Merge pull request #119 from Ensembl/Feature/BCFLocation

Feature/bcf location

modules/Bio/EnsEMBL/IO/Parser/BCF.pm

@@ -34,7 +34,7 @@ use warnings;
 use Carp;
 use Bio::DB::HTS::VCF;
 use Bio::DB::HTS::VCF::Iterator;
-
+use Cwd qw(getcwd);
 use parent qw/Bio::EnsEMBL::IO::Parser/;
 
 sub open {
@@ -51,6 +51,21 @@ sub open {
   return $self;
 }
 
+sub open_with_location {
+  my ($caller, $filename, $location, @other_args) = @_;
+  my $class = ref($caller) || $caller;
+
+  # initialize generic parser
+  my $self = $class->SUPER::new(@other_args);
+  my $currentDir = getcwd();
+  chdir($location);
+  $self->{record} = undef;
+  $self->{bcf_file} = Bio::DB::HTS::VCF->new( filename => $filename );
+  $self->{iterator} = undef;
+  chdir($currentDir);
+  return $self;
+}
+
 sub seek {
   my ($self, $chrom, $start, $end) = @_;
 

modules/t/bcf.t

@@ -17,6 +17,7 @@ use warnings;
 
 use Test::More;
 use Bio::EnsEMBL::IO::Parser::BCF;
+use Cwd qw(getcwd);
 
 use FindBin qw( $Bin );
 
@@ -26,6 +27,14 @@ my $test_file = $Bin . '/input/test.bcf';
 ok (my $parser = Bio::EnsEMBL::IO::Parser::BCF->open($test_file), "BCF file open");
 is ($parser->num_variants(), 9, 'correct number of variants identified in file');
 
+#test open with $location
+my $currentDir = getcwd();
+chdir('/');
+ok ($parser = Bio::EnsEMBL::IO::Parser::BCF->open($test_file, $currentDir), "BCF file open with location");
+is ($parser->num_variants(), 9, 'correct number of variants identified in file');
+chdir($currentDir);
+
+
 ok (my $h = $parser->header(), "Got header");
 my $header_str = <<HEADER;
 ##fileformat=VCFv4.0