Files from @suhas-rao

#!/bin/bash

inputFile=$1

awk 'BEGIN{bytecounter=0}{

	if (bytecounter==0) {

		chr1=$2;

		chr2=$6;

		gsub(/ /, "", chr1);

		gsub(/ /, "", chr2);

		chr1=tolower(chr1);

		chr2=tolower(chr2);

		gsub(/chr/, "", chr1);

		gsub(/chr/, "", chr2);	

		chr1=toupper(chr1);

		chr2=toupper(chr2);

		print chr1"_"chr2 "," bytecounter;

		currentChr1 = chr1;

		currentChr2 = chr2;

	} 

	chr1=$2;

        chr2=$6;

        gsub(/ /, "", chr1);

        gsub(/ /, "", chr2);

        chr1=tolower(chr1);

        chr2=tolower(chr2);

        gsub(/chr/, "", chr1);

        gsub(/chr/, "", chr2);

        chr1=toupper(chr1);

        chr2=toupper(chr2);

	if (chr1!=currentChr1 || chr2!=currentChr2) {

		print chr1"_"chr2 "," bytecounter;

		currentChr1 = chr1;

		currentChr2 = chr2;

		bytecounter += length($0) + 1;

	} else {

		bytecounter += length($0) + 1;

	}

}' "$inputFile"

#!/bin/bash

inputFile=$1

awk '{chr1=$2;chr2=$6;gsub(/ /, "", chr1);gsub(/ /, "", chr2);chr1=tolower(chr1);chr2=tolower(chr2);gsub(/chr/, "", chr1);gsub(/chr/, "", chr2);chr1=toupper(chr1);chr2=toupper(chr2); print $0 >> "merged_nodups.txt_"chr1"_"chr2;}' "$inputFile"