Mercurial > repos > devteam > samtools_stats
diff test-data/12.2reads.overlap.expected @ 9:ab75c7ea49a5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author | iuc |
---|---|
date | Tue, 28 Sep 2021 16:08:22 +0000 |
parents | 8d500e0e0dbe |
children | 8fecc86e574a |
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--- a/test-data/12.2reads.overlap.expected Thu Oct 10 03:39:57 2019 -0400 +++ b/test-data/12.2reads.overlap.expected Tue Sep 28 16:08:22 2021 +0000 @@ -1,8 +1,11 @@ +# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats -t /tmp/tmp0r5zs075/files/2/a/2/dataset_2a2a3ee9-3133-4880-a37c-50b6354c9000.dat -@ 0 infile # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK 5b31676a b0edee94 471895da # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 2 +SN raw total sequences: 2 # excluding supplementary and secondary reads SN filtered sequences: 0 SN sequences: 2 SN is sorted: 1 @@ -17,6 +20,7 @@ SN reads MQ0: 0 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 +SN supplementary alignments: 0 SN total length: 200 # ignores clipping SN total first fragment length: 100 # ignores clipping SN total last fragment length: 100 # ignores clipping @@ -353,6 +357,107 @@ GCC 98 50.00 50.00 0.00 0.00 0.00 0.00 GCC 99 50.00 50.00 0.00 0.00 0.00 0.00 GCC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# ACGT content per cycle, read oriented. Use `grep ^GCT | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%] +GCT 1 50.00 0.00 50.00 0.00 +GCT 2 0.00 50.00 50.00 0.00 +GCT 3 0.00 50.00 0.00 50.00 +GCT 4 0.00 50.00 50.00 0.00 +GCT 5 0.00 0.00 50.00 50.00 +GCT 6 0.00 0.00 50.00 50.00 +GCT 7 0.00 50.00 0.00 50.00 +GCT 8 0.00 0.00 50.00 50.00 +GCT 9 0.00 50.00 0.00 50.00 +GCT 10 50.00 0.00 50.00 0.00 +GCT 11 0.00 0.00 100.00 0.00 +GCT 12 50.00 0.00 0.00 50.00 +GCT 13 0.00 50.00 50.00 0.00 +GCT 14 50.00 0.00 0.00 50.00 +GCT 15 0.00 0.00 50.00 50.00 +GCT 16 0.00 50.00 50.00 0.00 +GCT 17 0.00 50.00 0.00 50.00 +GCT 18 100.00 0.00 0.00 0.00 +GCT 19 50.00 0.00 0.00 50.00 +GCT 20 0.00 50.00 50.00 0.00 +GCT 21 50.00 0.00 0.00 50.00 +GCT 22 0.00 50.00 0.00 50.00 +GCT 23 0.00 0.00 0.00 100.00 +GCT 24 0.00 50.00 50.00 0.00 +GCT 25 0.00 0.00 0.00 100.00 +GCT 26 0.00 0.00 50.00 50.00 +GCT 27 0.00 100.00 0.00 0.00 +GCT 28 0.00 0.00 0.00 100.00 +GCT 29 50.00 0.00 50.00 0.00 +GCT 30 0.00 50.00 0.00 50.00 +GCT 31 0.00 50.00 0.00 50.00 +GCT 32 0.00 0.00 50.00 50.00 +GCT 33 0.00 50.00 0.00 50.00 +GCT 34 50.00 0.00 0.00 50.00 +GCT 35 0.00 50.00 0.00 50.00 +GCT 36 0.00 100.00 0.00 0.00 +GCT 37 0.00 50.00 0.00 50.00 +GCT 38 50.00 50.00 0.00 0.00 +GCT 39 100.00 0.00 0.00 0.00 +GCT 40 0.00 0.00 100.00 0.00 +GCT 41 0.00 50.00 0.00 50.00 +GCT 42 50.00 50.00 0.00 0.00 +GCT 43 0.00 0.00 50.00 50.00 +GCT 44 50.00 0.00 50.00 0.00 +GCT 45 50.00 0.00 50.00 0.00 +GCT 46 50.00 0.00 50.00 0.00 +GCT 47 50.00 0.00 50.00 0.00 +GCT 48 0.00 50.00 50.00 0.00 +GCT 49 50.00 0.00 0.00 50.00 +GCT 50 0.00 0.00 50.00 50.00 +GCT 51 0.00 0.00 100.00 0.00 +GCT 52 50.00 0.00 50.00 0.00 +GCT 53 0.00 50.00 0.00 50.00 +GCT 54 50.00 0.00 50.00 0.00 +GCT 55 50.00 0.00 0.00 50.00 +GCT 56 0.00 50.00 50.00 0.00 +GCT 57 100.00 0.00 0.00 0.00 +GCT 58 50.00 0.00 50.00 0.00 +GCT 59 100.00 0.00 0.00 0.00 +GCT 60 50.00 0.00 50.00 0.00 +GCT 61 0.00 0.00 0.00 100.00 +GCT 62 0.00 50.00 50.00 0.00 +GCT 63 50.00 0.00 0.00 50.00 +GCT 64 0.00 0.00 100.00 0.00 +GCT 65 50.00 50.00 0.00 0.00 +GCT 66 0.00 50.00 0.00 50.00 +GCT 67 0.00 0.00 0.00 100.00 +GCT 68 0.00 50.00 0.00 50.00 +GCT 69 0.00 50.00 0.00 50.00 +GCT 70 50.00 0.00 0.00 50.00 +GCT 71 0.00 0.00 0.00 100.00 +GCT 72 0.00 50.00 0.00 50.00 +GCT 73 0.00 0.00 0.00 100.00 +GCT 74 0.00 50.00 0.00 50.00 +GCT 75 50.00 0.00 0.00 50.00 +GCT 76 0.00 50.00 0.00 50.00 +GCT 77 50.00 0.00 0.00 50.00 +GCT 78 50.00 0.00 0.00 50.00 +GCT 79 50.00 0.00 0.00 50.00 +GCT 80 50.00 0.00 0.00 50.00 +GCT 81 50.00 0.00 0.00 50.00 +GCT 82 50.00 0.00 0.00 50.00 +GCT 83 50.00 0.00 0.00 50.00 +GCT 84 50.00 0.00 0.00 50.00 +GCT 85 50.00 0.00 0.00 50.00 +GCT 86 50.00 0.00 0.00 50.00 +GCT 87 50.00 0.00 0.00 50.00 +GCT 88 50.00 0.00 0.00 50.00 +GCT 89 50.00 0.00 0.00 50.00 +GCT 90 50.00 0.00 0.00 50.00 +GCT 91 50.00 0.00 50.00 0.00 +GCT 92 50.00 0.00 50.00 0.00 +GCT 93 50.00 0.00 50.00 0.00 +GCT 94 50.00 0.00 0.00 50.00 +GCT 95 50.00 0.00 50.00 0.00 +GCT 96 50.00 0.00 50.00 0.00 +GCT 97 50.00 0.00 50.00 0.00 +GCT 98 50.00 0.00 50.00 0.00 +GCT 99 50.00 0.00 50.00 0.00 +GCT 100 50.00 0.00 0.00 50.00 # ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 @@ -454,6 +559,8 @@ FBC 98 0.00 100.00 0.00 0.00 0.00 0.00 FBC 99 0.00 100.00 0.00 0.00 0.00 0.00 FBC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +FTC 50 21 14 15 0 # ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 LBC 2 0.00 0.00 100.00 0.00 0.00 0.00 @@ -555,6 +662,26 @@ LBC 98 100.00 0.00 0.00 0.00 0.00 0.00 LBC 99 100.00 0.00 0.00 0.00 0.00 0.00 LBC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters +LTC 41 20 23 16 0 +# ACGT content per cycle for barcodes. Use `grep ^BCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N counts as a percentage of all A/C/G/T bases [%] +BCC1 2 0.00 0.00 100.00 0.00 0.00 +BCC1 3 0.00 0.00 0.00 100.00 0.00 +BCC1 4 0.00 100.00 0.00 0.00 0.00 +BCC1 5 0.00 0.00 0.00 100.00 0.00 +BCC1 6 100.00 0.00 0.00 0.00 0.00 +BCC1 7 0.00 0.00 0.00 100.00 0.00 +BCC1 8 0.00 100.00 0.00 0.00 0.00 +# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number. +QTQ1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +QTQ1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +QTQ1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 +QTQ1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +QTQ1 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +QTQ1 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +QTQ1 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +QTQ1 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 # Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs IS 0 0 0 0 0 IS 1 0 0 0 0