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#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fastq_reader;
my $usage = "\n\nusage: $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 $left_fastq_reader = new Fastq_reader($left_fq);
my $right_fastq_reader = new Fastq_reader($right_fq);
while (1) {
my $left_fq = $left_fastq_reader->next();
if ($left_fq) {
print $left_fq->get_fastq_record();
}
my $right_fq = $right_fastq_reader->next();
if ($right_fq) {
print $right_fq->get_fastq_record();
}
if ($left_fq && $right_fq) {
my $left_core_read_name = $left_fq->get_core_read_name();
my $right_core_read_name = $right_fq->get_core_read_name();
if ($left_core_read_name ne $right_core_read_name) {
die "Error, read names are out of synch: $left_core_read_name vs. $right_core_read_name ";
}
}
else {
last;
}
}
if ($left_fastq_reader->next() || $right_fastq_reader->next()) {
die "Error, unequal number of fastq records in left and right fq files.";
}
exit(0);
}
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