#!/usr/bin/perl -w


#### DEBUG

$DEBUG = 1;


#### TIME

my $time = time();


=head2


	APPLICATION     replaceAtQual


	PURPOSE


		REPLACE THE '@' QUALITY VALUE WITH 'A' (ONE VALUE HIGHER)


		BECAUSE IT INTERFERES WITH MAQ CONVERSION FROM solexa TO fastq


    INPUT


        1. solexa-FORMAT FASTQ FILE


    OUTPUT


        1. sanger-FORMAT FASTQ FILE


	USAGE


    ./replaceAtQual.pl  <--inputfile String> <--outputfile String> [--dot Integer] [-h]


        --inputfile		       :   /Full/path/to/inputfile 

        --outputfile		   :   /Full/path/to/outputfile 

        --dot                  :   Print counter every 'dot' number of records

        --help                 :   print help info


    EXAMPLES



perl /nethome/bioinfo/apps/agua/0.4/bin/apps/utils/replaceAtQual.pl \

--inputfile /mihg/data/NGS/syoung/base/pipeline/SRA/NA18507/samples/reads_1.1.fastq \

--outputfile /mihg/data/NGS/syoung/base/pipeline/SRA/NA18507/samples/reads_sanger_1.1.fastq \

--dot 100000


=cut


use strict;


#### USE LIBRARY

use FindBin qw($Bin);

use lib "$Bin/../../../lib";


#### FLUSH BUFFER

$| = 1;


#### GET TEMP DIRECTORY

my $configfile = "$Bin/../../../../conf/default.conf";

my $conf = Conf::Agua->new(inputfile=>$configfile);

my $tempdir = $conf->getKeyValue("agua", 'EXECUTION_TEMPDIR');


#### INTERNAL MODULES

use Sampler;

use Timer;

use Util;
use Conf::Agua;


#### EXTERNAL MODULES

use Term::ANSIColor qw(:constants);

use Getopt::Long;

use IO::Pipe;


#### SET DEFAULT SEPARATOR

my $DEFAULT_SEPARATOR = "\\s+";


#### SAVE ARGUMENTS

my @arguments = @ARGV;


#### GET OPTIONS

my $inputfile;

my $outputfile;

my $dot = 10000;

my $help;

if ( not GetOptions (

    'inputfile=s' => \$inputfile,

    'outputfile=s' => \$outputfile,

    'dot=i' => \$dot,

    'help' => \$help

) )

{ print "Use option --help for usage instructions.\n";  exit;    };


#### PRINT HELP

if ( defined $help )	{	usage();	}


#### CHECK INPUTS

die "Input file not defined (Use --help for usage)\n" if not defined $inputfile;

#die "Output file not defined (Use --help for usage)\n" if not defined $outputfile;


#### GET THE INFO FILES AND TOTAL READ COUNTS FOR EACH DIRECTORY

my $args =

{

	'inputfile'		=>	$inputfile,

	'outputfile'	=>	$outputfile,

	'dot'			=>	$dot

};


#### SET FILES

Sampler::replaceAtQual($args);


#### PRINT RUN TIME

my $runtime = Timer::runtime( $time, time() );

print "\nRun time: $runtime\n";

print "Completed $0\n";

print Util::datetime(), "\n";

print "****************************************\n\n\n";

exit;


#:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

#									SUBROUTINES

#:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


sub usage

{

	print `perldoc $0`;

    exit;

}