Class org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMakerIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.fasta > FastaAlternateReferenceMakerIntegrationTest
17

tests
0

failures
0

ignored
2.021s

duration
100%

successful

Tests

Test Duration Result
testAlternateReferenceContiguousDiffContigs 0.125s passed
testAlternateReferenceContiguousSameContig 0.117s passed
testBadIupacInput 0.110s passed
testIupac 0.124s passed
testNoMask[0](src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1.fasta) 0.127s passed
testNoMask[1](src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps2.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2.fasta) 0.117s passed
testSnpMask[0](src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps2.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2.fasta, false) 0.123s passed
testSnpMask[1](src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps2.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2_priority.fasta, true) 0.120s passed
testSnpMask[2](src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps2.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.fasta, false) 0.123s passed
testSnpMask[3](src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps2.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.fasta, true) 0.116s passed
testSnpMask[4](src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snpsAndIndels.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.fasta, false) 0.116s passed
testSnpMask[5](src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snpsAndIndels.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.fasta, true) 0.116s passed
testSnpMask[6](src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snpsAndIndels.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/overlapsIndelsMask.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.fasta, false) 0.117s passed
testSnpMask[7](src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snpsAndIndels.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/overlapsIndelsMask.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.fasta, true) 0.119s passed
testSpanDel 0.113s passed
testSpanDelIUPAC[0](NA1, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.fasta) 0.123s passed
testSpanDelIUPAC[1](NA3, src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.fasta) 0.115s passed

Standard error

[May 19, 2025 at 4:07:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456
[May 19, 2025 at 4:07:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1841299456