#!/usr/bin/env perl

=begin
generates vep input file from myseq vcf src files for single myseq run
=cut

BEGIN {
	use lib '/home/raj/perl5/lib/perl5'; # ensure FindBin from local-lib
 	use FindBin; # warn $FindBin::Bin; exit;
    use lib (
        $FindBin::Bin . '/../../lib',
        $FindBin::Bin . '/../..', # for ngs.sqlite db
    );
}
    
use Data::Dumper::Concise;
use Modern::Perl '2012';
use IO::All;
use NGS::DB;

my $db = NGS::DB->new(); # warn $db->dbix;
my $gene_strand = $db->dbix->select('gene_strand', [qw/gene_name strand/])->map;
my $hotspots = $db->dbix->select('hotspots', ['position', 1])->map;
    # warn Dumper [$hotspots, $gene_strand]; exit;

my $src_dir = $FindBin::Bin . '/src';
my @dirs = io($src_dir)->all; # print "$_ is a " . $_->type . "\n" for @dirs;
    
my $a = my $b = 0;

my %samples;
# collect filenames from each dir, add to %samples hash:
for my $d (@dirs) { # warn Dumper $_;
    next unless $d->type eq 'dir'; # skip eg png's
	my @files = io($d)->all; # Dumper \@files;  
	for my $f (@files) { # warn $f->filename;
		my $filename = $f->filename;
		next unless $filename =~ /vcf\Z/; # warn $f->filename;
		push @{ $samples{$filename} }, $f; # io object
	}
} # warn Dumper keys %samples; exit;

my @vep;

FILE:
while ( my($sample, $o) = each %samples ) {
	# parse file content in each directory:
	for my $f(@$o) { # warn $f->name;
		my $data = parse($f); # warn Dumper $data; # arrayref
        push @vep, @$data;
	}  warn Dumper @vep;
}

warn $a;
warn $b;

sub parse {
	my $f = shift; # io object
    
	my @folders = $f->splitdir; # warn $folders[-2]; # array of dirs in full path
	my @lines   = io($f->name)->slurp; # warn Dumper \@lines;
    
	my @data = ();

	LINE: for (@lines) {
		next LINE if /^#/; # skip comments
		my @fields = split "\t", $_;
		
		my $start_pos = $fields[1] || next LINE; # warn $start_pos;
        {
            my $vals = _parse_fields(\@fields) || next LINE; # hashref
            # add sample name:
            $vals->{sample} = $folders[-1]; # warn $folders[-1];
            push @data, $vals;
        }
	}    
    return \@data;
}

sub _parse_fields {
    my $data = shift; # arrayref of tab-separated vcf row entries

	my $chr     = $data->[0]; # warn $chr;
    my $pos     = $data->[1]; # warn $pos;
	my $ref     = $data->[3]; # warn $ref;
	my $alt     = $data->[4]; # warn $alt;
	my $filter  = $data->[6]; # warn $filter;
    my $info    = $data->[7]; # warn $info
	my $results = $data->[9]; # warn $results;

	my $vf = (split ':', $results)[3]; # warn $vf;
	my ($depth) = $info =~ /DP=(\d+)/; # warn $depth;
    my ($genes) = $info =~ /GI=(.*?)\;/; # warn $genes; # non-greedy match

    my ($chromosome) = $chr =~ /chr([\w\d]+)/; # warn Dumper [$chr, $chromosome];
    
    my @genes = do { # remove duplicate genes: eg TP53,TP53,TP53
        no warnings 'uninitialized'; # eg if regex failed due to malformed str
        my %seen = map { $_ => 1 } split ',', $genes;    
        keys %seen;
    } || warn 'no GI entry'; # warn @genes;
    
#$a++;     
    # skip unless VF > 5% cutoff or start position is a known hotspot:
    return 0 unless $vf > 0.05 || $hotspots->{$pos};
#$b++;    
    
    my $start_pos = my $end_pos = $pos;
    
    my $allele;
    # insertion:
    if ( length $alt > 1 ) {
        $start_pos += 1;
        my @bases = split //, $alt; # warn Dumper \@bases;
        shift @bases;
        $allele = sprintf '-/%s', join '', @bases; # warn Dumper [$alt,$allele];
    }
    # deletion:
    elsif ( length $ref > 1 ) {
        $start_pos += 1;
        $end_pos += ( (length $ref) - 1 );
        my @bases = split //, $ref; # warn Dumper \@bases;
        shift @bases;
        $allele = sprintf '%s/-', join '', @bases; # warn Dumper [$ref,$allele];
    } # warn Dumper [$pos,$alt,$ref,$start_pos,$end_pos];
    # substitution:
    $allele ||= sprintf '%s/%s', $ref, $alt; # warn $allele;
    
    my %h = (
        chromosome => $chromosome,
        start_pos  => $start_pos,
        end_pos    => $end_pos,
        allele     => $allele,
        strand     => '+', # don't need to use gene_strand table
    );
=begin # not splitting genes, not using gene_strand table
    GENE:
    for my $gene (@genes) {
        # + or - strand from gene_strand table:
        my $strand = $gene_strand->{$gene};
        unless ($strand) {
            warn "$gene not in gene_strand table";
            next GENE;
        } # warn Dumper [ $chromosome, $start_pos, $end_pos, $allele, $strand ];
        $h{strand} = $strand;
    }
=cut
    return \%h;
}