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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;
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