Mercurial > repos > devteam > samtools_stats
comparison test-data/12.2reads.nooverlap.expected @ 12:541082d03bef draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author | iuc |
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date | Sun, 08 Sep 2024 03:27:04 +0000 |
parents | e28839a4b932 |
children |
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11:fed4aa48ba09 | 12:541082d03bef |
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1 # This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats | 1 # This file was produced by samtools stats (1.20+htslib-1.20) and can be plotted using plot-bamstats |
2 # This file contains statistics for all reads. | 2 # This file contains statistics for all reads. |
3 # The command line was: stats -t /tmp/tmp0r5zs075/files/b/2/1/dataset_b2175431-044e-449d-8f60-1bfd33679b61.dat -p -@ 0 infile | 3 # The command line was: stats -t /tmp/tmp5q_kwqc0/files/5/e/6/dataset_5e6cda5d-79e8-4b8f-9e14-97f3be9f87de.dat -p -@ 0 infile |
4 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities | 4 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities |
5 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) | 5 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) |
6 CHK 5b31676a b0edee94 471895da | 6 CHK 5b31676a b0edee94 471895da |
7 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. | 7 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. |
8 SN raw total sequences: 2 # excluding supplementary and secondary reads | 8 SN raw total sequences: 2 # excluding supplementary and secondary reads |
853 RL 100 2 | 853 RL 100 2 |
854 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count | 854 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count |
855 FRL 100 1 | 855 FRL 100 1 |
856 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count | 856 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count |
857 LRL 100 1 | 857 LRL 100 1 |
858 # Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count | |
859 MAPQ 7 1 | |
860 MAPQ 37 1 | |
858 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions | 861 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions |
859 ID 2 0 1 | 862 ID 2 0 1 |
860 ID 3 1 0 | 863 ID 3 1 0 |
861 # 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) | 864 # 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) |
862 IC 90 1 0 0 0 | 865 IC 90 1 0 0 0 |