Extract a specific ratio of reads from a BAM file

random_line_extraction.using_ratio.pl

#This is probably not the best way to go about this, but it basically works.
#Keep in mind that PERL's "rand()" function isn't really random, but for this purpose it doesn't really matter.
#Suggested usage: samtools view -h <in.bam> | perl random_line_extraction.using_ratio.pl <ratio in decimal form> | samtools view -bS - > <out.bam>

$num=shift;
while($line=<STDIN>) {
    chomp($line);
    if($line =~ m/^@/) {
        print "$line\n";
    }
    else {
        my $rnum = rand();
        if($rnum<=$num) {
            print "$line\n";
        }
    }
}