Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Description: Bio::Variation::SNP is unmaintained and no longer released

So remove references to it
--- libbio-cluster-perl.orig/lib/Bio/ClusterIO/dbsnp.pm
+++ libbio-cluster-perl/lib/Bio/ClusterIO/dbsnp.pm
@@ -65,7 +65,6 @@
 $Bio::ClusterIO::dbsnp::VERSION = '1.7.3';
 use strict;
 use Bio::Root::Root;
-use Bio::Variation::SNP;
 use XML::SAX;
 use Data::Dumper;
 use IO::File;
@@ -167,108 +166,8 @@
   $DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0);
 }
 
-=head2 next_cluster
-
- Title   : next_cluster
- Usage   : $dbsnp = $stream->next_cluster()
- Function: returns the next refSNP in the stream
- Returns : Bio::Variation::SNP object representing composite refSNP
-           and its component subSNP(s).
- Args    : NONE
-
-=cut
-
-###
-#Adapted from Jason's blastxml.pm
-###
-
-# you shouldn't have to preparse this; the XML is well-formed and refers
-# accurately to a remote DTD/schema
-
-sub next_cluster {
-  my $self = shift;
-  my $data = '';
-  my($tfh);
-
-  if( $self->use_tempfile ) {
-	$tfh = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!");
-	$tfh->autoflush(1);
-  }
-
-  my $start = 1;
-  while( defined( $_ = $self->_readline ) ){
-	#skip to beginning of refSNP entry
-	if($_ !~ m{<Rs[^>]*>} && $start){
-	  next;
-	} elsif($_ =~ m{<Rs[^>]*>} && $start){
-	  $start = 0;
-	} 
-
-	#slurp up the data
-	if( defined $tfh ) {
-	  print $tfh $_;
-	} else {
-	  $data .= $_;
-	}
-
-	#and stop at the end of the refSNP entry
-	last if $_ =~ m{</Rs>};
-  }
-
-  #if we didn't find a start tag
-  return if $start;
-
-  my %parser_args;
-  if( defined $tfh ) {
-	seek($tfh,0,0);
-	%parser_args = ('Source' => { 'ByteStream' => $tfh },
-					'Handler' => $self);
-  } else {
-	%parser_args = ('Source' => { 'String' => $data },
-					'Handler' => $self);
-  }
-
-  my $starttime;
-  my $result;
-
-  if(  $DEBUG ) {  $starttime = [ Time::HiRes::gettimeofday() ]; }
-
-  eval {
-	$result = $self->{'_xmlparser'}->parse(%parser_args);
-  };
-
-  if( $@ ) {
-	$self->warn("error in parsing a report:\n $@");
-	$result = undef;
-  }
-
-  if( $DEBUG ) {
-	$self->debug( sprintf("parsing took %f seconds\n", Time::HiRes::tv_interval($starttime)));
-  }
-
-  return $self->refsnp;
-}
-
 =head2 SAX methods
 
-=cut
-
-=head2 start_document
-
- Title   : start_document
- Usage   : $parser->start_document;
- Function: SAX method to indicate starting to parse a new document.
-           Creates a Bio::Variation::SNP
- Returns : none
- Args    : none
-
-=cut
-
-sub start_document{
-  my ($self) = @_;
-  $self->{refsnp} = Bio::Variation::SNP->new;
-}
-
 sub refsnp {
   return shift->{refsnp};
 }
--- libbio-cluster-perl.orig/META.json
+++ libbio-cluster-perl/META.json
@@ -46,7 +46,6 @@
             "Bio::Root::RootI" : "0",
             "Bio::Seq::SeqFactory" : "0",
             "Bio::Species" : "0",
-            "Bio::Variation::SNP" : "0",
             "Data::Dumper" : "0",
             "IO::File" : "0",
             "Time::HiRes" : "0",
--- libbio-cluster-perl.orig/META.yml
+++ libbio-cluster-perl/META.yml
@@ -39,7 +39,6 @@
   Bio::Root::RootI: '0'
   Bio::Seq::SeqFactory: '0'
   Bio::Species: '0'
-  Bio::Variation::SNP: '0'
   Data::Dumper: '0'
   IO::File: '0'
   Time::HiRes: '0'
--- libbio-cluster-perl.orig/Makefile.PL
+++ libbio-cluster-perl/Makefile.PL
@@ -30,7 +30,6 @@
     "Bio::Root::RootI" => 0,
     "Bio::Seq::SeqFactory" => 0,
     "Bio::Species" => 0,
-    "Bio::Variation::SNP" => 0,
     "Data::Dumper" => 0,
     "IO::File" => 0,
     "Time::HiRes" => 0,
@@ -69,7 +68,6 @@
   "Bio::Root::Test" => 0,
   "Bio::Seq::SeqFactory" => 0,
   "Bio::Species" => 0,
-  "Bio::Variation::SNP" => 0,
   "Data::Dumper" => 0,
   "File::Spec" => 0,
   "IO::File" => 0,
--- libbio-cluster-perl.orig/t/ClusterIO.t
+++ libbio-cluster-perl/t/ClusterIO.t
@@ -7,7 +7,7 @@
     use lib '.';
 	use Bio::Root::Test;
 	
-	test_begin(-tests => 12,
+	test_begin(-tests => 4,
 			   -requires_module => 'Time::HiRes');
     
 	use_ok('Bio::ClusterIO');
@@ -22,16 +22,16 @@
 					'-format' => 'dbsnp',
 					'-file'   => test_input_file('LittleChrY.dbsnp.xml'));
     
-	$result = $clusterio->next_cluster;
-	ok($result);
-	is($result->observed, 'C/T');
-	is($result->type, 'notwithdrawn');
-	ok($result->seq_5);
-	ok($result->seq_3);
-	my @ss = $result->each_subsnp;
-	is scalar @ss,  5;
-	is($ss[0]->handle, 'CGAP-GAI');
-	is($ss[1]->handle, 'LEE');
+	# $result = $clusterio->next_cluster;
+	# ok($result);
+	# is($result->observed, 'C/T');
+	# is($result->type, 'notwithdrawn');
+	# ok($result->seq_5);
+	# ok($result->seq_3);
+	# my @ss = $result->each_subsnp;
+	# is scalar @ss,  5;
+	# is($ss[0]->handle, 'CGAP-GAI');
+	# is($ss[1]->handle, 'LEE');
 	
 	# don't know if these were ever meant to work... cjf 3/7/07
 	#is($result->heterozygous, 0.208738461136818);
