Mercurial > repos > devteam > samtools_stats
diff test-data/1.stats.expected @ 4:8d500e0e0dbe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
| author | iuc |
|---|---|
| date | Thu, 27 Sep 2018 08:59:54 -0400 |
| parents | |
| children | ab75c7ea49a5 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.stats.expected Thu Sep 27 08:59:54 2018 -0400 @@ -0,0 +1,383 @@ +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 1a1c1362 29c426ae 7bab45da +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 2 +SN filtered sequences: 0 +SN sequences: 2 +SN is sorted: 1 +SN 1st fragments: 1 +SN last fragments: 1 +SN reads mapped: 2 +SN reads mapped and paired: 2 # paired-end technology bit set + both mates mapped +SN reads unmapped: 0 +SN reads properly paired: 2 # proper-pair bit set +SN reads paired: 2 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 0 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 70 # ignores clipping +SN total first fragment length: 35 # ignores clipping +SN total last fragment length: 35 # ignores clipping +SN bases mapped: 70 # ignores clipping +SN bases mapped (cigar): 70 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 0 # from NM fields +SN error rate: 0.000000e+00 # mismatches / bases mapped (cigar) +SN average length: 35 +SN average first fragment length: 35 +SN average last fragment length: 35 +SN maximum length: 35 +SN maximum first fragment length: 35 +SN maximum last fragment length: 35 +SN average quality: 255.0 +SN insert size average: 100.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 1 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +SN percentage of properly paired reads (%): 100.0 +# First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +FFQ 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 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 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 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 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 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 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 +FFQ 2 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 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 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 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 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 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 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Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 28.39 0 +GCF 58.29 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 21.36 0 +GCL 43.97 1 +# ACGT content per cycle. Use `grep ^GCC | 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 [%] +GCC 1 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 2 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 3 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 4 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 5 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 6 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 7 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 8 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 9 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 10 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 11 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 12 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 13 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 14 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 15 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 16 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 17 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 18 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 19 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 20 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 21 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 22 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 23 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 24 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 25 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 26 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 27 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 28 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 29 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 30 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 31 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 32 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 33 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 34 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 35 0.00 0.00 50.00 50.00 0.00 0.00 +# 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 +FBC 3 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 4 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 5 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 6 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 7 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 8 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 9 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 10 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 11 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 12 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 13 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 14 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 15 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 16 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 17 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 18 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 19 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 20 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 21 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 22 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 23 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 24 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 25 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 26 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 27 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 28 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 29 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 30 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 31 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 32 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 33 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 34 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 35 0.00 0.00 100.00 0.00 0.00 0.00 +# 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 0.00 100.00 0.00 0.00 +LBC 3 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 4 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 5 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 6 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 7 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 8 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 9 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 10 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 11 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 12 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 13 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 14 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 15 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 16 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 17 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 18 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 19 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 20 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 21 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 22 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 23 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 24 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 25 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 26 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 27 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 28 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 29 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 30 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 31 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 32 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 33 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 34 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 35 0.00 0.00 0.00 100.00 0.00 0.00 +# 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 +IS 2 0 0 0 0 +IS 3 0 0 0 0 +IS 4 0 0 0 0 +IS 5 0 0 0 0 +IS 6 0 0 0 0 +IS 7 0 0 0 0 +IS 8 0 0 0 0 +IS 9 0 0 0 0 +IS 10 0 0 0 0 +IS 11 0 0 0 0 +IS 12 0 0 0 0 +IS 13 0 0 0 0 +IS 14 0 0 0 0 +IS 15 0 0 0 0 +IS 16 0 0 0 0 +IS 17 0 0 0 0 +IS 18 0 0 0 0 +IS 19 0 0 0 0 +IS 20 0 0 0 0 +IS 21 0 0 0 0 +IS 22 0 0 0 0 +IS 23 0 0 0 0 +IS 24 0 0 0 0 +IS 25 0 0 0 0 +IS 26 0 0 0 0 +IS 27 0 0 0 0 +IS 28 0 0 0 0 +IS 29 0 0 0 0 +IS 30 0 0 0 0 +IS 31 0 0 0 0 +IS 32 0 0 0 0 +IS 33 0 0 0 0 +IS 34 0 0 0 0 +IS 35 0 0 0 0 +IS 36 0 0 0 0 +IS 37 0 0 0 0 +IS 38 0 0 0 0 +IS 39 0 0 0 0 +IS 40 0 0 0 0 +IS 41 0 0 0 0 +IS 42 0 0 0 0 +IS 43 0 0 0 0 +IS 44 0 0 0 0 +IS 45 0 0 0 0 +IS 46 0 0 0 0 +IS 47 0 0 0 0 +IS 48 0 0 0 0 +IS 49 0 0 0 0 +IS 50 0 0 0 0 +IS 51 0 0 0 0 +IS 52 0 0 0 0 +IS 53 0 0 0 0 +IS 54 0 0 0 0 +IS 55 0 0 0 0 +IS 56 0 0 0 0 +IS 57 0 0 0 0 +IS 58 0 0 0 0 +IS 59 0 0 0 0 +IS 60 0 0 0 0 +IS 61 0 0 0 0 +IS 62 0 0 0 0 +IS 63 0 0 0 0 +IS 64 0 0 0 0 +IS 65 0 0 0 0 +IS 66 0 0 0 0 +IS 67 0 0 0 0 +IS 68 0 0 0 0 +IS 69 0 0 0 0 +IS 70 0 0 0 0 +IS 71 0 0 0 0 +IS 72 0 0 0 0 +IS 73 0 0 0 0 +IS 74 0 0 0 0 +IS 75 0 0 0 0 +IS 76 0 0 0 0 +IS 77 0 0 0 0 +IS 78 0 0 0 0 +IS 79 0 0 0 0 +IS 80 0 0 0 0 +IS 81 0 0 0 0 +IS 82 0 0 0 0 +IS 83 0 0 0 0 +IS 84 0 0 0 0 +IS 85 0 0 0 0 +IS 86 0 0 0 0 +IS 87 0 0 0 0 +IS 88 0 0 0 0 +IS 89 0 0 0 0 +IS 90 0 0 0 0 +IS 91 0 0 0 0 +IS 92 0 0 0 0 +IS 93 0 0 0 0 +IS 94 0 0 0 0 +IS 95 0 0 0 0 +IS 96 0 0 0 0 +IS 97 0 0 0 0 +IS 98 0 0 0 0 +IS 99 0 0 0 0 +IS 100 1 1 0 0 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 35 2 +# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count +FRL 35 1 +# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count +LRL 35 1 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 70 +# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile +GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000