Class picard.analysis.replicates.CollectIndependentReplicatesMetricTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| simpleTest[0](multipleContigs.vcf, twopairsWithUMIsMultipleOrientations, {nSites=3, nDuplicateSets=3, nMismatchingUMIsInCoOrientedBiDups=2, nMismatchingUMIsInContraOrientedBiDups=1}) | 0.022s | passed |
| simpleTest[10](hets_pos22_IncorrectAlleles.vcf, aTriple, {nMismatchingAllelesTriDups=0}) | 0.003s | passed |
| simpleTest[11](hets.vcf, twoPairsWithUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=1, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=1, nBadBarcodes=0}) | 0.003s | passed |
| simpleTest[12](hets.vcf, twoPairsWithBadUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=0, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=0, nBadBarcodes=1}) | 0.003s | passed |
| simpleTest[1](hets.vcf, twoPairs, {nSites=1, nDuplicateSets=1, nDifferentAllelesTriDups=0, nDifferentAllelesBiDups=1, nReferenceAllelesBiDups=0, nAlternateAllelesBiDups=0, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nAlternateReads=1, nReferenceReads=1}) | 0.003s | passed |
| simpleTest[2](twoSamplesHet.vcf, twoPairs, {nDifferentAllelesBiDups=1, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nDifferentAllelesTriDups=0, nSites=1}) | 0.003s | passed |
| simpleTest[3](hets.vcf, aTriple, {nExactlyTriple=1, nExactlyDouble=1, nDuplicateSets=2, nAlternateReads=2, nReferenceReads=3}) | 0.003s | passed |
| simpleTest[4](multipleContigs.vcf, multipleContigs, {nDuplicateSets=8, nTotalReads=20, nSites=4}) | 0.005s | passed |
| simpleTest[5](hets_pos20.vcf, aTriple, {nAlternateAllelesTriDups=1, nMismatchingAllelesBiDups=0}) | 0.003s | passed |
| simpleTest[6](hets_pos21_HOMREF_G.vcf, aTriple, {nReferenceAllelesTriDups=1}) | 0.003s | passed |
| simpleTest[7](hets_pos20.vcf, twoPairs, {nAlternateAllelesBiDups=1}) | 0.003s | passed |
| simpleTest[8](hets_pos21_HOMREF_G.vcf, twoPairs, {nReferenceAllelesBiDups=1}) | 0.002s | passed |
| simpleTest[9](hets_pos22_IncorrectAlleles.vcf, twoPairs, {nSites=1, nThreeAllelesSites=1, nAlternateAllelesTriDups=0, nMismatchingAllelesBiDups=0}) | 0.003s | passed |
Standard error
INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Found 5 heterozygous sites in VCF. INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:11 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Found 5 heterozygous sites in VCF. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Found 2 heterozygous sites in VCF. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Found 2 heterozygous sites in VCF. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2025-04-24 13:00:12 CollectIndependentReplicateMetrics Iteration done. Emitting metrics.