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#!/usr/bin/env perl
use strict;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use SAM_reader;
use SAM_entry;
my $usage = "usage: $0 nameSorted.sam\n\n";
my $sam_file = $ARGV[0] or die $usage;
main: {
my $sam_reader = new SAM_reader($sam_file);
my $filtered_count = 0;
my $total_count = 0;
my $prev_core_read_name = "";
my @entries;
while ($sam_reader->has_next()) {
my $sam_entry = $sam_reader->get_next();
my $core_read_name = $sam_entry->get_core_read_name();
if ($core_read_name ne $prev_core_read_name) {
&process_entries(@entries);
@entries = ();
}
push (@entries, $sam_entry);
$prev_core_read_name = $core_read_name;
}
if (@entries) {
&process_entries(@entries);
}
exit(0);
}
####
sub process_entries {
my @entries = @_;
my %scaffolds;
foreach my $entry (@entries) {
my $scaff = $entry->get_scaffold_name();
$scaffolds{$scaff}++;
}
my $num_scaff = scalar(keys %scaffolds);
if ($num_scaff == 1) {
foreach my $entry (@entries) {
print $entry->toString() . "\n";
}
}
return;
}
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