20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,98 @@
+package SAM_reader;
+
+use strict;
+use warnings;
+use Carp;
+
+use SAM_entry;
+
+sub new {
+	my $packagename = shift;
+	my $filename = shift; 
+
+	unless ($filename) {
+		confess "Error, need SAM filename as parameter";
+	}
+	
+	my $self = { filename => $filename,
+				 _next => undef,
+				 _fh =>  undef,
+	};
+
+	bless ($self, $packagename);
+
+	$self->_init();
+
+	return($self);
+}
+
+
+####
+sub _init {
+	my ($self) = @_;
+
+	open ($self->{_fh}, $self->{filename}) or confess "Error, cannot open file " . $self->{filename};
+	
+	$self->_advance();
+
+	return;
+}
+
+####
+sub _advance {
+	my ($self) = @_;
+
+	my $fh = $self->{_fh};
+
+	my $next_line = <$fh>;
+	
+	if ($next_line) {
+		$self->{_next} = new SAM_entry($next_line);
+	}
+	else {
+		$self->{_next} = undef;
+	}
+	
+	return;
+}
+
+####
+sub has_next {
+	my $self = shift;
+	
+	if (defined $self->{_next}) {
+		return(1);
+	}
+	else {
+		return(0);
+	}
+}
+
+
+####
+sub get_next {
+	my $self = shift;
+	
+	my $next_entry = $self->{_next};
+
+	$self->_advance();
+	
+	if (defined $next_entry) {
+		return($next_entry);
+	}
+	else {
+		return(undef);
+	}
+}
+
+####
+sub preview_next {
+	my $self = shift;
+	return($self->{_next});
+}
+
+
+1;
+
+	
+