view test-data/markdupes_metrics.txt @ 4:9d85f5915da9 draft

planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 1c7680ac36888721d2c0b72f4e6d27415fe07b43
author gbcs-embl-heidelberg
date Tue, 01 Aug 2017 03:42:03 -0400
parents 101525093ba1
children
line wrap: on
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## htsjdk.samtools.metrics.StringHeader
# org.embl.gbcs.je.jeduplicates.MarkDuplicatesWithMolecularCode MISMATCHES=2 MAX_NUMBER_OF_N=1 BARCODE_FILE=/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_5.dat SLOTS=[-1, -2] INPUT=[/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_4.dat] OUTPUT=/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_6.dat METRICS_FILE=/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_7.dat COMMENT=[test-run] REMOVE_DUPLICATES=true ASSUME_SORTED=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    SPLIT_CHAR=: TRIM_HEADERS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMolecularCode COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Nov 10 17:01:18 CET 2015

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
Unknown Library	196	674	196	186	467	0	0.725389	216

## HISTOGRAM	java.lang.Double
BIN	VALUE
1.0	0.997418
2.0	1.041445
3.0	1.043389
4.0	1.043474
5.0	1.043478
6.0	1.043478
7.0	1.043478
8.0	1.043478
9.0	1.043478
10.0	1.043478
11.0	1.043478
12.0	1.043478
13.0	1.043478
14.0	1.043478
15.0	1.043478
16.0	1.043478
17.0	1.043478
18.0	1.043478
19.0	1.043478
20.0	1.043478
21.0	1.043478
22.0	1.043478
23.0	1.043478
24.0	1.043478
25.0	1.043478
26.0	1.043478
27.0	1.043478
28.0	1.043478
29.0	1.043478
30.0	1.043478
31.0	1.043478
32.0	1.043478
33.0	1.043478
34.0	1.043478
35.0	1.043478
36.0	1.043478
37.0	1.043478
38.0	1.043478
39.0	1.043478
40.0	1.043478
41.0	1.043478
42.0	1.043478
43.0	1.043478
44.0	1.043478
45.0	1.043478
46.0	1.043478
47.0	1.043478
48.0	1.043478
49.0	1.043478
50.0	1.043478
51.0	1.043478
52.0	1.043478
53.0	1.043478
54.0	1.043478
55.0	1.043478
56.0	1.043478
57.0	1.043478
58.0	1.043478
59.0	1.043478
60.0	1.043478
61.0	1.043478
62.0	1.043478
63.0	1.043478
64.0	1.043478
65.0	1.043478
66.0	1.043478
67.0	1.043478
68.0	1.043478
69.0	1.043478
70.0	1.043478
71.0	1.043478
72.0	1.043478
73.0	1.043478
74.0	1.043478
75.0	1.043478
76.0	1.043478
77.0	1.043478
78.0	1.043478
79.0	1.043478
80.0	1.043478
81.0	1.043478
82.0	1.043478
83.0	1.043478
84.0	1.043478
85.0	1.043478
86.0	1.043478
87.0	1.043478
88.0	1.043478
89.0	1.043478
90.0	1.043478
91.0	1.043478
92.0	1.043478
93.0	1.043478
94.0	1.043478
95.0	1.043478
96.0	1.043478
97.0	1.043478
98.0	1.043478
99.0	1.043478
100.0	1.043478