_samtools

 1#compdef samtools
 2#autoload
 3
 4local curcontext="$curcontext" state line ret=1
 5local -a _files
 6
 7_arguments -C \
 8  '1: :->cmds' \
 9  '2:: :->args' && ret=0
10
11case $state in
12  cmds)
13    _values "samtools command" \
14        "view[SAM<->BAM conversion]" \
15        "sort[sort alignment file]" \
16        "mpileup[multi-way pileup]" \
17        "depth[compute the depth]" \
18        "faidx[index/extract FASTA]" \
19        "tview[text alignment viewer]" \
20        "index[index alignment]" \
21        "idxstats[BAM index stats (r595 or later)]" \
22        "fixmate[fix mate information]" \
23        "flagstat[simple stats]" \
24        "calmd[recalculate MD/NM tags and '=' bases]" \
25        "merge[merge sorted alignments]" \
26        "rmdup[remove PCR duplicates]" \
27        "reheader[replace BAM header]" \
28        "cat[concatenate BAMs]" \
29        "bedcov[read depth per BED region]" \
30        "targetcut[cut fosmid regions (for fosmid pool only)]" \
31        "phase[phase heterozygotes]" \
32        "bamshuf[shuffle and group alignments by name]"
33    ret=0
34    ;;
35  *)
36    _files
37    ;;
38esac
39
40return ret