#!/bin/csh
rm -f out_full
touch out_full
foreach s1   ( *.fna )
    set notcompared = 0;
    foreach s2 ( *.fna )
	if ( ${s1} != ${s2} && $notcompared) then 
	    echo "${s1} ${s2}"
	    nice +19 yass -M 3  -r 2  ${s1} ${s2} -d 1 -i 0 -O 1000 -X 100 -w 0 -o out_yass
	endif
	cat out_yass | grep ".*||.*\|\*(" >> out_full;
	if ( ${s1} == ${s2} ) then
	    set notcompared = 1;
	endif
  end
end
