Class org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSparkIntegrationTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| test | 0.267s | passed |
| testCountReadsWithIntervals[0](, 8) | 0.178s | passed |
| testCountReadsWithIntervals[10](-L chr7:1-10 -L chr7:5-10 --interval-padding 10 --interval-set-rule INTERSECTION -XL chr7:21-200, 4) | 0.185s | passed |
| testCountReadsWithIntervals[1](-L chr7:1-20, 4) | 0.190s | passed |
| testCountReadsWithIntervals[2](-L chr1, 0) | 0.178s | passed |
| testCountReadsWithIntervals[3](-L chr1 -L chr7, 7) | 0.181s | passed |
| testCountReadsWithIntervals[4](-XL chr7, 0) | 0.180s | passed |
| testCountReadsWithIntervals[5](-XL chr7:2-404, 3) | 0.181s | passed |
| testCountReadsWithIntervals[6](-L chr7:1-30 -L chr7:10-15 --interval-set-rule INTERSECTION, 3) | 0.180s | passed |
| testCountReadsWithIntervals[7](-L chr7:1 --interval-padding 19, 4) | 0.181s | passed |
| testCountReadsWithIntervals[8](-L src/test/resources/org/broadinstitute/hellbender/tools/chr7_1_20_interval.list, 4) | 0.180s | passed |
| testCountReadsWithIntervals[9](-L chr7:1-100 -XL chr7:2-100, 3) | 0.181s | passed |
| testCountReads[0](count_reads.sam, null, 8) | 0.111s | passed |
| testCountReads[1](count_reads.bam, null, 8) | 0.270s | passed |
| testCountReads[2](count_reads.cram, count_reads.fasta, 8) | 0.223s | passed |
| testCountReads[3](count_reads_sorted.sam, null, 8) | 0.101s | passed |
| testCountReads[4](count_reads_sorted.bam, null, 8) | 0.180s | passed |
| testCountReads[5](count_reads_sorted.cram, count_reads.fasta, 8) | 0.160s | passed |
| testNoNPRWhenOutputIsUnspecified | 0.269s | passed |
Standard output
8 8 8 8 8 8 8 8 4 0 7 0 3 3 4 4 3 4 8
Standard error
[October 27, 2025 at 5:47:01 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:01 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:01 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:01 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:01 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:01 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:02 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:02 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:02 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:02 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:02 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:03 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:03 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:03 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:03 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:03 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:03 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:04 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280 [October 27, 2025 at 5:47:04 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1604321280