"Options:\n",
" -r, --refseq <file.fa> The reference sequence, required when indels are present.\n",
" -s, --snps-only Ignore indels.\n",
+ " -t, --column-title <string> The column title.\n",
" -h, -?, --help This help message.\n",
"\n";
}
while (my $arg=shift(@ARGV))
{
if ( $arg eq '-r' || $arg eq '--refseq' ) { $opts{refseq}=shift(@ARGV); next; }
+ if ( $arg eq '-t' || $arg eq '--column-title' ) { $opts{title}=shift(@ARGV); next; }
if ( $arg eq '-s' || $arg eq '--snps-only' ) { $opts{snps_only}=1; next; }
if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
my ($prev_chr,$prev_pos,$prev_ref);
my $refseq;
my $ignore_indels = $$opts{snps_only} ? 1 : 0;
+ my $title = exists($$opts{title}) ? $$opts{title} : 'data';
print $fh_out
qq[##fileformat=VCFv3.3\n],
qq[##FORMAT=GT,1,String,"Genotype"\n],
qq[##FORMAT=GQ,1,Integer,"Genotype Quality"\n],
qq[##FORMAT=DP,1,Integer,"Read Depth"\n],
- qq[#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tdata\n]
+ qq[#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t$title\n]
;
while (my $line=<$fh_in>)