Shell Programming and Scripting

cat input

chr1 1000 2000
chr1 600 699
chr1 701 1000
chr1 600 1710
chr2 900 1800

Record1.Col2 - Record2.Col2
Record1.Col2 - Record2.Col3
Record1.Col3 - Record2.Col2
Record1.Col3 - Record2.Col3

cat output
chr1 600 699
chr2 900 1800

chr1 1000 2000 chr1 600 699
chr1 1000 2000 chr1 701 1000
chr1 1000 2000 chr1 600 1710
chr1 1000 2000 chr2 900 1800

$2-$5, $2-$6, $3-$5 and $3-$6

chr1 1000 2000 chr1 600 (400&1400) 699(301&1301) - This one will qualify, because the values are greater than 300.
chr1 1000 2000 chr1 701(299&1299) 1000(0&1000) - This record should be deleted, because the values are less than 300.
chr1 1000 2000 chr1 600(400&1400) 1710(-710&290) - This is same as above. You can ignore the negative sign while calculating.
chr1 1000 2000 chr2 900 1800 - This one will remain because the col1 and col4 don't match.

awk ' NR == 1 {
                c1 = $2
                c2 = $3
                p  = $1
                next

} p == $1 {
                d1 = c1 - $2
                d2 = c1 - $3

                d3 = c2 - $2
                d4 = c2 - $3

                d1 = (d1 < 0)?d1*-1:d1
                d2 = (d2 < 0)?d2*-1:d2
                d3 = (d3 < 0)?d3*-1:d3
                d4 = (d4 < 0)?d4*-1:d4

                if ( d1 > 300 && d2 > 300 && d3 > 300 && d4 > 300 )
                        print
} p != $1 {
                c1 = $2
                c2 = $3
                p  = $1
                print
} ' input