use strict;
use warnings;
use File::Basename; 
use Cwd;
use File::Path qw(make_path remove_tree);
die qq(
Bad numbr of inputs

) if(!@ARGV);

my @bam_list_entries;

my $player_options = "--bowtie2 -p 4 ";
my $bam_output;
my $summary;
my $genome;
my $singles = "";
my $mates1 = "";
my $mates2 = "";
my $directional="";
my $format="";
my $log_file="";


foreach my $input (@ARGV) 
{
	my @tmp = split "::", $input;
	if($tmp[0] eq "GENOME") 
	{
		$genome=$tmp[1];	
	} 
	elsif($tmp[0] eq "MATES") 
	{
		$mates1 = $tmp[1];
		$mates2 = $tmp[2];
	}
	elsif($tmp[0] eq "SINGLES") 
	{
		$singles = $tmp[1];
	} 
	elsif($tmp[0] eq "FORMAT") 
	{
		$format = $tmp[1];
	} 
	elsif($tmp[0] eq "DIRECTIONAL") 
	{
		$directional = $tmp[1];
	} 
	elsif($tmp[0] eq "SUMMARY") 
	{
		$summary = $tmp[1];
	} 
        elsif($tmp[0] eq "OUTPUT") 
	{
		$bam_output = $tmp[1];
	} 

	else 
	{
		die("Unknown Input: $input\n");
	}
}


my $working_dir = cwd()."/BISMARK_OUTPUT";
make_path($working_dir);


#run bismark 

if ($singles eq "")
{
	system ("bismark $player_options $directional $format $genome -o $working_dir -1 $mates1 -2 $mates2 > $summary 2>&1 ");
	
}
else
{
	system ("bismark $player_options $directional $format $genome -o $working_dir $singles > $summary 2>&1");
	
}


move_files($working_dir);


sub move_files
{
	my $name;
	my $suffix;
	my $path;
	my $local_dir = $_[0];
	opendir(DIR, $local_dir);
	#print ("Openning: $local_dir\n");
	my @FILES= readdir(DIR); 
	closedir(DIR);
	foreach my $file (@FILES) 
	{
		if ($file eq "." || $file eq "..")
		{
			#print ("./ or ../ skipped\n");
		}
		elsif (-d "$local_dir/$file")
		{
			#print ("moving to: $local_dir/$file\n");
			move_files("$local_dir/$file");
		}
		elsif (-f "$local_dir/$file")
		{
			($name,$path,$suffix) = fileparse($file,qr"\.[^.]*$");
			if ($suffix eq ".sam")
			{
				#converto to BAM and Delete SAM
				system ("MergeSamFiles.sh MAX_RECORDS_IN_RAM=2000000 I=$local_dir/$file O=$bam_output VALIDATION_STRINGENCY=LENIENT SO=coordinate USE_THREADING=true CREATE_INDEX=true > /dev/null 2>&1");
				system ("rm -rf $local_dir/$file");
				
			}
			elsif($suffix eq ".txt")
			{
				system ("mv $local_dir/$file $summary");
			}
		}
		else
		{
			die("Unrecognized file generated: $file\n");
		}
		
	}
}