#!/bin/sh
# $Id: spanblocks,v 1.6 1992/04/01 21:43:25 schwartz Exp $

USAGE='usage: spanblocks [-msa] alignfile startblock [endblock] [prefuzz postfuzz]';
case $# in
0) echo $USAGE 2>&1; exit 1;;
esac

MSA=1
case "$1" in
-m*) MSA=0; shift;;
esac

tmp1=msa.$$
tmp2=msa.output

msaselect $* >$tmp1 &&
  (msa $tmp1 >$tmp2 2>/dev/null ; msa2lav $tmp1 $tmp2)

case $MSA in
0) rm $tmp1;;
1) mv $tmp1 msa.input;;
esac