139 lines
2.7 KiB
Perl
139 lines
2.7 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 SAM_reader;
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use SAM_entry;
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my $usage = "\n\nusage: name_sorted_paired_reads.sam\n\n";
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my $sam_file = $ARGV[0] or die $usage;
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main: {
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my $prev_read_name = "";
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my $prev_scaff_name = "";
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my @reads;
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my $sam_reader = new SAM_reader($sam_file);
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while ($sam_reader->has_next()) {
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my $read = $sam_reader->get_next();
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my $scaff_name = $read->get_scaffold_name();
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my $core_read_name = $read->get_core_read_name();
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if ($core_read_name ne $prev_read_name) {
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if (@reads) {
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&process_pairs(@reads);
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@reads = ();
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}
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}
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push (@reads, $read);
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$prev_read_name = $core_read_name;
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$prev_scaff_name = $scaff_name;
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}
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&process_pairs(@reads);
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exit(0);
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}
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####
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sub process_pairs {
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my (@reads) = @_;
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my %scaffold_to_reads;
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foreach my $read (@reads) {
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my $scaff_name = $read->get_scaffold_name();
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push (@{$scaffold_to_reads{$scaff_name}}, $read);
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}
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foreach my $scaff (keys %scaffold_to_reads) {
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my @scaff_reads = @{$scaffold_to_reads{$scaff}};
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&process_scaffold_pairs(@scaff_reads);
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}
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return;
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}
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sub process_scaffold_pairs {
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my @reads = @_;
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my @left_reads;
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my @right_reads;
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foreach my $read (@reads) {
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my $read_name = $read->get_read_name();
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#print "processing: $read_name\n";
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if ($read_name =~ m|/1$|) {
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push (@left_reads, $read);
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}
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elsif ($read_name =~ m|/2$|) {
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push (@right_reads, $read);
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}
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}
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unless (@left_reads && @right_reads) {
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#print "\t** no pairs...\n";
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return;
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}
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my $left_read = shift @left_reads;
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my $left_aligned_pos = $left_read->get_aligned_position();
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my $scaffold_name = $left_read->get_scaffold_name();
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my $right_read = shift @right_reads;
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my $right_aligned_pos = $right_read->get_aligned_position();
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$left_read->set_mate_scaffold_name($scaffold_name);
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$left_read->set_mate_scaffold_position($right_aligned_pos);
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$right_read->set_mate_scaffold_name($scaffold_name);
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$right_read->set_mate_scaffold_position($left_aligned_pos);
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$left_read->set_paired(1);
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$right_read->set_paired(1);
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$left_read->set_proper_pair(1);
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$right_read->set_proper_pair(1);
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$left_read->set_first_in_pair(1);
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$right_read->set_second_in_pair(1);
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print $left_read->toString() . "\n";
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print $right_read->toString() . "\n";
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return;
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}
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