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#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fastq_reader;
my $usage = "usage: $0 left.fq right.fq\n\n";
my $left_fq = $ARGV[0] or die $usage;
my $right_fq = $ARGV[1] or die $usage;
main: {
my $left_fq_reader = new Fastq_reader($left_fq);
my $right_fq_reader = new Fastq_reader($right_fq);
my $ok_counter = 0;
my $error_counter = 0;
while (my $left_fq_record = $left_fq_reader->next()) {
my $right_fq_record = $right_fq_reader->next() or die "Error, no next record in $right_fq";
my $left_core_acc = $left_fq_record->get_core_read_name();
my $left_full_acc = $left_fq_record->get_full_read_name();
my $right_core_acc = $right_fq_record->get_core_read_name();
my $right_full_acc = $right_fq_record->get_full_read_name();
if ($left_core_acc eq $right_core_acc) {
$ok_counter++;
}
else {
$error_counter++;
print join("\t", $left_full_acc, $right_full_acc, $left_core_acc, $right_core_acc, "ERROR") . "\n\n";
print STDERR "\r[$ok_counter ok, $error_counter error] ";
die "Error, found out-of-order pairing. Stopping now.";
}
if ($ok_counter % 1000 == 0) {
print STDERR "\r[$ok_counter ok, $error_counter error] ";
}
}
exit(0);
}
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