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