inodb · May 16, 2014 15:14
diff --git a/mummer_duplicate_contigs b/mummer_duplicate_contigs
 for row in $(cat nucmer.coords | awk -v OFS=, '{if ($10 == 100.00 && $11 == 100.00 && $7 == 100.00 && $12 != $13) {print $12,$13}}')
 do
    echo $row | tr ',' '\n' | sort | tr '\n' ',' | sed 's/,$//'
    echo
 done | cut -d, -f2 | sort -u > duplicatecontigs.txt
	for row in $(cat nucmer.coords \| awk -v OFS=, '{if ($10 == 100.00 && $11 == 100.00 && $7 == 100.00 && $12 != $13) {print $12,$13}}')
	do
	echo $row \| tr ',' '\n' \| sort \| tr '\n' ',' \| sed 's/,$//'
	echo
	done \| cut -d, -f2 \| sort -u > duplicatecontigs.txt