#!/usr/bin/perl

use warnings;
use strict;

use lib '/home/raj/perl5/lib/perl5';

use IO::All;
use FindBin; # warn $FindBin::Bin;
use Data::Dumper;

use lib $FindBin::Bin . '/../lib';
use ChartMaker;

my $src = $ARGV[0];

unless ($src) {
	print "need a vcf file identifier !!\n\n"; exit;
}

my $src_dir = $FindBin::Bin . '/vcf';

my @dirs = io($src_dir)->all; # print "$_ is a " . $_->type . "\n" for @dirs;
    
my %h; # start-position indexer

# data structure for chartdirector:
my %chart = ( data_title => $src );

# extract files from each dir, skip all except matching supplied filename:
for my $d (@dirs) { # warn Dumper $_;
    next unless $d->type eq 'dir';
	my @files = io($d)->all; # Dumper \@files;  
	for my $f (@files) { # warn $f->filename;
		next unless $f->filename =~ /^$src/; # warn $f->filename;
		parse($f->name);
	}
} # warn Dumper \%h; exit;

# printf "| %9s | %s |\n", $_, $h{$_}{count} for sort by_frequency keys %h;
# map { print Dumper $h{$_} }
#    grep { $h{$_}{count} == 1 }
#        sort by_start_pos keys %h;

my $format = "| %9s | %6s | %8s | %10s | %4s | %6s |\n";
my @dividr = ( '=' x 9, '=' x 6, '=' x 8, '=' x 10, '=' x 4, '=' x 6 );

printf $format, qw( START REF ALT FILTER DP VF );
printf $format, @dividr;

for my $location ( sort by_start_pos keys %h ) { # warn $location;
	next unless $h{$location}{count} == 1;
	my $data = $h{$location}{data}; # warn Dumper $data;

	for (@$data) {
		push @{ $chart{x_data} }, $_->{depth};
		push @{ $chart{y_data} }, $_->{vf};		
	}
	printf $format, $location, @{$_}{ qw/ref alt filter depth vf/ } for @$data;
	printf $format, @dividr;
}

# generate chart of depth (x) vs variable frequency (y):
@chart{ qw/x_title y_title chart_title/ } = ( 'Depth', 'VF', 'VCF analysis' ); 
ChartMaker::make_chart(\%chart);

exit 0;

#===============================================================================

sub parse {
	my $filename = shift;
	my @lines = io($filename)->slurp; # warn Dumper \@lines;
	
	my %i; # counter localised to individual file
	LINE: for (@lines) {
		next LINE if /^#/; # skip comments
		my @fields = split "\t", $_;
		
		my $start_pos  = $fields[1] || next LINE; # warn $start_pos;
		my ($ref,$alt) = @fields[3,4]; # warn Dumper [$ref,$alt];
		my $filter     = $fields[6]; # warn $filter;
		my ($depth)    = $fields[7] =~ /DP=(\d+)/; # warn $depth;
		my $results    = $fields[-1]; # warn $results;		
		my $vf = (split ':', $results)[3]; # warn $vf;
		
		my %r = (
			filter => $filter,
			depth  => $depth,
			ref    => $ref,
			alt    => $alt,
			vf     => $vf,
		);
        # add %r data as array(ref) - can have multiple entries per file:
		push @{ $h{$start_pos}{data} }, \%r;
        # auto-increment intra-file start position counter:
		$i{$start_pos}++;

#		$h{$start_pos}{depth}  ||= $depth;
#		$h{$start_pos}{ref}    ||= $ref;
#		$h{$start_pos}{alt}    ||= $alt;
#		$h{$start_pos}{vf}     ||= $vf;
	}
	# auto-increment %h start position key once for each start position key in
    # %i (don't care how many times start position entry appears in each file):
	for my $start_position (keys %i) { $h{$start_position}{count}++ }
}

sub by_start_pos {
	return $a <=> $b;
}

sub by_frequency { # 1st by frequency, 2nd by start position:
	return $h{$b}{count} <=> $h{$a}{count} || $a <=> $b;
}