Class org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparatorIntegrationTest
Tests
| Test |
Duration |
Result |
| testAnnotationDifferences[0]( -L chr1:186475, expected_warning_as_vqslod.txt) |
0.179s |
passed |
| testAnnotationDifferences[1]( -L chr1:186475 --ignore-attribute AS_VQSLOD, empty_file.txt) |
0.176s |
passed |
| testAnnotationDifferences[2]( -L chr1:187471 --ignore-attribute AS_VQSLOD, expected_warning_filter.txt) |
0.169s |
passed |
| testAnnotationDifferences[3]( -L chr1:186475-945669 --ignore-attribute VQSLOD --ignore-attribute AS_VQSLOD --ignore-filters --ignore-attribute culprit --ignore-attribute AS_culprit --ignore-attribute AS_FilterStatus --ignore-attribute ExcessHet --ignore-attribute AS_SOR --ignore-attribute AS_FS --ignore-attribute AS_BaseQRankSum --ignore-attribute AS_ReadPosRankSum --ignore-attribute AS_MQRankSum, empty_file.txt) |
0.184s |
passed |
| testAnnotationDifferences[4]( -L chr1:945670 --ignore-attribute VQSLOD --ignore-attribute AS_VQSLOD --ignore-filters --ignore-attribute culprit --ignore-attribute AS_culprit --ignore-attribute AS_FilterStatus --ignore-attribute ExcessHet --ignore-attribute AS_SOR --ignore-attribute AS_FS --ignore-attribute AS_BaseQRankSum --ignore-attribute AS_ReadPosRankSum --ignore-attribute AS_MQRankSum, qual_diff_warning.txt) |
0.177s |
passed |
| testAnnotationDifferences[5]( -L chr1:945670 --qual-change-allowed 0.1 --ignore-attribute AS_VQSLOD, empty_file.txt) |
0.176s |
passed |
| testAnnotationDifferences[6]( -L chr1:186475 --mute-acceptable-diffs, empty_file.txt) |
0.185s |
passed |
| testExpectedFailure |
0.339s |
passed |
| testGvcfs[0]( -L chr1:864084-864610, empty_file.txt) |
0.162s |
passed |
| testGvcfs[1]( -L chr1:54682-347969, ref_block_warning.txt) |
0.159s |
passed |
| testGvcfs[2]( -L chr1:792417, tree_score_warning.txt) |
0.168s |
passed |
| testGvcfs[3]( -L chr1:792417 --ignore-non-ref-data --annotations-to-keep TREE_SCORE, tree_score_warning.txt) |
0.166s |
passed |
| testGvcfs[4]( -L chr1:792417 --ignore-attribute TREE_SCORE --ignore-non-ref-data, empty_file.txt) |
0.158s |
passed |
| testGvcfs[5]( -L chr1:792417 --ignore-attribute TREE_SCORE, empty_file.txt) |
0.156s |
passed |
| testGvcfs[6]( -L chr1:950542, depth_warning.txt) |
0.163s |
passed |
| testGvcfs[7]( -L chr1:950542 --ignore-gq0, empty_file.txt) |
0.155s |
passed |
| testMixedPloidy |
0.203s |
passed |
Standard output
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[22:55:12] Executing test VCFComparatorIntegrationTest:testVcfs
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[22:55:12] Executing test VCFComparatorIntegrationTest:testVcfs
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[22:55:12] Executing test VCFComparatorIntegrationTest:testVcfs
--------------------------------------------------------------------------------
[22:55:12] Executing test VCFComparatorIntegrationTest:testVcfs
--------------------------------------------------------------------------------
[22:55:12] Executing test VCFComparatorIntegrationTest:testVcfs
--------------------------------------------------------------------------------
[22:55:12] Executing test VCFComparatorIntegrationTest:testVcfs
--------------------------------------------------------------------------------
[22:55:13] Executing test VCFComparatorIntegrationTest:testVcfs
--------------------------------------------------------------------------------
[22:55:13] Executing test VCFComparatorIntegrationTest:testGvcfs
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[22:55:13] Executing test VCFComparatorIntegrationTest:testGvcfs
--------------------------------------------------------------------------------
[22:55:13] Executing test VCFComparatorIntegrationTest:testGvcfs
--------------------------------------------------------------------------------
[22:55:14] Executing test VCFComparatorIntegrationTest:testGvcfs
--------------------------------------------------------------------------------
[22:55:14] Executing test VCFComparatorIntegrationTest:testGvcfs
--------------------------------------------------------------------------------
[22:55:14] Executing test VCFComparatorIntegrationTest:testGvcfs
--------------------------------------------------------------------------------
[22:55:14] Executing test VCFComparatorIntegrationTest:testGvcfs
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[22:55:14] Executing test VCFComparatorIntegrationTest:testGvcfs
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[22:55:14] Executing test VCFComparatorIntegrationTest:testMixedPloidy
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[22:55:15] Executing test VCFComparatorIntegrationTest:testMixedPloidy
Standard error
[March 28, 2025 at 10:55:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424