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|
#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
my $pair_stats_file;
my $max_cov;
my $min_cov;
my $max_pct_stdev;
my $usage = <<__EOUSAGE__;
#############################################################
#
# Required:
#
# --stats_file <string> : pairs.stats.sorted
#
# --max_cov <int> : maximum coverage
#
# --min_cov <int> : minimum coverage
#
# --max_pct_stdev <int> : maximum pct stdev
#
#
#############################################################
__EOUSAGE__
;
my $help_flag;
&GetOptions ( 'h' => \$help_flag,
'stats_file=s' => \$pair_stats_file,
'max_cov=i' => \$max_cov,
'min_cov=i' => \$min_cov,
'max_pct_stdev=i' => \$max_pct_stdev,
);
unless ($pair_stats_file &&
$max_cov &&
defined($min_cov) &&
$max_pct_stdev) {
die $usage;
}
main: {
my $count_no_cov = 0;
my $count_aberrant_and_discarded = 0;
my $count_selected = 0;
my $count_total = 0;
my $count_below_min_cov = 0;
open (my $fh, $pair_stats_file) or die $!;
while (<$fh>) {
$count_total++;
chomp;
my $line = $_;
my ($med_cov, $avg_cov, $stdev, $pct_dev, $core_acc) = split(/\t/);
$core_acc =~ s|/[12]$||;
if ($med_cov < 1) {
$count_no_cov++; ## this shouldn't happen in modern versions of this process. (bh 10-2013)
next;
}
if ($med_cov < $min_cov) {
$count_below_min_cov++;
next;
}
if ($pct_dev > $max_pct_stdev) {
# print STDERR "// excluding $_ as aberrant\n";
$count_aberrant_and_discarded++;
next;
}
if (rand(1) <= $max_cov/$med_cov) {
print "$core_acc\n";
$count_selected++;
}
}
close $fh;
print STDERR "$count_selected / $count_total = " . sprintf("%.2f", $count_selected/$count_total*100) . "% reads selected during normalization.\n";
print STDERR "$count_aberrant_and_discarded / $count_total = " . sprintf("%.2f", $count_aberrant_and_discarded/$count_total*100) . "% reads discarded as likely aberrant based on coverage profiles.\n";
print STDERR "$count_no_cov / $count_total = " . sprintf("%.2f", $count_no_cov/$count_total*100) . "% reads missing kmer coverage (N chars included?).\n";
print STDERR "$count_below_min_cov / $count_total = " . sprintf("%.2f", $count_below_min_cov/$count_total*100) . "% reads discarded as below minimum coverage threshold=$min_cov\n";
exit(0);
}
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