#! /usr/bin/perl

use strict;

print "Enter the csfasta file name: ";
my $inputFile1 = <STDIN>;
chomp ($inputFile1);
if (not (-e "$inputFile1"))
{
	print "File does not exist. Exiting program\n";
	exit;
}

print "Enter the quality score file name: ";
my $inputFile2 = <STDIN>;
chomp ($inputFile2);
if (not (-e "$inputFile2"))
{
	print "File does not exist. Exiting program\n";
	exit;
}
#my $inputFile2 = "QV_1.qual";
#my $inputFile1 = "CS_1.csfasta";
print "Enter the number of nodes available:";
my $grids = <STDIN>;

print "Enter the reference genome file name: ";
my $ref = <STDIN>;
chomp ($ref);

print "Enter the output base name: ";
my $out = <STDIN>;
chomp ($out);

print "Enter the number of mismatches: ";
my $mismatch = <STDIN>;
chomp ($mismatch);

print "Enter the RAM available: ";
my $reads = <STDIN>;
chomp ($reads);

print "Enter the number of threads: ";
my $threads = <STDIN>;
chomp ($threads);

print "Splitting csfasta...\n";
my ($totalLen, $length) = divideCS();
print "Splitting quality file\n";
divideQual();
print "Creating preference files...\n";
makeOption($totalLen, $length);

sub divideCS
  {
    open (INPUT, "$inputFile1");

    my $line;
    my $numLines = 1;
    my $header = '';
    my $i;
    my $j;
    my $len;
    my $filename;
    my $numheader = 0;

    while (defined ($line = <INPUT>))
      {
		if ($line=~/#/)
	  	{
	    	$header .=$line;
	    	$numheader++;
	  	}
	  	else
	  	{
	  		last;
	  	}
      }
   
    #print $header, "\n\n";
    while (defined ($line = <INPUT>))
      {
      	$numLines++;
      }
    
    $numLines = $numLines/2;
    my $len;
    $len = int ($numLines/$grids);
    #print $len, " :len\n";

    seek (INPUT, 0, 0);
    my $i;
    for ($i = 0; $i < $numheader; $i++)
      {
	$line = <INPUT>;
      }

       
    for ($j = 1; $j < $grids; $j++)
      {
	$filename = "CS_".$j.".csfasta";
	open (INPUT1, ">$filename");
	#print $header, "\n";
	print INPUT1 $header;
	#print $j, "\n";
	for ($i = 0; $i < $len; $i++)
	  {
	    $line = <INPUT>;
	    print INPUT1 $line;
	    $line = <INPUT>;
	    print INPUT1 $line;
	  }
	close INPUT1;
      }
    $filename = "CS_".$j.".csfasta";
    open (INPUT1, ">$filename");
    print INPUT1 $header;

    while (defined ($line = <INPUT>))
      {
	print INPUT1 $line;
      }
    close INPUT1;
    close INPUT;
    return ($numLines, $len);
  }

sub divideQual
    {
      open (INPUT, "$inputFile2");

      my $line;
      my $numLines = 1;
      my $header = "";
      my $i;
      my $j;
      my $len;
      my $filename;

      my $numheader = 0;

      while (defined ($line = <INPUT>))
      {
	if ($line =~/#/)
	  {
	    $header .=$line;
	    $numheader++;
	  }
	  else
	  {
	  	last;
	  }
      }
      #print $numheader, "\n";

      #print $header, "\n\n";
      while (defined ($line = <INPUT>))
	{
	  $numLines++;
	}
     
      $numLines = $numLines/2;
      my $len;
      $len = int ($numLines/$grids);
      #print $len, " :len\n";

      seek (INPUT, 0, 0);
      for ($i = 0; $i < $numheader; $i++)
	{
	  $line = <INPUT>;
	}
      
      for ($j = 1; $j < $grids; $j++)
      {
	$filename = "QV_".$j.".qual";
	open (INPUT1, ">$filename");
	#print $header, "\n";
	print INPUT1 $header;
	for ($i = 0; $i < $len; $i++)
	  {
	    $line = <INPUT>;
	    print INPUT1 $line;
	    $line = <INPUT>;
	    print INPUT1 $line;
	  }
	close INPUT1;
      }
    $filename = "QV_".$j.".qual";
    open (INPUT1, ">$filename");
    print INPUT1 $header;

    while (defined ($line = <INPUT>))
      {
	print INPUT1 $line;
      }
    close INPUT1;
    close INPUT;

    }
    
    
sub makeOption
{
	my $total  = shift;
	my $len = shift;
	my $i;
	my $start;
	my $inputFile;
	for ($i = 1; $i <= $grids; $i++)
	{
		$start = ($i - 1) * $len;
		
		$inputFile = "part$i.pref";
		open (INPUT, ">$inputFile");

		print INPUT "$ref\n"; 
		print INPUT "CS_$i.csfasta\n";
		print INPUT "QV_$i.qual\n";
		print INPUT "$out$i\n";
		print INPUT "$mismatch\n";
		print INPUT "$reads\n";
		print INPUT "$threads\n";
		print INPUT "false\n";
		print INPUT "false\n";
		print INPUT "$start\n";
		
		close INPUT;
	}
}