#!/software/bin/perl

use strict;
use warnings ;
use File::Copy;
use File::Basename;
use File::Listing;

my $rootdir  = $ARGV[0];
my $celfile = $ARGV[1];
my $cfile = fileparse($celfile);
my $sample = $ARGV[2];

my $cdfdir = $rootdir . "/cdf";
my $celdir = $rootdir . "/cel";
my $outdir = $rootdir . "/outdir";
mkdir($cdfdir, 0755) || print "Couldn't make dir $!\n";
mkdir($celdir,0755) || print "Couldn't make Celdir $!\n";

my $cdffile = "/nfs/team78pc/Individuals_Folders/cdg/TRANSFER/viewer/picnicGUI_unix/src/GenomeWideSNP_6.fromDB.cdf";
copy("$cdffile", "$cdfdir/GenomeWideSNP_6.fromDB.cdf") or die "copy failed $!\n";
copy("$celfile", "$celdir/$cfile") or die "copy of celfile failed $!\n";
mkdir ($outdir,0755) || print "Couldn't create outputdir : $!\n";
 
 
chdir($rootdir) || die "Can't change directory $!\n";




my $cmd1 = "java -Xmx2G -jar $rootdir/celConverter/CelFileConverter.jar -m $rootdir/celConverter/Snp6FeatureMappings.csv -c $rootdir/cdf/GenomeWideSNP_6.fromDB.cdf -s $celdir/ -t $rootdir/outdir/raw";
system($cmd1);

my $dir = "$rootdir/outdir/output2/$sample" . "_feature.TXT";

opendir(DIR, "$rootdir/outdir/raw") || "Cannot open the directory $!\n";
opendir(ODIR,"$dir") || "Cannot open output2directory $! \n";
 
foreach my $file (readdir(DIR)){
 if($file =~ /feature_intensity$/){
 
  #my $cmd = "sh run_preprocessing.sh $rootdir/Matlab_Compilet_Runtime/v710/ $file $rootdir/info/ $rootdir/outdir/raw/ $rootdir/outdir/output/  $rootdir/outdir/ PRIMARY 0.5";
  #warn "Running $cmd... \n"; 
  #system($cmd); #outputs ploidy_3456_feature.TXT.csv
  
  foreach my $file2(readdir(ODIR)){
    
   if($file2 =~ /^ploidy\_$sample\_feature\.TXT\.csv$/){
    open(FILE, "<$dir/$file2") || "Cannot open the file $file2 $!\n"; #output from the previous system cmd. 
    while(<FILE>){
     chomp;
     my ($in_pi,$in_ploidy,$in_alpha) = split(/,/);
     my $cmd2 = "sh run_HMM.sh $rootdir/Matlab_Compilet_Runtime/v710/ $file $rootdir/info/ $rootdir/outdir/output/ $rootdir/outdir/ 10 $in_pi $in_ploidy $in_alpha";
     warn "Running $cmd2\n";
     system($cmd2);
     
     }
     close FILE;
    }
   }

 }


}