Author: Steffen Moeller <steffen_moeller@gmx.de>
Description: Fixes a series of errors indicated by Perl 5.18.
Forwarded: https://sourceforge.net/p/perlprimer/patches/6/

Index: git/perlprimer.pl
===================================================================
--- git.orig/perlprimer.pl
+++ git/perlprimer.pl
@@ -3093,23 +3093,24 @@
 	# and because it's 3' primer-dimers that are the real problem in PCR.
 	
 	# create a binding array for each of the four bases
-	for $l (0 .. $pfl-1) {
+	foreach $l (0 .. $pfl-1) {
 		my $mbase = substr($fprimer_r, $l, 1);
 		$primer_hash{$mbase}[$l]=1;
-		for $k qw(a g c t) {
+		my @nucleotides = qw(a g c t);
+		foreach $k (@nucleotides) {
 			$primer_hash{$k}[$l] ||=0;
 		}
 	}
 		
 	# create the primer matrix
 	my @primer_comp;
-	for $k (0 .. $prl-1) {
+	foreach $k (0 .. $prl-1) {
 		$primer_comp[$k]=$primer_hash{substr($rcomprlc, $k, 1)};
 	}
 		
 	# read each combination from the matrix, calculate dG for each dimer
 	my $pd_len = ($pd_full ? $pfl+$prl-1 : $pl-2);
-	for $k (0 .. $pd_len) {
+	foreach $k (0 .. $pd_len) {
 		$score[$k]=0;
 		my $bind;
 		my $score_p=0;
@@ -3129,7 +3130,7 @@
 		# }
 		
 		# read the binding data
-		for $l (0 .. $prl-1) {
+		foreach $l (0 .. $prl-1) {
 			if (($k-$l)<$pfl) {
 				$bind .= $primer_comp[$l][$k-$l] if ($k-$l)>=0;
 			} else {
@@ -3148,7 +3149,7 @@
 		
 		# Find start and end of similarity
 		my ($pb_init,$pb_end);
-		for $l (0 .. length($bind)-1) {
+		foreach $l (0 .. length($bind)-1) {
 			# at first I tried finding the initiating terminal bases with
 			# regexps, but that was much slower ...
 			if (substr($bind, $l, 1) eq "1") {
@@ -3159,7 +3160,7 @@
 				
 		if (defined($pb_init)) {
 			# deltaG calculation
-			for $l ($pb_init .. $pb_end-1) {
+			foreach $l ($pb_init .. $pb_end-1) {
 				next if substr($bind, $l, 2) eq "00";
 				next if substr($bind, $l, 1) eq "2";
 				$score_p+=$oligo_dG{substr($primer_f, $pfl-$k+$l-1, 2).substr($rprimer_r, $l, 2)};
@@ -3228,44 +3229,44 @@
 	# and because it's 3' primer-dimers that are the real problem in PCR.
 	
 	# create a binding array for each of the four bases
-	for $l (0 .. $pfl-1) {
+	foreach $l (0 .. $pfl-1) {
 		my $mbase = substr($fprimer_r, $l, 1);
 		$primer_hash{$mbase}[$l]=1;
-		for $k qw(a g c t) {
+		foreach $k (qw(a g c t)) {
 			$primer_hash{$k}[$l] ||=0;
 		}
 	}
 		
 	# create the primer matrix
 	my @primer_comp;
-	for $k (0 .. $prl-1) {
-		$primer_comp[$k]=$primer_hash{substr($rcomprlc, $k, 1)};
+	foreach my $kk (0 .. $prl-1) {
+		$primer_comp[$kk]=$primer_hash{substr($rcomprlc, $kk, 1)};
 	}
 	
 	# print the matrix - for debugging
 	print "$primer_f vs. $primer_r - full pd = $pd_full\n";
 	print "  \t";
-	for $l (0 .. $pfl-1) {
+	foreach $l (0 .. $pfl-1) {
 		my $mbase = substr($fprimer_r, $l, 1);
 		print "$mbase ";
 	}
 	print "\n";
-	for $k (0 .. $prl-1) {
-		my $base = substr($rprimer_r, $k, 1);
-		print "$base:\t@{$primer_comp[$k]}\n";
+	foreach my $kk (0 .. $prl-1) {
+		my $base = substr($rprimer_r, $kk, 1);
+		print "$base:\t@{$primer_comp[$kk]}\n";
 	}
 	
 	my @binding_data;
 	# read each combination from the matrix, calculate dG for each dimer
 	my $pd_len = ($pd_full ? $pfl+$prl-1 : $pl-2);
-	for my $k (0 .. $pd_len) {
-		$score[$k]=0;
+	foreach my $kk (0 .. $pd_len) {
+		$score[$kk]=0;
 		my $bind;
 		my $score_p=0;
 		
 		# starting coords
-		my $pf_coord_start = ($k >= $pfl ? $pfl-1 : $k);
-		my $pr_coord_start = ($k - $pfl > 0 ? $k - $pfl : 0);
+		my $pf_coord_start = ($kk >= $pfl ? $pfl-1 : $kk);
+		my $pr_coord_start = ($kk - $pfl > 0 ? $kk - $pfl : 0);
 		my ($pf_coord, $pr_coord, $first, $flag);
 		
 		# read through each combination finding multiple matches
@@ -3285,7 +3286,7 @@
 				}
 			} elsif ($flag) {
 				# end of a binding stretch
-				push @binding_data, [$k, $first, $bind] if $bind > 1;
+				push @binding_data, [$kk, $first, $bind] if $bind > 1;
 				$bind=0;
 				$flag=0;
 			}
@@ -3325,7 +3326,7 @@
 		# # }
 				# 
 		# # read the binding data
-		# for $l (0 .. $prl-1) {
+		# foreach $l (0 .. $prl-1) {
 			# if (($k-$l)<$pfl) {
 				# $bind .= $primer_comp[$l][$k-$l] if ($k-$l)>=0;
 			# } else {
@@ -3344,7 +3345,7 @@
 		# 
 		# # Find start and end of similarity
 		# my ($pb_init,$pb_end);
-		# for $l (0 .. length($bind)-1) {
+		# foreach $l (0 .. length($bind)-1) {
 			# # at first I tried finding the initiating terminal bases with
 			# # regexps, but that was much slower ...
 			# if (substr($bind, $l, 1) eq "1") {
@@ -3355,7 +3356,7 @@
 				# 
 		# if (defined($pb_init)) {
 			# # deltaG calculation
-			# for $l ($pb_init .. $pb_end-1) {
+			# foreach $l ($pb_init .. $pb_end-1) {
 				# next if substr($bind, $l, 2) eq "00";
 				# next if substr($bind, $l, 1) eq "2";
 				# $score_p+=$oligo_dG{substr($primer_f, $pfl-$k+$l-1, 2).substr($rprimer_r, $l, 2)};