From afdbc56e71488d2cf662d3679556a8419883100b Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Thu, 18 Dec 2014 10:31:13 +0000
Subject: [PATCH 1/2] Stopping redefined subroutine warnings.

Perl 5.16 and upwards did a lot of undefined subroutine warnings which
really clutter up output. I moved the functions into a single XS package
and had TabixIterator use the Tabix XS module directly. It probably
isn't the best solution but it does stop the problem.
---
 .gitignore            | 58 +++++++++++++++++++++++++++++++++++++++++++
 perl/Tabix.pm         | 30 ++++++++++++++++++++--
 perl/Tabix.xs         |  2 --
 perl/TabixIterator.pm | 41 ------------------------------
 4 files changed, 86 insertions(+), 45 deletions(-)
 create mode 100644 .gitignore
 delete mode 100644 perl/TabixIterator.pm

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..98a26d4
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,58 @@
+#### General stuff
+/tabix
+/bgzip
+/perl/Tabix*.c
+
+#### C stuff
+# Object files
+*.o
+*.ko
+*.obj
+*.elf
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Libraries
+*.lib
+*.a
+*.la
+*.lo
+
+# Shared objects (inc. Windows DLLs)
+*.dll
+*.so
+*.so.*
+*.dylib
+
+# Executables
+*.exe
+*.out
+*.app
+*.i*86
+*.x86_64
+*.hex
+
+#### Perl stuff
+/perl/blib/
+/perl/.build/
+/perl/_build/
+/perl/cover_db/
+/perl/inc/
+/perl/Build
+/perl/!Build/
+/perl/Build.bat
+/perl/.last_cover_stats
+/perl/Makefile
+/perl/Makefile.old
+/perl/MANIFEST.bak
+/perl/META.yml
+/perl/META.json
+/perl/MYMETA.*
+nytprof.out
+/perl/pm_to_blib
+*.o
+*.bs
+
+/.perl-version
diff --git a/perl/Tabix.pm b/perl/Tabix.pm
index fd7165d..e5aa4e2 100644
--- a/perl/Tabix.pm
+++ b/perl/Tabix.pm
@@ -4,8 +4,6 @@ use strict;
 use warnings;
 use Carp qw/croak/;
 
-use TabixIterator;
-
 require Exporter;
 
 our @ISA = qw/Exporter/;
@@ -72,5 +70,33 @@ sub getnames {
   return tabix_getnames($self->{_});
 }
 
+package TabixIterator;
+
+use strict;
+use warnings;
+
+sub new {
+  my $invocant = shift;
+  my $class = ref($invocant) || $invocant;
+  my $self = {};
+  bless($self, $class);
+  return $self;
+}
+
+sub set {
+  my ($self, $iter) = @_;
+  $self->{_} = $iter;
+}
+
+sub get {
+  my $self = shift;
+  return $self->{_};
+}
+
+sub DESTROY {
+  my $self = shift;
+  Tabix::tabix_iter_free($self->{_}) if ($self->{_});
+}
+
 1;
 __END__
diff --git a/perl/Tabix.xs b/perl/Tabix.xs
index 50dabb1..b18134d 100644
--- a/perl/Tabix.xs
+++ b/perl/Tabix.xs
@@ -62,8 +62,6 @@ tabix_getnames(t)
 		XPUSHs(sv_2mortal(newSVpv(names[i], 0)));
 	free(names);
 
-MODULE = Tabix PACKAGE = TabixIterator
-
 void
 tabix_iter_free(iter)
 	ti_iter_t iter
diff --git a/perl/TabixIterator.pm b/perl/TabixIterator.pm
deleted file mode 100644
index 335194a..0000000
--- a/perl/TabixIterator.pm
+++ /dev/null
@@ -1,41 +0,0 @@
-package TabixIterator;
-
-use strict;
-use warnings;
-use Carp qw/croak/;
-
-require Exporter;
-
-our @ISA = qw/Exporter/;
-our @EXPORT = qw/tabix_iter_free/;
-
-our $VERSION = '0.2.0';
-
-require XSLoader;
-XSLoader::load('Tabix', $VERSION);
-
-sub new {
-  my $invocant = shift;
-  my $class = ref($invocant) || $invocant;
-  my $self = {};
-  bless($self, $class);
-  return $self;
-}
-
-sub set {
-  my ($self, $iter) = @_;
-  $self->{_} = $iter;
-}
-
-sub get {
-  my $self = shift;
-  return $self->{_};
-}
-
-sub DESTROY {
-  my $self = shift;
-  tabix_iter_free($self->{_}) if ($self->{_});
-}
-
-1;
-__END__

From 1db5ef6669a9a9e98cee726bab8983bc0e3ce3bb Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Fri, 19 Dec 2014 12:00:42 +0000
Subject: [PATCH 2/2] TabixIterator.pm has gone so removed from MANIFEST

---
 perl/MANIFEST | 1 -
 1 file changed, 1 deletion(-)

diff --git a/perl/MANIFEST b/perl/MANIFEST
index 877da96..b27d9e2 100644
--- a/perl/MANIFEST
+++ b/perl/MANIFEST
@@ -2,7 +2,6 @@ MANIFEST
 typemap
 Tabix.xs
 Tabix.pm
-TabixIterator.pm
 Makefile.PL
 t/01local.t
 t/02remote.t
\ No newline at end of file