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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 Data::Dumper;
my $usage = "usage: $0 file.sam\n\n";
my $sam_file = $ARGV[0] or die $usage;
main: {
my $sam_reader = new SAM_reader($sam_file);
print "chr1\tcoord1\tstrand1\tchr2\tcoord2\tstrand2\n";
my @entries;
my $curr_read_name = "";
while (my $sam_entry = $sam_reader->get_next()) {
my $core_read_name = $sam_entry->get_core_read_name();
if ($core_read_name ne $curr_read_name) {
if (scalar(@entries) > 1) {
&process_entries(@entries);
}
@entries = ();
}
$curr_read_name = $core_read_name;
push (@entries, $sam_entry);
}
# get last ones
if (scalar(@entries) > 1) {
&process_entries(@entries);
}
exit(0);
}
####
sub process_entries {
my @entries = @_;
my @left_entries;
my @right_entries;
foreach my $entry (@entries) {
if ($entry->get_scaffold_name() eq "*") { next; } # unaligned read
if ($entry->is_first_in_pair()) {
push (@left_entries, $entry);
}
elsif ($entry->is_second_in_pair()) {
push (@right_entries, $entry);
}
else {
die "Error, not left or right seq of pair: " . Dumper($entry);
}
}
if (scalar(@left_entries) > 1 || scalar(@right_entries) > 1) {
print STDERR "Error, should only have single read mappings, but have more than one:"
. Dumper(\@left_entries) . Dumper(\@right_entries);
return;
}
if (scalar(@left_entries) == 1 && scalar(@right_entries) == 1) {
## all good.
my $left_entry = $left_entries[0];
my $right_entry = $right_entries[0];
# "chr1\tcoord1\tstrand1\tchr2\tcoord2\tstrand2\n";
print join("\t",
$left_entry->get_scaffold_name(), $left_entry->get_scaffold_position(), $left_entry->get_query_strand(),
$right_entry->get_scaffold_name(), $right_entry->get_scaffold_position(), $right_entry->get_query_strand())
. "\n";
}
return;
}
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