Class org.broadinstitute.hellbender.tools.ClipReadsIntegrationTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testClipper[0](clippingReadsTest.withRG.hg19, null, .bam, -QT 0, QT_0, true) | 0.123s | passed |
| testClipper[10](clippingReadsTest.withRG.hg19, null, .bam, -QT 10 -CR WRITE_Q0S, QT_10_CR_WRITE_Q0S, true) | 0.073s | passed |
| testClipper[11](clippingReadsTest.withRG.hg19, null, .bam, -QT 10 -CR SOFTCLIP_BASES, QT_10_CR_SOFTCLIP_BASES, true) | 0.128s | passed |
| testClipper[12](clippingReadsTest.withRG.hg19, null, .bam, -XF /home/runner/work/gatk/gatk/src/test/resources/seqsToClip.fasta, XF, true) | 0.075s | passed |
| testClipper[13](clippingReadsTest.withRG.hg19, null, .bam, -QT 10 -CT 1-5 -X CCCCC -XF /home/runner/work/gatk/gatk/src/test/resources/seqsToClip.fasta, QT_10_CT_15_X_CCCCC_XF, true) | 0.126s | passed |
| testClipper[14](clippingReadsTestCRAM, valid.fasta, .cram, -QT 10, QT_10, true) | 0.089s | passed |
| testClipper[15](clippingReadsTestCRAM, valid.fasta, .cram, -QT 10, QT_10, false) | 0.087s | passed |
| testClipper[16](clipAdapters, null, .bam, --clip-adapter -CR HARDCLIP_BASES --min-read-length-to-output 1, CA, true) | 0.112s | passed |
| testClipper[1](clippingReadsTest.withRG.hg19, null, .bam, -QT 0, QT_0, false) | 0.073s | passed |
| testClipper[2](clippingReadsTest.withRG.hg19, null, .bam, -QT 2, QT_2, true) | 0.074s | passed |
| testClipper[3](clippingReadsTest.withRG.hg19, null, .bam, -QT 10, QT_10, true) | 0.074s | passed |
| testClipper[4](clippingReadsTest.withRG.hg19, null, .bam, -QT 20, QT_20, true) | 0.070s | passed |
| testClipper[5](clippingReadsTest.withRG.hg19, null, .bam, -CT 1-5, CT_15, true) | 0.075s | passed |
| testClipper[6](clippingReadsTest.withRG.hg19, null, .bam, -CT 1-5,11-15, CT_15_1115, true) | 0.075s | passed |
| testClipper[7](clippingReadsTest.withRG.hg19, null, .bam, -X CCCCC, X_CCCCC, true) | 0.072s | passed |
| testClipper[8](clippingReadsTest.withRG.hg19, null, .bam, -X CCCCC, X_CCCCC, false) | 0.074s | passed |
| testClipper[9](clippingReadsTest.withRG.hg19, null, .bam, -QT 10 -CR WRITE_NS, QT_10_CR_WRITE_NS, true) | 0.082s | passed |
Standard output
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 0
Percent of clipped reads 0.00
Number of examined bases 988
Number of clipped bases 0
Percent of clipped bases 0.00
Number of quality-score clipped bases 0
Number of range clipped bases 0
Number of sequence clipped bases 0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 0
Percent of clipped reads 0.00
Number of examined bases 988
Number of clipped bases 0
Percent of clipped bases 0.00
Number of quality-score clipped bases 0
Number of range clipped bases 0
Number of sequence clipped bases 0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 13
Percent of clipped reads 100.00
Number of examined bases 988
Number of clipped bases 126
Percent of clipped bases 12.75
Number of quality-score clipped bases 126
Number of range clipped bases 0
Number of sequence clipped bases 0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 13
Percent of clipped reads 100.00
Number of examined bases 988
Number of clipped bases 126
Percent of clipped bases 12.75
Number of quality-score clipped bases 126
Number of range clipped bases 0
Number of sequence clipped bases 0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 13
Percent of clipped reads 100.00
Number of examined bases 988
Number of clipped bases 198
Percent of clipped bases 20.04
Number of quality-score clipped bases 198
Number of range clipped bases 0
Number of sequence clipped bases 0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 13
Percent of clipped reads 100.00
Number of examined bases 988
Number of clipped bases 65
Percent of clipped bases 6.58
Number of quality-score clipped bases 0
Number of range clipped bases 65
Number of sequence clipped bases 0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 13
Percent of clipped reads 100.00
Number of examined bases 988
Number of clipped bases 130
Percent of clipped bases 13.16
Number of quality-score clipped bases 0
Number of range clipped bases 130
Number of sequence clipped bases 0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 2
Percent of clipped reads 15.38
Number of examined bases 988
Number of clipped bases 10
Percent of clipped bases 1.01
Number of quality-score clipped bases 0
Number of range clipped bases 0
Number of sequence clipped bases 10
10 clip sites matching CCCCC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 2
Percent of clipped reads 15.38
Number of examined bases 988
Number of clipped bases 10
Percent of clipped bases 1.01
Number of quality-score clipped bases 0
Number of range clipped bases 0
Number of sequence clipped bases 10
10 clip sites matching CCCCC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 13
Percent of clipped reads 100.00
Number of examined bases 988
Number of clipped bases 126
Percent of clipped bases 12.75
Number of quality-score clipped bases 126
Number of range clipped bases 0
Number of sequence clipped bases 0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 13
Percent of clipped reads 100.00
Number of examined bases 988
Number of clipped bases 126
Percent of clipped bases 12.75
Number of quality-score clipped bases 126
Number of range clipped bases 0
Number of sequence clipped bases 0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 13
Percent of clipped reads 100.00
Number of examined bases 988
Number of clipped bases 126
Percent of clipped bases 12.75
Number of quality-score clipped bases 126
Number of range clipped bases 0
Number of sequence clipped bases 0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 6
Percent of clipped reads 46.15
Number of examined bases 988
Number of clipped bases 43
Percent of clipped bases 4.35
Number of quality-score clipped bases 0
Number of range clipped bases 0
Number of sequence clipped bases 43
8 clip sites matching GAGG
35 clip sites matching TATTATA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 13
Number of clipped reads 13
Percent of clipped reads 100.00
Number of examined bases 988
Number of clipped bases 244
Percent of clipped bases 24.70
Number of quality-score clipped bases 126
Number of range clipped bases 65
Number of sequence clipped bases 53
10 clip sites matching CCCCC
8 clip sites matching GAGG
35 clip sites matching TATTATA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 8
Number of clipped reads 8
Percent of clipped reads 100.00
Number of examined bases 808
Number of clipped bases 345
Percent of clipped bases 42.70
Number of quality-score clipped bases 345
Number of range clipped bases 0
Number of sequence clipped bases 0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 8
Number of clipped reads 8
Percent of clipped reads 100.00
Number of examined bases 808
Number of clipped bases 345
Percent of clipped bases 42.70
Number of quality-score clipped bases 345
Number of range clipped bases 0
Number of sequence clipped bases 0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Number of examined reads 500
Number of clipped reads 500
Percent of clipped reads 100.00
Number of examined bases 110332
Number of clipped bases 18453
Percent of clipped bases 16.72
Number of quality-score clipped bases 0
Number of range clipped bases 0
Number of sequence clipped bases 0
Number of adapter clipped bases 18453
--------------------------------------------------------------------------------
Standard error
[June 2, 2025 at 2:11:42 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:42 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:42 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:43 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:43 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:43 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:43 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:43 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:43 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:43 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:43 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:43 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:43 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:43 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:43 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:44 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [June 2, 2025 at 2:11:44 PM UTC] org.broadinstitute.hellbender.tools.ClipReads done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000