Class org.broadinstitute.hellbender.engine.AssemblyRegionIteratorUnitTest

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

tests
0

failures
0

ignored
12.841s

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) 8.035s 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) 1.960s 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) 1.921s 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) 0.925s passed

Standard error

20:25:06.320 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-b2a05c7-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_utils.so
20:25:06.324 INFO  NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/gatk/gatk-package-b2a05c7-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
20:25:06.325 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:25:06.326 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:25:06.333 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-b2a05c7-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
20:25:06.348 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:25:06.349 INFO  IntelPairHmm - Available threads: 4
20:25:06.349 INFO  IntelPairHmm - Requested threads: 4
20:25:06.349 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:25:14.338 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:25:14.338 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:25:14.338 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:25:14.338 INFO  IntelPairHmm - Available threads: 4
20:25:14.338 INFO  IntelPairHmm - Requested threads: 4
20:25:14.339 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:25:16.298 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:25:16.298 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:25:16.298 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:25:16.298 INFO  IntelPairHmm - Available threads: 4
20:25:16.298 INFO  IntelPairHmm - Requested threads: 4
20:25:16.299 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:25:18.219 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:25:18.220 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:25:18.220 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:25:18.220 INFO  IntelPairHmm - Available threads: 4
20:25:18.220 INFO  IntelPairHmm - Requested threads: 4
20:25:18.220 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation