#!/usr/bin/perl -w

=head
 Title    : apt_SNPCall_report
 Function : To combine the results from the different reports based on the batch list.
=cut
#-------------------------------------------------------------------------------
# use and library files
use strict;
use Getopt::Long;

#-------------------------------------------------------------------------------
# Get options
my ($help, $batch, $list);
my $output = "genotyping_results.txt";
my ($good_batch, $out_name, $out_dir_name);
my (@list_files, %sample);


sub help {
  print <<EOH;

Description:
Using the apt_SNP_batch_call will generate reports for each of the separate samples that failed QC together with either samples that passed QC or HapMap reference samples. This script will combine the results from each of the report files into one table containing the SNP call rate and the pm_mean (average intensity).

Input files
The script will search for the customer samples using

Known issues/bug/beware...
NA

Use:
  perl $0 [options]

Options and arguments:
-help              this
--batch            Name of the file that contains the batches used for genotyping       [mandatory]
--list             File containing the list of CEL files of interest                    [mandatory]
--output           Name of output file                                                  [optional]

EOH
  $help  =  1;
  exit;
}

#-------------------------------------------------------------------------------
# Options:
GetOptions(
           'help'      => \$help,
	   'batch=s'   => \$batch,
	   'list=s'    => \$list,
	   'output=s'  => \$output
           );
if ((! $batch) or (! $list) or $help){ 
  &help();
}

# File opening:
open (BATCH, $batch) || die "Cannot open input file $batch: $!\n";
open (LIST, $list) || die "Cannot open input file $list: $!\n";
open (W, ">$output") || die "Error to open $!";

#-------------------------------------------------------------------------------
# Script

#print W "SampleName\tcall_rate\tpm_mean\n";
print "SampleName\tcall_rate\tpm_mean\n";

while (<LIST>) {
    chomp;
    my ($path, $file) = ($_ =~ /(.*\/)(.*)/);
    push (@list_files, $file);
}
close LIST;

while (<BATCH>) {
    chomp;
    s/\r//;
    my $filename = $_;
    $out_name = $filename;
    $out_name =~ s/\.txt//;
    $out_dir_name = "apt_SNPCall_".$out_name;
    foreach my $lf (@list_files){
	open (SAMPLE, "$out_dir_name/birdseed-v2.report.txt") || die "Error to open: $!";
	while (<SAMPLE>) {
	    chomp;
	    my @tab = split("\t", $_);
	    if ($tab[0] eq $lf){
		my $sample = $lf;
		$sample =~ s/\.CEL//;
		print $sample."\t".$tab[2]."\t".$tab[22]."\n"; #I get problems here
#		print W $sample."\t".$tab[2]."\t".$tab[22]."\n";
	    }

	}
    }
}

close SAMPLE;
close W;
close BATCH;

###################################
# Functions