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comparison test-data/picard_CollectHsMetrics_test1.tab @ 24:b9fbec5ac6b2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
author iuc
date Fri, 31 May 2019 03:21:52 -0400
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children 3f254c5ced1d
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23:1cd1cf786389 24:b9fbec5ac6b2
1 ## htsjdk.samtools.metrics.StringHeader
2 # CollectHsMetrics BAIT_INTERVALS=[/tmp/tmpMGxxyd/files/000/dataset_2.dat] TARGET_INTERVALS=[/tmp/tmpMGxxyd/files/000/dataset_3.dat] INPUT=picard_CollectHsMetrics_bam OUTPUT=/tmp/tmpMGxxyd/files/000/dataset_4.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 TMP_DIR=[/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 SAMPLE_SIZE=10000 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
3 ## htsjdk.samtools.metrics.StringHeader
4 # Started on: Thu May 30 21:41:26 UTC 2019
5
6 ## METRICS CLASS picard.analysis.directed.HsMetrics
7 BAIT_SET GENOME_SIZE BAIT_TERRITORY TARGET_TERRITORY BAIT_DESIGN_EFFICIENCY TOTAL_READS PF_READS PF_UNIQUE_READS PCT_PF_READS PCT_PF_UQ_READS PF_UQ_READS_ALIGNED PCT_PF_UQ_READS_ALIGNED PF_BASES_ALIGNED PF_UQ_BASES_ALIGNED ON_BAIT_BASES NEAR_BAIT_BASES OFF_BAIT_BASES ON_TARGET_BASES PCT_SELECTED_BASES PCT_OFF_BAIT ON_BAIT_VS_SELECTED MEAN_BAIT_COVERAGE MEAN_TARGET_COVERAGE MEDIAN_TARGET_COVERAGE MAX_TARGET_COVERAGE PCT_USABLE_BASES_ON_BAIT PCT_USABLE_BASES_ON_TARGET FOLD_ENRICHMENT ZERO_CVG_TARGETS_PCT PCT_EXC_DUPE PCT_EXC_MAPQ PCT_EXC_BASEQ PCT_EXC_OVERLAP PCT_EXC_OFF_TARGET FOLD_80_BASE_PENALTY PCT_TARGET_BASES_1X PCT_TARGET_BASES_2X PCT_TARGET_BASES_10X PCT_TARGET_BASES_20X PCT_TARGET_BASES_30X PCT_TARGET_BASES_40X PCT_TARGET_BASES_50X PCT_TARGET_BASES_100X HS_LIBRARY_SIZE HS_PENALTY_10X HS_PENALTY_20X HS_PENALTY_30X HS_PENALTY_40X HS_PENALTY_50X HS_PENALTY_100X AT_DROPOUT GC_DROPOUT HET_SNP_SENSITIVITY HET_SNP_Q SAMPLE LIBRARY READ_GROUP
8 dataset_2 16569 303 183 0.60396 543 543 543 1 1 543 1 48712 48712 1545 8432 38735 911 0.204816 0.795184 0.154856 5.09901 4.978142 4 11 0.031614 0.018641 1.734388 0 0 0 0 0.008088 0.99146 2.489071 1 0.994536 0.125683 0 0 0 0 0 0 0 0 0 0 0 0 0 0.879902 9
9
10 ## HISTOGRAM java.lang.Integer
11 coverage_or_base_quality high_quality_coverage_count unfiltered_baseq_count
12 0 0 0
13 1 1 0
14 2 71 0
15 3 13 0
16 4 13 0
17 5 24 0
18 6 0 0
19 7 4 0
20 8 12 0
21 9 22 0
22 10 18 0
23 11 5 0
24 12 0 0
25 13 0 0
26 14 0 0
27 15 0 0
28 16 0 0
29 17 0 0
30 18 0 0
31 19 0 0
32 20 0 0
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35 23 0 0
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38 26 0 0
39 27 0 0
40 28 0 0
41 29 0 0
42 30 0 0
43 31 0 0
44 32 0 0
45 33 0 6
46 34 0 0
47 35 0 0
48 36 0 0
49 37 0 0
50 38 0 3
51 39 0 1
52 40 0 0
53 41 0 1
54 42 0 0
55 43 0 0
56 44 0 0
57 45 0 0
58 46 0 1
59 47 0 0
60 48 0 0
61 49 0 6
62 50 0 4
63 51 0 2
64 52 0 1
65 53 0 4
66 54 0 4
67 55 0 2
68 56 0 8
69 57 0 4
70 58 0 11
71 59 0 2
72 60 0 14
73 61 0 17
74 62 0 26
75 63 0 20
76 64 0 21
77 65 0 65
78 66 0 125
79 67 0 56
80 68 0 70
81 69 0 69
82 70 0 95
83 71 0 117
84 72 0 156
85 73 0 0
86 74 0 0
87 75 0 0
88 76 0 0
89 77 0 0
90 78 0 0
91 79 0 0
92 80 0 0
93 81 0 0
94 82 0 0
95 83 0 0
96 84 0 0
97 85 0 0
98 86 0 0
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100 88 0 0
101 89 0 0
102 90 0 0
103 91 0 0
104 92 0 0
105 93 0 0
106 94 0 0
107 95 0 0
108 96 0 0
109 97 0 0
110 98 0 0
111 99 0 0
112 100 0 0
113 101 0 0
114 102 0 0
115 103 0 0
116 104 0 0
117 105 0 0
118 106 0 0
119 107 0 0
120 108 0 0
121 109 0 0
122 110 0 0
123 111 0 0
124 112 0 0
125 113 0 0
126 114 0 0
127 115 0 0
128 116 0 0
129 117 0 0
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131 119 0 0
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134 122 0 0
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136 124 0 0
137 125 0 0
138 126 0 0
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140 128 0 0
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142 130 0 0
143 131 0 0
144 132 0 0
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148 136 0 0
149 137 0 0
150 138 0 0
151 139 0 0
152 140 0 0
153 141 0 0
154 142 0 0
155 143 0 0
156 144 0 0
157 145 0 0
158 146 0 0
159 147 0 0
160 148 0 0
161 149 0 0
162 150 0 0
163 151 0 0
164 152 0 0
165 153 0 0
166 154 0 0
167 155 0 0
168 156 0 0
169 157 0 0
170 158 0 0
171 159 0 0
172 160 0 0
173 161 0 0
174 162 0 0
175 163 0 0
176 164 0 0
177 165 0 0
178 166 0 0
179 167 0 0
180 168 0 0
181 169 0 0
182 170 0 0
183 171 0 0
184 172 0 0
185 173 0 0
186 174 0 0
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203 191 0 0
204 192 0 0
205 193 0 0
206 194 0 0
207 195 0 0
208 196 0 0
209 197 0 0
210 198 0 0
211 199 0 0
212 200 0 0
213