#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
