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#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use SAM_reader;
use SAM_entry;
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);
while (my $sam_entry = $sam_reader->get_next()) {
my ($genome_coords_aref, $read_coords_aref) = $sam_entry->get_alignment_coords();
my $read_name = $sam_entry->get_read_name();
my $scaffold = $sam_entry->get_scaffold_name();
print join("\t", $scaffold, &get_coord_string($genome_coords_aref),
$read_name, &get_coord_string($read_coords_aref)) . "\n";
}
exit(0);
}
####
sub get_coord_string {
my ($coords_aref) = @_;
my $text = "";
foreach my $coordset (@$coords_aref) {
my ($lend, $rend) = @$coordset;
if ($text) {
$text .= ",";
}
$text .= "$lend-$rend";
}
return($text);
}
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