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Diffstat (limited to 'plugins/samtools/_samtools')
| -rw-r--r-- | plugins/samtools/_samtools | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/plugins/samtools/_samtools b/plugins/samtools/_samtools new file mode 100644 index 000000000..ddb002ae2 --- /dev/null +++ b/plugins/samtools/_samtools @@ -0,0 +1,40 @@ +#compdef samtools +#autoload + +local curcontext="$curcontext" state line ret=1 +local -a _files + +_arguments -C \ + '1: :->cmds' \ + '2:: :->args' && ret=0 + +case $state in + cmds) + _values "samtools command" \ + "view[SAM<->BAM conversion]" \ + "sort[sort alignment file]" \ + "mpileup[multi-way pileup]" \ + "depth[compute the depth]" \ + "faidx[index/extract FASTA]" \ + "tview[text alignment viewer]" \ + "index[index alignment]" \ + "idxstats[BAM index stats (r595 or later)]" \ + "fixmate[fix mate information]" \ + "flagstat[simple stats]" \ + "calmd[recalculate MD/NM tags and '=' bases]" \ + "merge[merge sorted alignments]" \ + "rmdup[remove PCR duplicates]" \ + "reheader[replace BAM header]" \ + "cat[concatenate BAMs]" \ + "bedcov[read depth per BED region]" \ + "targetcut[cut fosmid regions (for fosmid pool only)]" \ + "phase[phase heterozygotes]" \ + "bamshuf[shuffle and group alignments by name]" + ret=0 + ;; + *) + _files + ;; +esac + +return ret |