Test Summary
|
84%
successful |
Failed tests
- DetermineGermlineContigPloidyIntegrationTest. testCohort
- DetermineGermlineContigPloidyIntegrationTest. testCohortDuplicateFiles
- DetermineGermlineContigPloidyIntegrationTest. testCohortWithSingleSample
- DetermineGermlineContigPloidyIntegrationTest. testCohortWithoutContigPloidyPriors
- GermlineCNVCallerIntegrationTest. testCaseWithHiddenArguments
- GermlineCNVCallerIntegrationTest. testCaseWithoutModel
- GermlineCNVCallerIntegrationTest. testCohortWithAnnotatedIntervals
- GermlineCNVCallerIntegrationTest. testCohortWithTwoIntervals
- GermlineCNVCallerIntegrationTest. testCohortWithoutIntervalAnnotations
- GermlineCNVCallerIntegrationTest. testNumericalAccuracy
- PostprocessGermlineCNVCallsIntegrationTest. testBadAutosomalContigs
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentInvalidInput[0](0, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentInvalidInput[10](1, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentInvalidInput[11](2, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentInvalidInput[1](1, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentInvalidInput[2](2, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentInvalidInput[3](0, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentInvalidInput[4](1, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentInvalidInput[5](2, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentInvalidInput[6](0, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentInvalidInput[7](1, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentInvalidInput[8](2, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentInvalidInput[9](0, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentValidInput[0](0, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentValidInput[1](1, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentValidInput[2](2, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentValidInput[3](0, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentValidInput[4](1, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentValidInput[5](2, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentValidInput[6](0, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentValidInput[7](1, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testDifferentValidInput[8](2, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-calls, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-calls], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_1-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_0-model, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-postprocess/shard_2-model])
- PostprocessGermlineCNVCallsIntegrationTest. testQualScoreCalculationWithBreakpoints
Ignored tests
Packages
| Package | Tests | Failures | Ignored | Duration | Success rate |
|---|---|---|---|---|---|
| org.broadinstitute.hellbender.tools.copynumber | 39 | 33 | 4 | 1m17.16s | 5% |
| org.broadinstitute.hellbender.tools.copynumber.plotting | 6 | 0 | 0 | 3.671s | 100% |
| org.broadinstitute.hellbender.tools.examples | 6 | 0 | 0 | 2.377s | 100% |
| org.broadinstitute.hellbender.tools.spark.pipelines.metrics | 31 | 0 | 0 | 13.800s | 100% |
| org.broadinstitute.hellbender.tools.walkers.bqsr | 6 | 0 | 0 | 11.891s | 100% |
| org.broadinstitute.hellbender.tools.walkers.varianteval | 1 | 0 | 0 | 3.120s | 100% |
| org.broadinstitute.hellbender.tools.walkers.vqsr | 2 | 0 | 0 | 49.280s | 100% |
| org.broadinstitute.hellbender.tools.walkers.vqsr.scalable | 41 | 0 | 0 | 1m37.19s | 100% |
| org.broadinstitute.hellbender.utils.R | 10 | 0 | 0 | 1.644s | 100% |
| org.broadinstitute.hellbender.utils.python | 70 | 0 | 0 | 18.851s | 100% |
| org.broadinstitute.hellbender.utils.runtime | 11 | 0 | 0 | 0.469s | 100% |