mirror of
https://github.com/ohmyzsh/ohmyzsh.git
synced 2024-12-25 05:41:58 +00:00
41 lines
1.1 KiB
Text
41 lines
1.1 KiB
Text
|
#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
|