Imported Upstream version 0.2.0

[tabix.git] / perl / Tabix.pm

diff --git a/perl/Tabix.pm b/perl/Tabix.pm
new file mode 100644 (file)
index 0000000..fd7165d
--- /dev/null
+++ b/perl/Tabix.pm
@@ -0,0 +1,76 @@
+package Tabix;
+
+use strict;
+use warnings;
+use Carp qw/croak/;
+
+use TabixIterator;
+
+require Exporter;
+
+our @ISA = qw/Exporter/;
+our @EXPORT = qw/tabix_open tabix_close tabix_read tabix_query tabix_getnames tabix_iter_free/;
+
+our $VERSION = '0.2.0';
+
+require XSLoader;
+XSLoader::load('Tabix', $VERSION);
+
+sub new {
+  my $invocant = shift;
+  my %args = @_;
+  $args{-data} || croak("-data argument required");
+  my $class = ref($invocant) || $invocant;
+  my $self = {};
+  bless($self, $class);
+  $self->open($args{-data}, $args{-index});
+  return $self;
+}
+
+sub open {
+  my ($self, $fn, $fnidx) = @_;
+  $self->close;
+  $self->{_fn} = $fn;
+  $self->{_fnidx} = $fnidx;
+  $self->{_} = $fnidx? tabix_open($fn, $fnidx) : tabix_open($fn);
+}
+
+sub close {
+  my $self = shift;
+  if ($self->{_}) {
+       tabix_close($self->{_});
+       delete($self->{_}); delete($self->{_fn}); delete($self->{_fnidx});
+  }
+}
+
+sub DESTROY {
+  my $self = shift;
+  $self->close;
+}
+
+sub query {
+  my $self = shift;
+  my $iter;
+  if (@_) {
+       $iter = tabix_query($self->{_}, @_);
+  } else {
+       $iter = tabix_query($self->{_});
+  }
+  my $i = TabixIterator->new;
+  $i->set($iter);
+  return $i;
+}
+
+sub read {
+  my $self = shift;
+  my $iter = shift;
+  return tabix_read($self->{_}, $iter->get);
+}
+
+sub getnames {
+  my $self = shift;
+  return tabix_getnames($self->{_});
+}
+
+1;
+__END__