File: vcfnoindels

package info (click to toggle)
libvcflib 1.0.0~rc2%2Bdfsg-2
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 51,048 kB
  • sloc: cpp: 30,004; perl: 474; sh: 247; makefile: 206; python: 200; ansic: 148
file content (25 lines) | stat: -rwxr-xr-x 430 bytes parent folder | download 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
 
#!/usr/bin/env perl
#

while (<STDIN>) {
    if ($_ =~ /^#/) {
        print;
    } else {
        $_ =~ /^(.+?)\t(.+?)\t(.+?)\t(.+?)\t(.+?)\t/;
        $chrom = $1;
        $pos = $2;
        $tag = $3;
        $ref = $4;
        $alts = $5;
	$hasindel = 0;
	@alts = split(/,/, $alts);
	foreach $alt (@alts) {
	    if (length($alt ) != length($ref)) {
		$hasindel = 1;
	    }
        }
	if (! $hasindel) {
	    print;
	}
    }
}