my %bwa = ();
my @splitstore=();
my @s1 = ();
my @s2 = ();
my @s3 = ();
my @s4 = ();
my @s5 = ();
my $ssl=(0);
my $splitstoreD=(0);
my $splitstoreI=(0);
my $file1 = shift;
open (FILE1, "$file1") || die "Failed to open $file1 for reading : $!"; # Open second file

while (<FILE1>) { # Reading second hash
    if ($_ =~ /^[^@]/s) {
        chomp;
        my @line = split /\s+/, $_;
        my $ID;
        if ($line[2] =~ /[^*]/) {
            $ID = $line[0];
            push @{$bwa{$ID}}, @line[0,2,5,12,15,16,17,18,3];

            #$bwa{$ID}[0] = $line[0];  # seq ID
            #$bwa{$ID}[1] = $line[2];  # Ref ID
            #$bwa{$ID}[2] = $line[5];  # CIGAR ID for insertion
            #$bwa{$ID}[3] = @line[9];  # Processed seq (already C->T)
            #$bwa{$ID}[3] = $line[12]; # Edit distance (edited area by # of base) : NM
            #$bwa{$ID}[4] = $line[15]; # No. of mismatches in the alignment : XM
            #$bwa{$ID}[5] = $line[16]; # No. of gap opens for insertion : XO
            #$bwa{$ID}[6] = $line[17]; # No. of gap extensions for deletion :XG
            #$bwa{$ID}[7] = $line[18]; # Mismatching positions / bases : MD
            #$bwa{$ID}[8] = $line[3];  # Starting position
            

            # These are not from my input, I made these so I can save some data for parsing the CIGAR ID.
            #$bwa{$ID}[10] = Total Number of Bases
            #$bwa{$ID}[11] = Deletion (0 if no)
            #$bwa{$ID}[12] = Insertion (0 if no)
            #$bwa{$ID}[13] = Number of bases until deletion
            #$bwa{$ID}[14] = Number of bases until insertion
            
            # Modifying CIGAR ID's to keep track of matches, deletions, insertions
            @splitstore = split /[A-Z]/, $bwa{$ID}[2];
            if ($bwa{$ID}[2] =~ /[D]/) { $splitstoreD = 1; } else { $splitstoreD = 0 }
            if ($bwa{$ID}[2] =~ /[I]/) { $splitstoreI = 1; } else { $splitstoreI = 0 }
            
            #Storing Total Bases
            $ssl = scalar @splitstore;
            if($ssl>1){
                if ($ssl>4){ #If there is both a deletion and insertion...
                    $bwa{$ID}[10] = $splitstore[0]+$splitstore[2]+$splitstore[$ssl-1]; #add first, third and last nubmers to get total bases
                }
                else{
                $bwa{$ID}[10] = $splitstore[0]+$splitstore[$ssl-1];} #add first and last numbers to get total bases
            }
            else { $bwa{$ID}[10] = $splitstore[0]; } #just the first number
            
            #Defining Deletions
            if($splitstoreD == 1) { $bwa{$ID}[11]="Del" } else { $bwa{$ID}[11]=0 }
            
            #Defining Insertions
            if($splitstoreI == 1) { $bwa{$ID}[12]="Ins" } else { $bwa{$ID}[12]=0 }
            
            #Defining Position of Deletion
            if ($bwa{$ID}[2] =~ /(\d*(?=D))/) {
                @s1 = split /(\d)/, $bwa{$ID}[2];
                @s2 = split /(\d+M)/, @s1;
                @s3 = split /(\d+M)/, @s2;
                @s4 = split /(\d+I)/, @s3;
                @s5 = split /[D]/, @s4;
                    $bwa{$ID}[13]=@s5;
            }
            
            
            
            print "@splitstore\t";
            print "$splitstoreI\t";
            print "$splitstoreD\t";
            print "$bwa{$ID}[10]\n";     
            print "@s1\t";
            print "@s2\t";
            print "@s3\t";
            print "@s4\t";
            print "@s5\t";
            print "$bwa{$ID}[13]\n";  
            
            @s1 = ();
            @s2 = ();
            @s3 = ();
            @s4 = ();
            @s5 = ();  
        }
    }
}
close FILE1 || die "Failed to close $file1 : $!";