Class org.broadinstitute.hellbender.tools.validation.CompareBaseQualitiesIntegrationTest

all > org.broadinstitute.hellbender.tools.validation > CompareBaseQualitiesIntegrationTest
6

tests
0

failures
0

ignored
0.652s

duration
100%

successful

Tests

Test Duration Result
identicalBamTest 0.070s passed
singleReadDiffTest[0](src/test/resources/org/broadinstitute/hellbender/tools/validation/single.read.bam, src/test/resources/org/broadinstitute/hellbender/tools/validation/single.read.bam, null, /tmp/local116208583777069067979/toolstemp.diff2269613974180570299.txt, [10, 20, 30, 40], single.read.qual.diff.txt) 0.065s passed
singleReadDiffTest[1](src/test/resources/org/broadinstitute/hellbender/tools/validation/single.read.bam, src/test/resources/org/broadinstitute/hellbender/tools/validation/another.single.read.bam, null, /tmp/local116208583777069067979/toolstemp.diff2269613974180570299.txt, [10, 20, 30, 40], two.reads.qual.diff.txt) 0.077s passed
singleReadDiffTest[2](src/test/resources/org/broadinstitute/hellbender/tools/validation/single.read.cram, src/test/resources/org/broadinstitute/hellbender/tools/validation/another.single.read.cram, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, /tmp/local116208583777069067979/toolstemp.diff2269613974180570299.txt, [10, 20, 30, 40], two.reads.qual.diff.txt) 0.207s passed
singleReadDiffTest[3](src/test/resources/org/broadinstitute/hellbender/tools/validation/single.read.bam, src/test/resources/org/broadinstitute/hellbender/tools/validation/another.single.read.cram, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, /tmp/local116208583777069067979/toolstemp.diff2269613974180570299.txt, [10, 20, 30, 40], two.reads.qual.diff.txt) 0.113s passed
singleReadDiffTest[4](src/test/resources/org/broadinstitute/hellbender/tools/validation/single.read.cram, src/test/resources/org/broadinstitute/hellbender/tools/validation/another.single.read.bam, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, /tmp/local116208583777069067979/toolstemp.diff2269613974180570299.txt, [10, 20, 30, 40], two.reads.qual.diff.txt) 0.120s passed

Standard output

-----------CompareMatrix summary------------
all 152510 quality scores are the same

---------CompareMatrix full matrix (non-zero entries) ----------
QRead1	QRead2	diff	count
1	1	0	13
2	2	0	16089
3	3	0	37
4	4	0	75
5	5	0	65
6	6	0	101
7	7	0	138
8	8	0	120
9	9	0	121
10	10	0	162
11	11	0	183
12	12	0	134
13	13	0	152
14	14	0	175
15	15	0	204
16	16	0	280
17	17	0	358
18	18	0	429
19	19	0	489
20	20	0	590
21	21	0	777
22	22	0	890
23	23	0	1008
24	24	0	1187
25	25	0	1466
26	26	0	1763
27	27	0	2023
28	28	0	2114
29	29	0	2590
30	30	0	2790
31	31	0	2890
32	32	0	3940
33	33	0	4569
34	34	0	5688
35	35	0	8157
36	36	0	12865
37	37	0	25225
38	38	0	35567
39	39	0	16205
40	40	0	819
41	41	0	62
-----------CompareMatrix-binned summary------------
all 152510 quality scores are the same

---------CompareMatrix-binned full matrix (non-zero entries) ----------
QRead1	QRead2	diff	count
1	1	0	13
2	2	0	16089
3	3	0	37
4	4	0	75
5	5	0	65
6	6	0	101
7	7	0	138
8	8	0	120
9	9	0	121
10	10	0	162
11	11	0	183
12	12	0	134
13	13	0	152
14	14	0	175
15	15	0	204
16	16	0	280
17	17	0	358
18	18	0	429
19	19	0	489
20	20	0	590
21	21	0	777
22	22	0	890
23	23	0	1008
24	24	0	1187
25	25	0	1466
26	26	0	1763
27	27	0	2023
28	28	0	2114
29	29	0	2590
30	30	0	2790
31	31	0	2890
32	32	0	3940
33	33	0	4569
34	34	0	5688
35	35	0	8157
36	36	0	12865
37	37	0	25225
38	38	0	35567
39	39	0	16205
40	40	0	819
41	41	0	62

Standard error

[March 28, 2025 at 10:46:29 PM UTC] org.broadinstitute.hellbender.tools.validation.CompareBaseQualities done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=658505728
[March 28, 2025 at 10:46:30 PM UTC] org.broadinstitute.hellbender.tools.validation.CompareBaseQualities done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=658505728
[March 28, 2025 at 10:46:30 PM UTC] org.broadinstitute.hellbender.tools.validation.CompareBaseQualities done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=658505728
[March 28, 2025 at 10:46:30 PM UTC] org.broadinstitute.hellbender.tools.validation.CompareBaseQualities done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:46:30 PM UTC] org.broadinstitute.hellbender.tools.validation.CompareBaseQualities done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=589299712
[March 28, 2025 at 10:46:30 PM UTC] org.broadinstitute.hellbender.tools.validation.CompareBaseQualities done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424