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#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use SAM_reader;
use SAM_entry;
use Carp;
use Data::Dumper;
my $usage = "usage: $0 file.sam number_records_to_check=10\n\n";
my $sam_file = $ARGV[0] or die $usage;
my $num_records_to_check = $ARGV[1] || 10;
main: {
my $sam_reader = new SAM_reader($sam_file);
my $num_records_checked = 0;
while (my $sam_entry = $sam_reader->get_next()) {
my $core_read_name = $sam_entry->get_read_name();
if (! $sam_entry->is_paired()) {
confess "ERROR, only paired reads should exist in bam file. Encountered unpaired read: " . Dumper($sam_entry);
}
$num_records_checked++;
if ($num_records_checked >= $num_records_to_check) {
last;
}
}
print STDERR "paired read check for $sam_file is OK.\n";
exit(0); # all good!
}
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