Added more information about SNP filtering and processing to the manual

SNPsplit_genome_preparation

@@ -35,7 +35,13 @@ my %snps; # storing all filtered SNPs
 my %snps_dual_genome; # storing all SNPs for dual genome
 
 my $snp_file_strain =   "all_SNPs_${strain}_GRCm38.txt.gz";
-my $snp_file_strain2 = "all_SNPs_${strain2}_GRCm38.txt.gz";
+my $snp_file_strain2;
+if ($strain2){
+    $snp_file_strain2 = "all_SNPs_${strain2}_GRCm38.txt.gz";
+}
+else{
+    $snp_file_strain2 = 'irrelevant_for_single_hybrid_mode';
+}
 my $new_ref_snp_annoations; # this will store the new Ref/SNP annotations for dual hybrids
 
 warn "Summarising SNPsplit Genome Preparation Parameters\n";
@@ -993,7 +999,7 @@ sub detect_strains{
 	my @strains = split (/\t/);
 
 	foreach my $index(0..$#strains){
-	    next if ($index <= 8); # The first 6 fields are irrelevant: #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  
+	    next if ($index <= 8); # The first 8 fields are irrelevant: #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  
 	    $strains{$strains[$index]} = $index; 
 	    # warn "$index\t$strains[$index]\n";
 	}

copy_SNPsplit_files_for_release.pl

@@ -0,0 +1,44 @@
+#!/usr/bin/perl
+use warnings;
+use strict;
+use File::Copy "cp";
+
+my $dir = shift@ARGV;
+
+die "Please provide a directory to copy files to!\n\n" unless ($dir);
+
+unless (-d $dir){
+  warn "Specified directory '$dir' doesn't exist. Creating it for you...\n\n";
+  mkdir $dir or die "Failed to create directory: $!\n\n";
+}
+
+my @files = ('RELEASE_NOTES.txt','SNPsplit','tag2sort','SNPsplit_User_Guide.pdf','license.txt','SNPsplit_genome_preparation');
+
+foreach my $file (@files){
+  copy_and_warn($file);
+}
+
+sub copy_and_warn{
+    my $file = shift;
+    warn "Now copying '$file' to $dir\n";
+    cp($file,"$dir/") or die "Copy failed: $!";
+
+}
+
+@files = ('SNPsplit','tag2sort','SNPsplit_genome_preparation');
+
+foreach my $file (@files){
+    set_permissions($file);
+}
+
+sub set_permissions{
+    my $file = shift;
+    warn "Setting permissions for ${dir}/$file\n";
+    chmod 0755, "${dir}/$file";
+}
+
+
+### Taring up the folder
+$dir =~ s/\/$//;
+warn "Tar command:\ntar czvf ${dir}.tar.gz $dir\n\n";
+system ("tar czvf ${dir}.tar.gz $dir/");