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

all > org.broadinstitute.hellbender.tools.sv.cluster > SVClusterEngineTest
98

tests
0

failures
0

ignored
1.051s

duration
100%

successful

Tests

Test Duration Result
testAdd 0.019s passed
testAddMaxCliqueLarge 0.075s passed
testAddVaryPositions[0](10000, 20001, 12000, 22001, 14000, 24001, SINGLE_LINKAGE, 1) 0.001s passed
testAddVaryPositions[1](10000, 20001, 12000, 22001, 14001, 24002, SINGLE_LINKAGE, 2) 0s passed
testAddVaryPositions[2](10000, 20001, 12001, 22002, 14002, 24003, SINGLE_LINKAGE, 3) 0s passed
testAddVaryPositions[3](10000, 20001, 11000, 21001, 12000, 22001, MAX_CLIQUE, 1) 0s passed
testAddVaryPositions[4](10000, 20001, 12000, 22001, 14000, 24001, MAX_CLIQUE, 2) 0s passed
testAddVaryPositions[5](10000, 20001, 12001, 22002, 14002, 24003, MAX_CLIQUE, 3) 0.001s passed
testClusterTogether 0s passed
testClusterTogetherCNVs 0s passed
testClusterTogetherInsertedComplex[0](chr1, 1000, chr1, 1000, dDUP, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@2a363b8d], true) 0s passed
testClusterTogetherInsertedComplex[1](chr1, 1010, chr1, 1010, dDUP, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@2a39291f], true) 0s passed
testClusterTogetherInsertedComplex[2](chr1, 2000, chr1, 3000, dDUP, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@2a39291f], false) 0.001s passed
testClusterTogetherInsertedComplex[3](chr1, 1000, chr1, 1000, dDUP_iDEL, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@2a363b8d], false) 0s passed
testClusterTogetherInsertedComplex[4](chr1, 1000, chr1, 1000, dDUP, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@2a63a48d], false) 0s passed
testClusterTogetherInsertedComplex[5](chr1, 1000, chr1, 1000, dDUP, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@94c20b6b], false) 0s passed
testClusterTogetherIntervaledComplex[0](chr1, 1000, chr1, 2000, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@5b3f6ec6, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@947ea38f], true) 0s passed
testClusterTogetherIntervaledComplex[1](chr1, 1100, chr1, 1900, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@5b403086, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@947f5325], true) 0s passed
testClusterTogetherIntervaledComplex[2](chr2, 1000, chr2, 2000, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@5b3f6ec6, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@947ea38f], false) 0s passed
testClusterTogetherIntervaledComplex[3](chr1, 1600, chr1, 2400, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@5b3f6ec6, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@947ea38f], false) 0s passed
testClusterTogetherIntervaledComplex[4](chr1, 1000, chr1, 2000, delINVdel, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@5b3f6ec6, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@947ea38f], false) 0s passed
testClusterTogetherIntervaledComplex[5](chr1, 1000, chr1, 2000, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@5b3f6ec6], false) 0s passed
testClusterTogetherIntervaledComplex[6](chr1, 1000, chr1, 2000, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@5b3ad82a, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@947ea38f], false) 0s passed
testClusterTogetherIntervaledComplex[7](chr1, 1000, chr1, 2000, delINV, [org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@5b3f6ec6, org.broadinstitute.hellbender.tools.sv.SVCallRecord$ComplexEventInterval@29f2d3b1], false) 0s passed
testClusterTogetherInvalidInterval 0.001s passed
testClusterTogetherVaryAlgorithms 0s passed
testClusterTogetherVaryContigs 0.001s passed
testClusterTogetherVaryParameters 0s passed
testClusterTogetherVaryPositions[0](500, 1001, 1001, 1502, false) 0s passed
testClusterTogetherVaryPositions[10](1, 10001, 1, 10001, true) 0s passed
testClusterTogetherVaryPositions[11](248946422, 248956422, 248946422, 248956422, true) 0s passed
testClusterTogetherVaryPositions[12](100000, 200000, 101001, 201001, false) 0s passed
testClusterTogetherVaryPositions[13](100000, 200000, 101000, 201000, true) 0.001s passed
testClusterTogetherVaryPositions[1](500, 1001, 500, 1001, true) 0s passed
testClusterTogetherVaryPositions[2](500, 1001, 600, 1101, true) 0s passed
testClusterTogetherVaryPositions[3](500, 1001, 601, 1102, false) 0s passed
testClusterTogetherVaryPositions[4](500, 1000, 600, 1101, false) 0s passed
testClusterTogetherVaryPositions[5](500, 501, 500, 501, true) 0s passed
testClusterTogetherVaryPositions[6](500, 501, 500, 502, false) 0.001s passed
testClusterTogetherVaryPositions[7](500, 500, 500, 500, true) 0s passed
testClusterTogetherVaryPositions[8](500, 500, 501, 501, false) 0s passed
testClusterTogetherVaryPositions[9](1, 248956422, 1, 248956422, true) 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) 0.001s passed
testClusterTogetherWithSizeSimilarityInsertions[7](1000, 1000, 1000, 499, false) 0s 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) 0s 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
testCollapser 0.010s passed
testGetCarrierSamplesBiallelic[0](0, null, null, [I@ddca64d, [Ljava.lang.String;@5d39797a) 0.002s passed
testGetCarrierSamplesBiallelic[10](2, N*, <DEL>, [I@72e950ef, [Ljava.lang.String;@79e2aa2d) 0s passed
testGetCarrierSamplesBiallelic[11](2, N*, <DEL>, [I@21259314, [Ljava.lang.String;@19f3c1f7) 0s passed
testGetCarrierSamplesBiallelic[12](2, N*, <DEL>, [I@65263248, [Ljava.lang.String;@6816b0cb) 0s passed
testGetCarrierSamplesBiallelic[13](2, N*, <DUP>, [I@7fc8930f, [Ljava.lang.String;@2b284acc) 0s passed
testGetCarrierSamplesBiallelic[14](2, N*, <DUP>, [I@70cc0601, [Ljava.lang.String;@4b27a3fc) 0s passed
testGetCarrierSamplesBiallelic[15](3, N*, <DEL>, [I@7db644d5, [Ljava.lang.String;@6ddab96c) 0.001s passed
testGetCarrierSamplesBiallelic[16](3, N*, <DEL>, [I@49842c0d, [Ljava.lang.String;@74d6d5ca) 0s passed
testGetCarrierSamplesBiallelic[1](0, null, <DEL>, [I@1c461b90, [Ljava.lang.String;@518e6d6c) 0s passed
testGetCarrierSamplesBiallelic[2](0, N*, null, [I@77d771a2, [Ljava.lang.String;@5be17e53) 0s passed
testGetCarrierSamplesBiallelic[3](0, ., null, [I@2cde0397, [Ljava.lang.String;@60483dcf) 0s passed
testGetCarrierSamplesBiallelic[4](0, ., <DEL>, [I@7d0ae3d1, [Ljava.lang.String;@2114955c) 0s passed
testGetCarrierSamplesBiallelic[5](0, N*, <DEL>, [I@6e5506c9, [Ljava.lang.String;@446b74b9) 0s passed
testGetCarrierSamplesBiallelic[6](0, N*, <DEL>, [I@5a4f7911, [Ljava.lang.String;@1cea4fdf) 0s passed
testGetCarrierSamplesBiallelic[7](1, N*, <DEL>, [I@47970962, [Ljava.lang.String;@66b16770) 0s passed
testGetCarrierSamplesBiallelic[8](1, N*, <DEL>, [I@72788282, [Ljava.lang.String;@ddb59b6) 0s passed
testGetCarrierSamplesBiallelic[9](2, N*, <DEL>, [I@12e33c7b, [Ljava.lang.String;@24b9c037) 0s passed
testGetClusteringIntervalEdge 0s passed
testGetClusteringIntervalLists 0s passed
testGetMaxClusterableStartingPosition[0](100, 200) 0.001s passed
testGetMaxClusterableStartingPosition[1](50000, 500000) 0s passed
testGetMaxClusterableStartingPosition[2](1, 1) 0s passed
testGetMaxClusterableStartingPosition[3](1, 2) 0s passed
testIsDepthOnlyCall 0s passed
testLargeRandom 0.933s passed
testMatchCNVNoGT[0](0, [I@30c31e10, [I@74f446ba, true) 0s passed
testMatchCNVNoGT[10](2, [I@7d5238b4, [I@55a430b2, false) 0s passed
testMatchCNVNoGT[11](2, [I@2667a238, [I@4a9cb9d8, false) 0s passed
testMatchCNVNoGT[12](2, [I@5bc3c4e5, [I@402ecbc7, false) 0s passed
testMatchCNVNoGT[1](0, [I@2105c11b, [I@99e68b5, true) 0s passed
testMatchCNVNoGT[2](1, [I@264e0b8e, [I@294c1b45, true) 0s passed
testMatchCNVNoGT[3](2, [I@45070db0, [I@13437ce5, true) 0s passed
testMatchCNVNoGT[4](2, [I@6162d87c, [I@1cf5236d, true) 0s passed
testMatchCNVNoGT[5](2, [I@28261231, [I@5f709e71, false) 0s passed
testMatchCNVNoGT[6](2, [I@302ab67e, [I@28058dd0, false) 0s passed
testMatchCNVNoGT[7](2, [I@4040559d, [I@253c82ad, true) 0.001s passed
testMatchCNVNoGT[8](2, [I@3af8f1ef, [I@7856b790, true) 0s passed
testMatchCNVNoGT[9](2, [I@7d5e165, [I@7adf0ff9, false) 0s passed

Standard error

20:33:25.547 DEBUG ExecutorMetricsPoller - removing (45, 0) from stageTCMP
20:33:25.547 DEBUG ExecutorMetricsPoller - removing (43, 0) from stageTCMP
20:33:25.547 DEBUG ExecutorMetricsPoller - removing (40, 0) from stageTCMP
20:33:25.547 DEBUG ExecutorMetricsPoller - removing (38, 0) from stageTCMP
20:33:25.547 DEBUG ExecutorMetricsPoller - removing (46, 0) from stageTCMP
20:33:25.547 DEBUG ExecutorMetricsPoller - removing (44, 0) from stageTCMP
20:33:25.547 DEBUG ExecutorMetricsPoller - removing (41, 0) from stageTCMP
20:33:25.547 DEBUG ExecutorMetricsPoller - removing (37, 0) from stageTCMP
20:33:25.547 DEBUG ExecutorMetricsPoller - removing (39, 0) from stageTCMP