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comparison test-data/samtools_stats_out1.tab @ 12:541082d03bef draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:27:04 +0000
parents e28839a4b932
children
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11:fed4aa48ba09 12:541082d03bef
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 --ref-seq reference.fa -@ 0 infile 3 # The command line was: stats --ref-seq reference.fa -@ 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 1bd20fd8 58ad2167 29883386 6 CHK 1bd20fd8 58ad2167 29883386
1860 RL 251 200 1860 RL 251 200
1861 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count 1861 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count
1862 FRL 251 100 1862 FRL 251 100
1863 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count 1863 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count
1864 LRL 251 100 1864 LRL 251 100
1865 # Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count
1866 MAPQ 0 6
1867 MAPQ 3 6
1868 MAPQ 8 3
1869 MAPQ 23 2
1870 MAPQ 24 4
1871 MAPQ 40 2
1872 MAPQ 42 2
1865 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions 1873 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions
1866 ID 1 1 0 1874 ID 1 1 0
1867 ID 2 1 0 1875 ID 2 1 0
1868 ID 4 2 0 1876 ID 4 2 0
1869 ID 10 5 0 1877 ID 10 5 0