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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
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