Class org.broadinstitute.hellbender.engine.AssemblyRegionIteratorUnitTest

all > org.broadinstitute.hellbender.engine > AssemblyRegionIteratorUnitTest
4

tests
0

failures
0

ignored
12.681s

duration
100%

successful

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) 8.069s 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) 1.886s 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) 1.832s 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) 0.894s passed

Standard error

20:47:34.476 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-9eb1b78-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_utils.so
20:47:34.478 INFO  NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/gatk/gatk-package-9eb1b78-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
20:47:34.479 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:47:34.480 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:47:34.488 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-9eb1b78-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
20:47:34.503 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:47:34.503 INFO  IntelPairHmm - Available threads: 4
20:47:34.503 INFO  IntelPairHmm - Requested threads: 4
20:47:34.503 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:47:42.526 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:47:42.526 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:47:42.526 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:47:42.526 INFO  IntelPairHmm - Available threads: 4
20:47:42.526 INFO  IntelPairHmm - Requested threads: 4
20:47:42.526 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:47:44.412 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:47:44.412 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:47:44.412 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:47:44.412 INFO  IntelPairHmm - Available threads: 4
20:47:44.412 INFO  IntelPairHmm - Requested threads: 4
20:47:44.413 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:47:46.244 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:47:46.245 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:47:46.245 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:47:46.245 INFO  IntelPairHmm - Available threads: 4
20:47:46.245 INFO  IntelPairHmm - Requested threads: 4
20:47:46.245 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation