The format of the ooc file in Blat

[superligang]

Hi, I'm new here.

Blat produces ooc file to store the over-repetitive fragment in the chromosomes. I wonder whether the format specification of this ooc file is public, or there is any program to parse it.

Thanks a lot.

[lifeng.tian]

I wrote a PERL script to decode it.
The sequence database is a subset of hg19, including
chr1 to chr22, chrX, chrY, and chrM.

The tileSize I used is 11.

There are 30031 11-mer excluded in the ooc file.

The decoded file looks like:
1480676850
11
0
1
2
3
4
5
6
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
24
25
26
27
32
33
34
.....
4193279
4193535
4194046
4194047
4194303

Here is the code:
$in="11.ooc";
open(IN, "< $in");
binmode(IN);
open(OUT, "> out");
while (read(IN,$b,4)) {
$byteCount++;
$a=unpack("V",$b);
print(OUT $a."\n");
}

[superligang]

this is great, thank you.