](1001, 2000, 1902, 2900, DEL, false)	0s	passed
testGetClusteringIntervalEdge	0s	passed
testGetClusteringIntervalLists	0.001s	passed
testGetMaxClusterableStartingPosition[0](100, 200)	0s	passed
testGetMaxClusterableStartingPosition[1](50000, 500000)	0s	passed
testGetMaxClusterableStartingPosition[2](1, 1)	0.001s	passed
testGetMaxClusterableStartingPosition[3](1, 2)	0s	passed
testIsDepthOnlyCall	0s	passed
testMatchCNVNoGT[0](0, [I@339de67e, [I@55704859, true)	0.001s	passed
testMatchCNVNoGT[10](2, [I@2324e26c, [I@716205f9, false)	0.001s	passed
testMatchCNVNoGT[11](2, [I@234ad505, [I@27796482, false)	0s	passed
testMatchCNVNoGT[12](2, [I@2765c3fc, [I@52f2d8e8, false)	0s	passed
testMatchCNVNoGT[1](0, [I@55af9b48, [I@890196b, true)	0s	passed
testMatchCNVNoGT[2](1, [I@41b6ae51, [I@686a08f4, true)	0s	passed
testMatchCNVNoGT[3](2, [I@78494a59, [I@c79a727, true)	0s	passed
testMatchCNVNoGT[4](2, [I@1c83652d, [I@2eaaef66, true)	0s	passed
testMatchCNVNoGT[5](2, [I@3a8dd899, [I@3da068e8, false)	0s	passed
testMatchCNVNoGT[6](2, [I@72bd8702, [I@2620d0dc, false)	0s	passed
testMatchCNVNoGT[7](2, [I@1ff9d66b, [I@1e2c701, true)	0.001s	passed
testMatchCNVNoGT[8](2, [I@711329fe, [I@2088e339, true)	0s	passed
testMatchCNVNoGT[9](2, [I@342cc706, [I@5c9844a4, false)	0s	passed

Standard error

15:00:09.974 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
15:00:09.974 DEBUG GenomeLocParser -  1 (16000 bp)
15:00:09.974 DEBUG GenomeLocParser -  2 (16000 bp)
15:00:09.974 DEBUG GenomeLocParser -  3 (16000 bp)
15:00:09.974 DEBUG GenomeLocParser -  4 (16000 bp)