cgp-cavemanwrapper-fix-script.patch

diff -crB cgpCaVEManWrapper-1.15.2-orig/bin/caveman_merge_results.pl cgpCaVEManWrapper-1.15.2/bin/caveman_merge_results.pl
*** cgpCaVEManWrapper-1.15.2-orig/bin/caveman_merge_results.pl	2020-01-17 08:25:27.822179647 +0100
--- cgpCaVEManWrapper-1.15.2/bin/caveman_merge_results.pl	2020-01-17 08:26:26.735045998 +0100
***************
*** 41,47 ****
  {
    my $options = setup();
    merge_vcf($options->{'out'}.'.snps', $options->{'snp_vcf'});
!   merge_vcf($options->{'out'}.'.subs', $options->{'sub_vcf'});
    merge_bed($options->{'out'}.'.no_analysis', $options->{'na_bed'});
  }
  
--- 41,47 ----
  {
    my $options = setup();
    merge_vcf($options->{'out'}.'.snps', $options->{'snp_vcf'});
!   merge_vcf($options->{'out'}.'.muts', $options->{'mut_vcf'});
    merge_bed($options->{'out'}.'.no_analysis', $options->{'na_bed'});
  }
  
***************
*** 66,72 ****
  	my ($path_prefix, $bed_files) = @_;
    my $new_bed = $path_prefix.'.bed';
    my $new_tmp_bed = $path_prefix.'.tmp.bed';
!   system(qq{grep '^#' $bed_files->[0] > $new_tmp_bed});
    system(qq{cat @{$bed_files} | grep -v '^#' | sort -k1,1 -k2,2n >> $new_tmp_bed});
  
  	#Now merge the bed file with bedtools merge so we have a much smaller output file.
--- 66,72 ----
  	my ($path_prefix, $bed_files) = @_;
    my $new_bed = $path_prefix.'.bed';
    my $new_tmp_bed = $path_prefix.'.tmp.bed';
! #  system(qq{grep '^#' $bed_files->[0] > $new_tmp_bed});
    system(qq{cat @{$bed_files} | grep -v '^#' | sort -k1,1 -k2,2n >> $new_tmp_bed});
  
  	#Now merge the bed file with bedtools merge so we have a much smaller output file.
***************
*** 103,109 ****
      if($file =~ m/\.snps\.vcf$/) {
        push @{$opts{'snp_vcf'}}, $file;
      }elsif($file =~ m/\.muts\.vcf$/){
!     	push @{$opts{'snp_vcf'}}, $file;
      }
      elsif($file =~ m/\.no_analysis\.bed$/) {
        push @{$opts{'na_bed'}}, $file;
--- 103,109 ----
      if($file =~ m/\.snps\.vcf$/) {
        push @{$opts{'snp_vcf'}}, $file;
      }elsif($file =~ m/\.muts\.vcf$/){
!     	push @{$opts{'mut_vcf'}}, $file;
      }
      elsif($file =~ m/\.no_analysis\.bed$/) {
        push @{$opts{'na_bed'}}, $file;