debian/patches/non_lexical_loop_iterator.patch

+Description: Make sure that iterator variable is explicitely decalred as
+ a lexcical using my keyword. See PBP, page 108.  Add perl shebang.
+From: Alex Mestiashvili <amestia@rsh2.donotuse.de>
+--- gff2aplot.orig/src/gff2aplot.pl
++++ gff2aplot/src/gff2aplot.pl
+@@ -1,3 +1,4 @@
++#!/usr/bin/perl
+ #
+ # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ # %                          GFF2APLOT                               %
+@@ -1663,7 +1664,7 @@
+             &report( 'NO_CUSTOM_FOUND', $file );
+             last MAIN;
+         };
+-        LOAD: foreach $file (@custom_files) {
++        LOAD: foreach my $file (@custom_files) {
+             open( THIS, "< $file" )
+               || ( &warn( 'FILE_NO_OPEN', $T, $file ), next LOAD );
+             &report( 'READ_CUSTOM_FILE', $file );
+@@ -1934,7 +1935,7 @@
+ 
+ sub parse_GFF_files() {
+     &header("PARSING INPUT GFF RECORDS");
+-    LOAD: foreach $file (@data_files) {
++    LOAD: foreach my $file (@data_files) {
+         open( THIS, "< $file" )
+           || ( &warn( 'FILE_NO_OPEN', $T, $file ), next LOAD );
+         $file eq '-' && ( $file = 'STANDARD INPUT' );
+@@ -2665,13 +2666,13 @@
+     my ( $out, $v );
+     $out = 0;    #
+                  # print STDERR ("#"x40)."\n";
+-    foreach $v (qw/ FEATURE GROUP STRAND SOURCE SEQUENCE /) {
++    foreach my $v (qw/ FEATURE GROUP STRAND SOURCE SEQUENCE /) {
+ 
+         # print STDERR "### GET LAYER: $v ($name) : ".
+ #              (defined($Defaults{$v}{$name})?$Defaults{$v}{$name}:"undef")."\n";
+         defined( $Defaults{$v}{$name} ) && ( $out = $Defaults{$v}{$name} );
+     };    # foreach
+-    foreach $v (@refs) {
++    foreach my $v (@refs) {
+ 
+         # print STDERR "### GET LAYER: $v ($name) : ".
+         #              (defined($v->{$name})?$v->{$name}:"undef")."\n";
+@@ -3002,7 +3003,7 @@
+ 
+     #
+     ( $sq_a, $sq_b ) = @$_ra;
+-    foreach $naln (@$_ro) {
++    foreach my $naln (@$_ro) {
+         ( $nm_a, $nm_b ) = split /:/o, $naln->[0], 2;
+         ( "$nm_a" eq "$sq_a" && "$nm_b" eq "$sq_b" ) && do {
+             @$_ra = ( $nm_a, $nm_b );
+@@ -3010,7 +3011,7 @@
+         };
+     };    # foreach $naln
+           # swapping
+-    foreach $naln (@$_ro) {
++    foreach my $naln (@$_ro) {
+         ( $nm_a, $nm_b ) = split /:/o, $naln->[0], 2;
+         ( "$nm_a" eq "$sq_b" && "$nm_b" eq "$sq_a" ) && do {
+             @$_ra = ( $nm_a, $nm_b );
+@@ -3024,7 +3025,7 @@
+ sub search_seqname() {
+     my ( $sq_a, $sq_b, $_ro ) = @_;
+     my ( $a_found, $naln );
+-    foreach $naln (@$_ro) {
++    foreach my $naln (@$_ro) {
+         ( $sq_a eq '.+' && defined($sq_b) && "$naln->[0]" eq "$sq_b" ) && next;
+         ( $sq_a eq '.+' || "$naln->[0]" eq "$sq_a" ) && do {
+             $sq_a = $naln->[0];
+@@ -4279,13 +4280,13 @@
+     my ( $out,  $v );
+ 
+     # print STDERR ("#"x40)."\n";
+-    foreach $v (qw/ FEATURE GROUP STRAND SOURCE SEQUENCE /) {
++    foreach my $v (qw/ FEATURE GROUP STRAND SOURCE SEQUENCE /) {
+         defined( $Defaults{$v}{$name} ) && ( $out = $Defaults{$v}{$name} );
+ 
+         # print STDERR "### GET VAR VALUE: $v ($name) : ".
+ #              (defined($Defaults{$v}{$name})?$Defaults{$v}{$name}:"undef")."\n";
+     };    # foreach
+-    foreach $v (@$refs) {
++    foreach my $v (@$refs) {
+         defined( $v->[$_prop]{$name} ) && ( $out = $v->[$_prop]{$name} );
+ 
+         # print STDERR "### GET VAR VALUE: $v ($name) : ".

debian/patches/perl_5.28.patch

@@ -2,18 +2,20 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Mon, 10 Dec 2018 07:36:57 +0100
 Description: Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/bin/gff2aplot line 1737.
 
---- a/src/gff2aplot.pl
-+++ b/src/gff2aplot.pl
-@@ -1733,7 +1734,7 @@ sub varscheck() {
+--- gff2aplot.orig/src/gff2aplot.pl
++++ gff2aplot/src/gff2aplot.pl
+@@ -1734,8 +1734,8 @@
        || return $F;
      $flag && do {
          my @tmpary = ();
 -        defined( @{ $varec->{$class}{ $$rec[1] } } ) || do {
-+        @{ $varec->{$class}{ $$rec[1] } } || do {
-             @{ $varec->{$class}{ $$rec[1] } } = ();
+-            @{ $varec->{$class}{ $$rec[1] } } = ();
++        eval {exists $varec->{$class}{ $$rec[1] }} || do {
++          @{ $varec->{$class}{ $$rec[1] } } = ();
          };
          @tmpary = &find_regexp( $$rec[0] );
-@@ -2930,7 +2931,8 @@ sub set_page_axes() {
+         $tmpary[3] = lc( $tmpary[3] ) if ( $class eq 'FEATURE' );
+@@ -2931,7 +2931,8 @@
          ( $vrf->{_x_sequence_name}, $vrf->{_y_sequence_name} ) = split /:/o,
            $vrf->{alignment_name}, 2;
      }
@@ -23,7 +25,7 @@ Description: Can't use 'defined(@array)' (Maybe you should just omit the defined
          ( $vrf->{_x_sequence_name}, $vrf->{_y_sequence_name} ) = split /:/o,
            $Order{ALN}[0][0], 2;
      }
-@@ -3730,7 +3732,11 @@ sub fill_mid() {
+@@ -3731,7 +3732,11 @@
  
  sub counter {    # $_[0]~current_pos++ $_[1]~char
      my $str;

debian/patches/series

+non_lexical_loop_iterator.patch
 02-blat2gff.diff
 03-parseblast.diff
 use-dpkg-buildflags.patch