20251125

99.scripts/trinity_utils/PerlLib/KmerGraphLib/ReadTracker.pm

@@ -0,0 +1,67 @@
+package ReadTracker;
+
+use strict;
+use warnings;
+use Carp;
+use ReadManager;
+
+
+sub new {
+	my ($packagename) = shift;
+	
+	
+	my $self = { reads => {}, # read indices, use ReadManager to hold full acc strings.
+
+	};
+
+	bless ($self, $packagename);
+
+	return($self);
+}
+
+sub track_reads {
+	my $self = shift;
+	my @reads = @_;
+
+	foreach my $read (@reads) {
+		my $index = &ReadManager::get_read_index($read);
+		$self->{reads}->{$index}++;
+	}
+
+	return;
+}
+
+sub append_to_ReadTracker {
+	my $self = shift;
+	my $to_add_ReadTracker = shift;
+
+	foreach my $read_index (keys %{$to_add_ReadTracker->{reads}}) {
+		$self->{reads}->{$read_index} += $to_add_ReadTracker->{reads}->{$read_index};
+	}
+	
+	return;
+}
+
+sub get_tracked_read_indices {
+	my $self = shift;
+
+	return(keys %{$self->{reads}});
+}
+
+sub get_read_base_count {
+	my $self = shift;
+	my $read = shift;
+
+	unless (defined $self->{reads}->{$read}) {
+		confess "Error, no read index stored [$read] ";
+	}
+
+	return($self->{reads}->{$read});
+}
+
+	
+
+1; #EOM
+
+	
+