_samtools 1.1 KB

12345678910111213141516171819202122232425262728293031323334353637383940
  1. #compdef samtools
  2. #autoload
  3. local curcontext="$curcontext" state line ret=1
  4. local -a _files
  5. _arguments -C \
  6. '1: :->cmds' \
  7. '2:: :->args' && ret=0
  8. case $state in
  9. cmds)
  10. _values "samtools command" \
  11. "view[SAM<->BAM conversion]" \
  12. "sort[sort alignment file]" \
  13. "mpileup[multi-way pileup]" \
  14. "depth[compute the depth]" \
  15. "faidx[index/extract FASTA]" \
  16. "tview[text alignment viewer]" \
  17. "index[index alignment]" \
  18. "idxstats[BAM index stats (r595 or later)]" \
  19. "fixmate[fix mate information]" \
  20. "flagstat[simple stats]" \
  21. "calmd[recalculate MD/NM tags and '=' bases]" \
  22. "merge[merge sorted alignments]" \
  23. "rmdup[remove PCR duplicates]" \
  24. "reheader[replace BAM header]" \
  25. "cat[concatenate BAMs]" \
  26. "bedcov[read depth per BED region]" \
  27. "targetcut[cut fosmid regions (for fosmid pool only)]" \
  28. "phase[phase heterozygotes]" \
  29. "bamshuf[shuffle and group alignments by name]"
  30. ret=0
  31. ;;
  32. *)
  33. _files
  34. ;;
  35. esac
  36. return ret