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#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
###############################################################################
#
# Required:
#
# --left <string> left.fq.stats
# --right <string> right.fq.stats
#
# Optional
#
# --sorted flag indicating that entries are lexically sorted
# (this can account for differences in representation by
# reads in either file)
# Unpaired entries are ignored.
#
################################################################################
__EOUSAGE__
;
my $left_stats_file;
my $right_stats_file;
my $sorted_flag = 0;
&GetOptions( 'left=s' => \$left_stats_file,
'right=s' => \$right_stats_file,
'sorted' => \$sorted_flag,
);
unless ($left_stats_file && $right_stats_file) {
die $usage;
}
main: {
my ($left_fh, $right_fh);
print STDERR "-opening $left_stats_file\n";
if ($left_stats_file =~ /\.gz$/) {
open ($left_fh, "gunzip -c $left_stats_file | ") or die $!;
} elsif ($left_stats_file =~ /\.xz$/) {
open(${left_fh}, "xz -cd ${left_stats_file} | ") or die $!;
}
else {
open ($left_fh, $left_stats_file) or die $!;
}
print STDERR "-opening $right_stats_file\n";
if ($right_stats_file =~ /\.gz$/) {
open ($right_fh, "gunzip -c $right_stats_file | ") or die $!;
} elsif ($right_stats_file =~ /\.xz$/) {
open (${right_fh}, "xz -dc ${right_stats_file} | ") or die $!;
}
else {
open ($right_fh, $right_stats_file) or die $!;
}
print STDERR "-done opening files.\n";
my $left_text = <$left_fh>;
my $right_text = <$right_fh>;
while (1) {
#print STDERR "$left_text\n$right_text\n\n";
if ( (! $left_text) || (! $right_text)) {
last;
}
chomp $left_text;
chomp $right_text;
my ($left_median, $left_avg, $left_stdev, $left_pct, $left_acc, $left_cov) = split(/\t/, $left_text);
my ($right_median, $right_avg, $right_stdev, $right_pct, $right_acc, $right_cov) = split(/\t/, $right_text);
my $core_acc = $left_acc;
if ($left_acc =~ /^(\S+)\/\d$/) {
$core_acc = $1;
}
my $right_core = $right_acc;
if ($right_acc =~ /^(\S+)\/\d$/) {
$right_core = $1;
}
#print STDERR "$core_acc\t$right_core";
#if ($core_acc eq $right_core) { print STDERR "\tYES\n";} else { print STDERR "\n"; }
unless ($right_core eq $core_acc) {
if ($sorted_flag) {
if ($left_acc lt $right_acc) {
$left_text = <$left_fh>; # advance left
}
else {
# advance right
$right_text = <$right_fh>;
}
next;
}
else {
die "Error, core accs are not equivalent: [$core_acc] vs. [$right_core] reads, and --sorted flag wasn't used here.";
}
}
my $median_pair_cov = int( ($left_median+$right_median)/2 + 0.5);
my $avg_pair_cov = int ( ($left_avg + $right_avg)/2 + 0.5);
my $avg_stdev = int( ($left_stdev + $right_stdev)/2 + 0.5);
if ($median_pair_cov != 0) {
## ignore bad reads.
my $avg_pair_pct = int( ($left_pct + $right_pct) / 2 + 0.5);
print join("\t", $median_pair_cov, $avg_pair_cov, $avg_stdev, $avg_pair_pct, $core_acc) . "\n";
}
## advance next entries.
$left_text = <$left_fh>;
$right_text = <$right_fh>;
}
exit(0);
}
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