dotfiles/zsh/.local/share/oh-my-zsh/plugins/samtools/_samtools

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#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