Mercurial > repos > devteam > picard
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 |
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## 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