annotate test-data/picard_MD_output3.txt @ 3:bf1c3f9f8282

Fix for FastqToSam MAX_Q usage detection.
author Daniel Blankenberg <dan@bx.psu.edu>
date Fri, 03 May 2013 17:13:01 -0400
parents 1cd7f3b42609
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
1 ## net.sf.picard.metrics.StringHeader
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
2 # net.sf.picard.sam.MarkDuplicates INPUT=picard_input_tiny_coord.sam OUTPUT=picard_MD_output4_.sam METRICS_FILE=picard_MD_output3_.txt REMOVE_DUPLICATES=true ASSUME_SORTED=false READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/kpvincent VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
3 ## net.sf.picard.metrics.StringHeader
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
4 # Started on: Tue Apr 19 15:32:38 EDT 2011
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
6 ## METRICS CLASS net.sf.picard.sam.DuplicationMetrics
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
7 LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
8 1 3 1 1 1 0 0.428571 3
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
9
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
10 ## HISTOGRAM java.lang.Double
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
11 BIN VALUE
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
12 1.0 0.948181
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
13 2.0 1.296997
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
14 3.0 1.425319
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
15 4.0 1.472527
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
16 5.0 1.489893
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
17 6.0 1.496282
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
18 7.0 1.498632
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
19 8.0 1.499497
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
20 9.0 1.499815
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
21 10.0 1.499932
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
22 11.0 1.499975
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
23 12.0 1.499991
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
24 13.0 1.499997
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
25 14.0 1.499999
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
26 15.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
27 16.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
28 17.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
29 18.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
30 19.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
31 20.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
32 21.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
33 22.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
34 23.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
35 24.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
36 25.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
37 26.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
38 27.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
39 28.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
40 29.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
41 30.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
42 31.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
43 32.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
44 33.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
45 34.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
46 35.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
47 36.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
48 37.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
49 38.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
50 39.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
51 40.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
52 41.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
53 42.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
54 43.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
55 44.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
56 45.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
57 46.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
58 47.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
59 48.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
60 49.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
61 50.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
62 51.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
63 52.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
64 53.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
65 54.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
66 55.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
67 56.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
68 57.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
69 58.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
70 59.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
71 60.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
72 61.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
73 62.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
74 63.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
75 64.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
76 65.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
77 66.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
78 67.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
79 68.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
80 69.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
81 70.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
82 71.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
83 72.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
84 73.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
85 74.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
86 75.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
87 76.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
88 77.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
89 78.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
90 79.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
91 80.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
92 81.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
93 82.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
94 83.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
95 84.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
96 85.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
97 86.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
98 87.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
99 88.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
100 89.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
101 90.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
102 91.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
103 92.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
104 93.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
105 94.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
106 95.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
107 96.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
108 97.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
109 98.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
110 99.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
111 100.0 1.5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
112