Class org.broadinstitute.hellbender.engine.AssemblyRegionIteratorUnitTest

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

tests
0

failures
0

ignored
12.490s

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) 7.732s 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) 1.909s 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) 1.925s 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) 0.924s passed

Standard error

22:03:23.892 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-fa08e16-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_utils.so
22:03:23.894 INFO  NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/gatk/gatk-package-fa08e16-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
22:03:23.894 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:03:23.896 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
22:03:23.902 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-fa08e16-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
22:03:23.913 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:03:23.913 INFO  IntelPairHmm - Available threads: 4
22:03:23.913 INFO  IntelPairHmm - Requested threads: 4
22:03:23.913 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:03:31.607 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:03:31.607 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
22:03:31.607 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:03:31.608 INFO  IntelPairHmm - Available threads: 4
22:03:31.608 INFO  IntelPairHmm - Requested threads: 4
22:03:31.608 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:03:33.517 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:03:33.517 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
22:03:33.517 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:03:33.517 INFO  IntelPairHmm - Available threads: 4
22:03:33.517 INFO  IntelPairHmm - Requested threads: 4
22:03:33.517 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:03:35.442 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:03:35.442 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
22:03:35.442 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:03:35.443 INFO  IntelPairHmm - Available threads: 4
22:03:35.443 INFO  IntelPairHmm - Requested threads: 4
22:03:35.443 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation