#!/bin/csh -f
set opd = $1
set fileN = $2
cd opd
sort -n -k 5,5 $fileN.orth.pairs | awk '{if ($5==prev){i+=1}{prev=$5};printf ("%s %.3d %.5d %.5d ",$1,$2,$3,NR-i); print $5,$6,$7,$8,$9,$10,$11,$12}'  - | sort -n -k 10,10 - | awk '{if ($10==prev){i+=1}{prev=$10};printf ("%s %.3d %.5d %.5d %.5d %s %.3d %.5d %.5d %.5d %d %d\n",$1,$2,$3,$4,$5,$6,$7,$8,NR-i,$10,$11,$12)}'  - >! short.file
sort -n -k 5 -k 10 short.file >! $fileN.orth.pairs
awk -f ../../../../../../Programs/4AnChro/get.syntonorth2.awk $fileN.orth.pairs >! $fileN.orth.synt
rm short.file
exit

