#!/usr/bin/gawk -f BEGIN { FS="\t"; OFS="\t"; print "old", "oldStart", "oldEnd","new", "newStart", "newEnd","newgap"; } { offset = $1; oldName = $2; oldSize = $3; newName = $4; newSize = $5; } newName != curChrom { curChrom = newName; prevEnd = 0; } { print oldName, 0, oldSize, newName, offset, offset+oldSize, offset-prevEnd; prevEnd = offset+oldSize; }