Class org.broadinstitute.hellbender.engine.CRAMSupportIntegrationTest

all > org.broadinstitute.hellbender.engine > CRAMSupportIntegrationTest
45

tests
0

failures
0

ignored
1m36.01s

duration
100%

successful

Tests

Test Duration Result
testNoRefMulti[0](cramtest.sam, cramtest.cram, .bam) 0.116s passed
testNoRef[0](cramtest.cram, .sam) 0.116s passed
testReadCramWithIntervalsWithBAIIndex[0](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000], [d, e]) 0.173s passed
testReadCramWithIntervalsWithBAIIndex[10](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000], [d, e]) 0.126s passed
testReadCramWithIntervalsWithBAIIndex[11](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-1099], [d]) 0.170s passed
testReadCramWithIntervalsWithBAIIndex[12](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1-200, 1:1000-2000], [a, d, e]) 0.152s passed
testReadCramWithIntervalsWithBAIIndex[13](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.115s passed
testReadCramWithIntervalsWithBAIIndex[14](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000, 3:300-399], [d, e, i]) 0.121s passed
testReadCramWithIntervalsWithBAIIndex[15](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000], [d, e]) 0.154s passed
testReadCramWithIntervalsWithBAIIndex[16](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-1099], [d]) 0.161s passed
testReadCramWithIntervalsWithBAIIndex[17](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1-200, 1:1000-2000], [a, d, e]) 0.162s passed
testReadCramWithIntervalsWithBAIIndex[18](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.114s passed
testReadCramWithIntervalsWithBAIIndex[19](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000, 3:300-399], [d, e, i]) 0.110s passed
testReadCramWithIntervalsWithBAIIndex[1](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-1099], [d]) 0.176s passed
testReadCramWithIntervalsWithBAIIndex[20](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000], [d, e]) 0.149s passed
testReadCramWithIntervalsWithBAIIndex[21](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-1099], [d]) 0.118s passed
testReadCramWithIntervalsWithBAIIndex[22](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1-200, 1:1000-2000], [a, d, e]) 0.121s passed
testReadCramWithIntervalsWithBAIIndex[23](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.128s passed
testReadCramWithIntervalsWithBAIIndex[24](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000, 3:300-399], [d, e, i]) 0.127s passed
testReadCramWithIntervalsWithBAIIndex[25](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000], [d, e]) 0.116s passed
testReadCramWithIntervalsWithBAIIndex[26](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-1099], [d]) 0.122s passed
testReadCramWithIntervalsWithBAIIndex[27](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1-200, 1:1000-2000], [a, d, e]) 0.112s passed
testReadCramWithIntervalsWithBAIIndex[28](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.108s passed
testReadCramWithIntervalsWithBAIIndex[29](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000, 3:300-399], [d, e, i]) 0.114s passed
testReadCramWithIntervalsWithBAIIndex[2](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1-200, 1:1000-2000], [a, d, e]) 0.111s passed
testReadCramWithIntervalsWithBAIIndex[3](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.161s passed
testReadCramWithIntervalsWithBAIIndex[4](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000, 3:300-399], [d, e, i]) 0.170s passed
testReadCramWithIntervalsWithBAIIndex[5](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000], [d, e]) 0.165s passed
testReadCramWithIntervalsWithBAIIndex[6](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-1099], [d]) 0.155s passed
testReadCramWithIntervalsWithBAIIndex[7](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1-200, 1:1000-2000], [a, d, e]) 0.157s passed
testReadCramWithIntervalsWithBAIIndex[8](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.169s passed
testReadCramWithIntervalsWithBAIIndex[9](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000, 3:300-399], [d, e, i]) 0.167s passed
testReadEntireCram[0](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [a, b, c, d, e, f, g, h, i, j, k]) 0.152s passed
testReadEntireCram[1](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [a, b, c, d, e, f, g, h, i, j, k]) 0.159s passed
testReadEntireCram[2](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [a, b, c, d, e, f, g, h, i, j, k]) 0.103s passed
testReadEntireCram[3](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [a, b, c, d, e, f, g, h, i, j, k]) 0.162s passed
testReadEntireCram[4](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [a, b, c, d, e, f, g, h, i, j, k]) 0.121s passed
testReadEntireCram[5](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [a, b, c, d, e, f, g, h, i, j, k]) 0.124s passed
testRoundTripToCRAM[0](/gatkCloneMountPoint/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, true, false) 27.389s passed
testRoundTripToCRAM[1](/gatkCloneMountPoint/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, false, false) 32.137s passed
testRoundTripToCRAM[2](/gatkCloneMountPoint/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, false, false) 30.614s passed
testSamtoolsGeneratedCRAMSliceMD5Calculation 0.139s passed
testSerialQueriesOnRemoteFile[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000009-10000011, unmapped], [a, b, c, d, e, g, h, h, i, i], [g, h, h, i, i]) 0.208s passed
testSerialQueriesOnRemoteFile[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000009-10000013, unmapped], [a, b, c, d, e, f, f, g, h, h, i, i], [g, h, h, i, i]) 0.152s passed
testWrongRef[0](cramtest.cram, .sam, cramtestWrongRef.fasta) 0.115s passed

Standard error

[May 27, 2025 at 6:15:06 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:06 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:06 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:06 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:06 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:06 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:06 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:07 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:07 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:07 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:07 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:07 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:07 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:08 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:10 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:11 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:11 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:15:32 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.35 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 6:16:00 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.37 minutes.
Runtime.totalMemory()=1400897536
[May 27, 2025 at 6:16:31 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.35 minutes.
Runtime.totalMemory()=1684013056
[May 27, 2025 at 6:16:41 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1684013056
[May 27, 2025 at 6:16:41 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1684013056
[May 27, 2025 at 6:16:41 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1684013056
[May 27, 2025 at 6:16:41 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1684013056