view test-data/picard_output_gc_summary_alignment_stats.txt @ 2:9227b8c3093b

Updated command line format per dev team standards.
author devteam <devteam@galaxyproject.org>
date Tue, 02 Apr 2013 09:42:36 -0400
parents 1cd7f3b42609
children
line wrap: on
line source

## net.sf.picard.metrics.StringHeader
# net.sf.picard.analysis.CollectGcBiasMetrics REFERENCE_SEQUENCE=testdata/picard/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta INPUT=testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=output_test_gc_nodict/test_nodic_ref_gc_summary_alignment_stats_test.txt CHART_OUTPUT=output_test_gc_nodict/test_nodic_ref_gc_summary_alignment_stats_test.pdf    WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 TMP_DIR=/tmp/raphael VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## net.sf.picard.metrics.StringHeader
# Started on: Tue Oct 26 13:54:53 EDT 2010

## METRICS CLASS	net.sf.picard.analysis.GcBiasDetailMetrics
GC	WINDOWS	READ_STARTS	MEAN_BASE_QUALITY	NORMALIZED_COVERAGE	ERROR_BAR_WIDTH
6	3	0	0	0	0
7	7	0	0	0	0
8	6	0	0	0	0
9	45	0	0	0	0
10	54	0	0	0	0
11	83	0	0	0	0
12	110	0	0	0	0
13	83	0	0	0	0
14	130	0	0	0	0
15	178	0	0	0	0
16	276	0	0	0	0
17	352	0	0	0	0
18	519	0	0	0	0
19	658	0	0	0	0
20	1073	0	0	0	0
21	1543	0	0	0	0
22	2024	0	0	0	0
23	2631	0	0	0	0
24	3758	0	0	0	0
25	5087	0	0	0	0
26	6543	0	0	0	0
27	8020	0	0	0	0
28	10251	0	0	0	0
29	12241	0	0	0	0
30	14189	0	0	0	0
31	16295	0	0	0	0
32	17995	0	0	0	0
33	20131	0	0	0	0
34	22194	0	0	0	0
35	23848	0	0	0	0
36	25355	0	0	0	0
37	27310	0	0	0	0
38	28274	0	0	0	0
39	28818	0	0	0	0
40	28806	0	0	0	0
41	29651	0	0	0	0
42	30773	0	0	0	0
43	31217	0	0	0	0
44	31743	0	0	0	0
45	32727	0	0	0	0
46	34084	0	0	0	0
47	35307	0	0	0	0
48	36752	0	0	0	0
49	36917	0	0	0	0
50	36561	0	0	0	0
51	36399	0	0	0	0
52	35677	0	0	0	0
53	34354	1	1	29.352448	29.352448
54	32401	0	0	0	0
55	30417	0	0	0	0
56	28588	0	0	0	0
57	27083	0	0	0	0
58	24090	0	0	0	0
59	20995	0	0	0	0
60	17702	0	0	0	0
61	14252	0	0	0	0
62	11595	0	0	0	0
63	9077	0	0	0	0
64	6863	0	0	0	0
65	5394	0	0	0	0
66	4304	0	0	0	0
67	3551	0	0	0	0
68	2776	0	0	0	0
69	2321	0	0	0	0
70	1999	0	0	0	0
71	1777	0	0	0	0
72	1444	0	0	0	0
73	1367	0	0	0	0
74	1182	0	0	0	0
75	975	0	0	0	0
76	807	0	0	0	0
77	852	0	0	0	0
78	867	0	0	0	0
79	925	0	0	0	0
80	786	0	0	0	0
81	762	0	0	0	0
82	578	0	0	0	0
83	475	0	0	0	0
84	391	0	0	0	0
85	219	0	0	0	0
86	184	0	0	0	0
87	75	0	0	0	0
88	36	0	0	0	0
89	37	0	0	0	0
90	24	0	0	0	0
91	40	0	0	0	0
92	33	0	0	0	0
93	11	0	0	0	0
94	24	0	0	0	0
95	12	0	0	0	0
96	11	0	0	0	0
97	11	0	0	0	0
98	9	0	0	0	0