/usr/share/bash-completion/completions/kalign is in kalign 1:2.03+20110620-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 | # -*- mode: shell-script; sh-basic-offset: 8; indent-tabs-mode: t -*-
# ex: ts=8 sw=8 noet filetype=sh
#
# kalign(1) completion
#
have kalign && {
_kalign() {
local cur prev
COMPREPLY=()
cur=`_get_cword`
prev=${COMP_WORDS[COMP_CWORD-1]}
case "$prev" in
-@(i|input|infile|in|o|output|outfile|out))
_filedir
return 0
;;
-@(c|sort))
COMPREPLY=( $( compgen -W "input tree gaps" -- "$cur" ) )
return 0
;;
-@(g|feature))
# TODO: finish this list!
COMPREPLY=( $( compgen -W "all maxplp STRUCT PFAM-A" -- "$cur" ) )
return 0
;;
-@(d|distance))
COMPREPLY=( $( compgen -W "wu pair" -- "$cur" ) )
return 0
;;
-@(b|guide_tree|tree))
COMPREPLY=( $( compgen -W "nj upgma" -- "$cur" ) )
return 0
;;
-@(f|format))
COMPREPLY=( $( compgen -W "fasta msf aln clu macsim" -- "$cur" ) )
return 0
;;
esac
if [[ "$cur" == -* ]]; then
COMPREPLY=( $( compgen -W "-s -gapopen -gap_open -gpo \
-e -gapextension -gap_ext -gpe \
-t -terminal_gap_extension_penalty -tgpe \
-m -matrix_bonus -bonus \
-c -sort \
-g -feature -same_feature_score -diff_feature_score \
-d -distance \
-b -guide-tree -tree \
-z -zcutoff \
-i -input -infile -in \
-o -output -outfile -out \
-a -gap_inc \
-f -format \
-q -quiet" \
-- "$cur" ) )
else
_filedir
fi
return 0
}
complete -F _kalign $filenames kalign
}
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