Commit 26b71c76 authored by Takadonet's avatar Takadonet

sort all keys function that output to a file and/or screen

parent 88411be4
......@@ -729,7 +729,7 @@ my $unique_count = 1;
my %name_map; # used to map sample name to other information
my %sample_map; # keeps track of which samples have which unique ids (so we can properly increment unique_count)
my %total_positions_map; # keep track of total positions, and if valid/not
for my $chromosome (keys %$vcf_data)
for my $chromosome ( sort {$a cmp $b } keys %$vcf_data)
my ($alignment,$total_positions) = variants_alignment($vcf_data->{$chromosome}, $chromosome, $reference, \@samples_list, $mpileup_data, $coverage_cutoff,$invalid_pos,$keep_ambiguous);
$total_positions_map{$chromosome} = $total_positions;
......@@ -835,7 +835,7 @@ print $vfh "#Chromosome\tPosition\tStatus\tReference\t";
my @samples_sorted_list = sort {$a cmp $b} @samples_list;
print $vfh join("\t",@samples_sorted_list);
print $vfh "\n";
for my $chr (keys %total_positions_map)
for my $chr (sort { $a cmp $b } keys %total_positions_map)
my $positions = $total_positions_map{$chr};
for my $pos (sort {$a <=> $b} keys %$positions)
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