Class org.broadinstitute.hellbender.tools.CountReadsIntegrationTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testBogusArgs | 0.116s | passed |
| testCountBAMReadsWithIntervals[0](-L chr7:1, 3) | 0.124s | passed |
| testCountBAMReadsWithIntervals[10](-L chr7:1-100 -XL chr7:2-100, 3) | 0.131s | passed |
| testCountBAMReadsWithIntervals[11](-L chr7:1-10 -L chr7:5-10 --interval-padding 10 --interval-set-rule INTERSECTION -XL chr7:21-200, 4) | 0.128s | passed |
| testCountBAMReadsWithIntervals[1](, 8) | 0.115s | passed |
| testCountBAMReadsWithIntervals[2](-L chr7:1-20, 4) | 0.122s | passed |
| testCountBAMReadsWithIntervals[3](-L chr1, 0) | 0.121s | passed |
| testCountBAMReadsWithIntervals[4](-L chr1 -L chr7, 7) | 0.121s | passed |
| testCountBAMReadsWithIntervals[5](-XL chr7, 0) | 0.117s | passed |
| testCountBAMReadsWithIntervals[6](-XL chr7:2-404, 3) | 0.117s | passed |
| testCountBAMReadsWithIntervals[7](-L chr7:1-30 -L chr7:10-15 --interval-set-rule INTERSECTION, 3) | 0.098s | passed |
| testCountBAMReadsWithIntervals[8](-L chr7:1 --interval-padding 19, 4) | 0.099s | passed |
| testCountBAMReadsWithIntervals[9](-L src/test/resources/org/broadinstitute/hellbender/tools/chr7_1_20_interval.list, 4) | 0.099s | passed |
| testCountCRAMReadsWithIntervals[0](-L chr7:1, 3) | 0.134s | passed |
| testCountCRAMReadsWithIntervals[10](-L chr7:1-100 -XL chr7:2-100, 3) | 0.125s | passed |
| testCountCRAMReadsWithIntervals[11](-L chr7:1-10 -L chr7:5-10 --interval-padding 10 --interval-set-rule INTERSECTION -XL chr7:21-200, 4) | 0.130s | passed |
| testCountCRAMReadsWithIntervals[1](, 8) | 0.111s | passed |
| testCountCRAMReadsWithIntervals[2](-L chr7:1-20, 4) | 0.123s | passed |
| testCountCRAMReadsWithIntervals[3](-L chr1, 0) | 0.120s | passed |
| testCountCRAMReadsWithIntervals[4](-L chr1 -L chr7, 7) | 0.116s | passed |
| testCountCRAMReadsWithIntervals[5](-XL chr7, 0) | 0.119s | passed |
| testCountCRAMReadsWithIntervals[6](-XL chr7:2-404, 3) | 0.124s | passed |
| testCountCRAMReadsWithIntervals[7](-L chr7:1-30 -L chr7:10-15 --interval-set-rule INTERSECTION, 3) | 0.134s | passed |
| testCountCRAMReadsWithIntervals[8](-L chr7:1 --interval-padding 19, 4) | 0.123s | passed |
| testCountCRAMReadsWithIntervals[9](-L src/test/resources/org/broadinstitute/hellbender/tools/chr7_1_20_interval.list, 4) | 0.120s | passed |
| testCountReadsWithOutputFile[0](count_reads.sam, null) | 0.122s | passed |
| testCountReadsWithOutputFile[1](count_reads.bam, null) | 0.119s | passed |
| testCountReadsWithOutputFile[2](count_reads.cram, count_reads.fasta) | 0.120s | passed |
| testCountReadsWithOutputFile[3](count_reads_sorted.sam, null) | 0.126s | passed |
| testCountReadsWithOutputFile[4](count_reads_sorted.bam, null) | 0.125s | passed |
| testCountReadsWithOutputFile[5](count_reads_sorted.cram, count_reads.fasta) | 0.128s | passed |
| testCountReads[0](count_reads.sam, null) | 0.121s | passed |
| testCountReads[1](count_reads.bam, null) | 0.117s | passed |
| testCountReads[2](count_reads.cram, count_reads.fasta) | 0.124s | passed |
| testCountReads[3](count_reads_sorted.sam, null) | 0.135s | passed |
| testCountReads[4](count_reads_sorted.bam, null) | 0.120s | passed |
| testCountReads[5](count_reads_sorted.cram, count_reads.fasta) | 0.124s | passed |
| testNoArgs | 0.127s | passed |
Standard error
[May 27, 2025 at 6:20:02 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:02 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:02 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:02 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:02 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:02 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:03 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:03 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:03 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:03 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:03 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:03 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:03 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:03 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:04 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:04 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:04 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:04 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:04 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:04 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:04 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:04 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:05 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:05 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:05 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:05 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:05 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:05 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:05 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:05 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:06 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:06 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:06 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:06 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:06 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 6:20:06 PM GMT] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000