Class org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSparkIntegrationTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| test | 0.285s | passed |
| testCountReadsWithIntervals[0](, 8) | 0.192s | passed |
| testCountReadsWithIntervals[10](-L chr7:1-10 -L chr7:5-10 --interval-padding 10 --interval-set-rule INTERSECTION -XL chr7:21-200, 4) | 0.223s | passed |
| testCountReadsWithIntervals[1](-L chr7:1-20, 4) | 0.202s | passed |
| testCountReadsWithIntervals[2](-L chr1, 0) | 0.196s | passed |
| testCountReadsWithIntervals[3](-L chr1 -L chr7, 7) | 0.189s | passed |
| testCountReadsWithIntervals[4](-XL chr7, 0) | 0.191s | passed |
| testCountReadsWithIntervals[5](-XL chr7:2-404, 3) | 0.196s | passed |
| testCountReadsWithIntervals[6](-L chr7:1-30 -L chr7:10-15 --interval-set-rule INTERSECTION, 3) | 0.197s | passed |
| testCountReadsWithIntervals[7](-L chr7:1 --interval-padding 19, 4) | 0.190s | passed |
| testCountReadsWithIntervals[8](-L src/test/resources/org/broadinstitute/hellbender/tools/chr7_1_20_interval.list, 4) | 0.188s | passed |
| testCountReadsWithIntervals[9](-L chr7:1-100 -XL chr7:2-100, 3) | 0.192s | passed |
| testCountReads[0](count_reads.sam, null, 8) | 0.119s | passed |
| testCountReads[1](count_reads.bam, null, 8) | 0.274s | passed |
| testCountReads[2](count_reads.cram, count_reads.fasta, 8) | 0.228s | passed |
| testCountReads[3](count_reads_sorted.sam, null, 8) | 0.119s | passed |
| testCountReads[4](count_reads_sorted.bam, null, 8) | 0.192s | passed |
| testCountReads[5](count_reads_sorted.cram, count_reads.fasta, 8) | 0.172s | passed |
| testNoNPRWhenOutputIsUnspecified | 0.275s | passed |
Standard output
8 8 8 8 8 8 8 8 4 0 7 0 3 3 4 4 3 4 8
Standard error
[May 19, 2025 at 7:13:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:45 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184 [May 19, 2025 at 7:13:45 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1713373184