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package SAM_to_AlignGraph;
## Static class
use strict;
use warnings;
use AlignGraph;
use Carp;
use SAM_reader;
use SAM_entry;
sub construct_AlignGraph {
my ($sam_file) = @_;
my $graph = new AlignGraph();
my $sam_reader = new SAM_reader($sam_file);
my $counter = 0;
while ($sam_reader->has_next()) {
$counter++;
print STDERR "\r[$counter] " if $counter % 100 == 0;
my $sam_entry = $sam_reader->get_next();
my $scaff = $sam_entry->get_scaffold_name();
my $read_acc = $sam_entry->get_read_name();
if ($sam_entry->is_query_unmapped()) { next; }
my $query_strand = $sam_entry->get_query_transcribed_strand();
my ($genome_coords_aref, $query_coords_aref) = $sam_entry->get_alignment_coords();
$graph->add_alignment($read_acc, $scaff, $query_strand, $genome_coords_aref);
}
return($graph);
}
1; #EOM
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