Class org.broadinstitute.hellbender.engine.AssemblyRegionIteratorUnitTest
Tests
| Test |
Duration |
Result |
| testRegionsHaveCorrectReadsAndSize[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, [20:10000000-10100000], 50, 300, 100) |
8.420s |
passed |
| testRegionsHaveCorrectReadsAndSize[1](/gatkCloneMountPoint/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000000-10010000, 20:10040000-10050000, 20:10060000-10070000], 50, 300, 100) |
2.247s |
passed |
| testRegionsHaveCorrectReadsAndSize[2](/gatkCloneMountPoint/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000000-10020000, 20:10020050-10030000], 50, 300, 100) |
1.978s |
passed |
| testRegionsHaveCorrectReadsAndSize[3](/gatkCloneMountPoint/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000000-10010000, 21:10013000-10015000], 50, 300, 100) |
0.951s |
passed |
Standard error
21:17:35.831 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-40db79c-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_utils.so
21:17:35.833 INFO NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/gatk/gatk-package-40db79c-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
21:17:35.833 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
21:17:35.836 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
21:17:35.844 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-40db79c-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
21:17:35.859 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
21:17:35.860 INFO IntelPairHmm - Available threads: 4
21:17:35.860 INFO IntelPairHmm - Requested threads: 4
21:17:35.860 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
21:17:44.234 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
21:17:44.234 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
21:17:44.234 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
21:17:44.235 INFO IntelPairHmm - Available threads: 4
21:17:44.235 INFO IntelPairHmm - Requested threads: 4
21:17:44.235 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
21:17:46.481 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
21:17:46.482 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
21:17:46.482 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
21:17:46.482 INFO IntelPairHmm - Available threads: 4
21:17:46.482 INFO IntelPairHmm - Requested threads: 4
21:17:46.482 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
21:17:48.460 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
21:17:48.460 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
21:17:48.460 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
21:17:48.460 INFO IntelPairHmm - Available threads: 4
21:17:48.460 INFO IntelPairHmm - Requested threads: 4
21:17:48.460 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation