LINUX AWK command for a big file - awk

Question

I have encountered a problem that exceeds my basic unix knowledge and would really appreciate some help. I have a large file in the following format:
chr1 10495 10499 211
chr1 10496 10500 1
chr1 10587 10591 93
chr1 10588 10592 1
chr1 10639 10643 4
chr1 10668 10672 11
chr1 10697 10701 13
chr1 10726 10730 8
chr1 10755 10759 7
chr1 10784 10788 5
chr2 10856 10860 4
chr3 10932 10936 6
chr3 10933 10937 2
chr5 11056 11060 4
chr6 11155 11159 9
If the values in column one match and one number difference in column two, I want to sum the values in column 4 of both lines and replace the value of column 3 in line 1 with the value of column 3 in line 2 , else just the the values in the unique line without modifying any column.
So the output I am hoping for would look like this:
chr1 10495 10500 212
chr1 10587 10592 94
chr1 10639 10643 4
chr1 10668 10672 11
chr1 10697 10701 13
chr1 10726 10730 8
chr1 10755 10759 7
chr1 10784 10788 5
chr2 10856 10860 4
chr3 10932 10937 8
chr5 11056 11060 4
chr6 11155 11159 9

Answer 1

$ cat tst.awk
BEGIN { OFS="\t" }
NR>1 {
if ( ($1==p[1]) && ($2==(p[2]+1)) ) {
print p[1], p[2], $3, p[4]+$4
delete p[0]
next
}
else if (0 in p) {
print p[0]
}
}
{ split($0,p); p[0]=$0 }
END { if (0 in p) print p[0] }
$
$ awk -f tst.awk file
chr1 10495 10500 212
chr1 10587 10592 94
chr1 10639 10643 4
chr1 10668 10672 11
chr1 10697 10701 13
chr1 10726 10730 8
chr1 10755 10759 7
chr1 10784 10788 5
chr2 10856 10860 4
chr3 10932 10937 8
chr5 11056 11060 4
chr6 11155 11159 9

Answer 2

Haven't checked closely, but I think you want:
awk '{split(p,a)}
$1==a[1] && a[2]==$2-1{print a[1], a[2], $3, $4 + a[4]; p=""; next}
p {print p} {p=$0}
END {print}' OFS=\\t input
At any given step (except the first), p holds the value from the previous line. The 2nd line of the script checks if the first field in the current line matches the first field of the last line and that the 2nd field is one greater than the 2nd field of the last line. In that condition, it prints the first two fields from the previous line, the third from the current line, and the sum of the 4th fields and moves on to the next line. If they don't match, it prints the previous line. At the end, it just prints the line.

Answer 3

This script, I'm using to merge intervals in transcriptome data
awk '
NR==1{
n= split($0, first);
c=1;
for(i=1; i<=n; i++) d[c, i] = first[i];
}
NR>1{
n= split($0, actual);
#if(actual[1] != d[c, 1] || actual[2]>d[c, 3]){ #for interval fusion
if(actual[1] != d[c, 1] || actual[2]>d[c,2]+1){ #OP requirement
c++;
for(i=1; i<=n; i++) d[c, i] = actual[i];
}else{
if(actual[3] > d[c,3]) d[c,3] = actual[3];
d[c,4] = d[c,4] + actual[4];
}
}
END{
for(i=1; i<=c; i++){
print d[i, 1], d[i, 2], d[i, 3], d[i, 4]
}
}' file
you get:
chr1 10495 10500 212
chr1 10587 10592 94
chr1 10639 10643 4
chr1 10668 10672 11
chr1 10697 10701 13
chr1 10726 10730 8
chr1 10755 10759 7
chr1 10784 10788 5
chr2 10856 10860 4
chr3 10932 10937 8
chr5 11056 11060 4
chr6 11155 11159 9