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comparison test-data/2.stats.expected @ 12:8fecc86e574a 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 03:23:56 +0000
parents ab75c7ea49a5
children
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11:a95f78faca04 12:8fecc86e574a
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 1a1c1362 29c426ae 7bab45da 6 CHK 1a1c1362 29c426ae 7bab45da
417 RL 35 2 417 RL 35 2
418 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count 418 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count
419 FRL 35 1 419 FRL 35 1
420 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count 420 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count
421 LRL 35 1 421 LRL 35 1
422 # Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count
423 MAPQ 40 2
422 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions 424 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions
423 # 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) 425 # 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)
424 # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. 426 # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.
425 COV [1-1] 1 70 427 COV [1-1] 1 70
426 # 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 428 # 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