#!/usr/bin/perl -w
# a program to get indels
# the input is a MAF format 3-way alignment file from 3-way blocks only
# the output is a TABULAR format file containing the coordinates of indels determined based on the outgroup 
# the program translates seq2, seq3, etc coordinates to (5'-3') strand orientation if alignment orientation 
# is reverse complement
# the program gets only indels that satisfy the following conditions:
# 1. two gaps can not overlap unless they are identical, which means they start and end at the same coordinates
# 2. the indel must start after at least three bases from the beginning of the block and finish before at least three bases from the end of the block
# 3. a low score base (masked) can not exist within the indel interval in each of the three sequences
# 4. at lease three high score bases (ummasked) must exist on each side of the indel in each of the three sequences


use strict;
use warnings;

# declare and initialize variables
my $fh; # variable to store filehandle
my $record;
my $offset;
my $library = $ARGV[0]; 
my $count = 0;
my $count2 = 0;
my $count3 = 0;
my $count4 = 0;
my $start1 = my $start2 = my $start3 = my $start4 = my $start5 = my $start6 = 0;
my $orient = "";
my $outgroup = $ARGV[2];
my $ingroup1 = my $ingroup2 = "";
my $count_seq1insert = my $count_seq1delete = 0;
my $count_seq2insert = my $count_seq2delete = 0;
my $count_seq3insert = my $count_seq3delete = 0;
my @seq1_insert_lengths = my @seq1_delete_lengths = ();
my @seq2_insert_lengths = my @seq2_delete_lengths = ();
my @seq3_insert_lengths = my @seq3_delete_lengths = ();
my @seq1_insert =  my @seq1_delete =  my @seq2_insert =  my @seq2_delete =  my @seq3_insert =  my @seq3_delete = ();
my @seq1_insert_startOnly = my @seq1_delete_startOnly = my @seq2_insert_startOnly = my @seq2_delete_startOnly = ();
my @seq3_insert_startOnly = my @seq3_delete_startOnly = ();
my @indels = (); 

# check to make sure correct files
my $usage = "usage: parseMAF_smallIndels.pl [MAF.in] [small_Indels_summary_TABULAR.out] [outgroup]\n";
die $usage unless @ARGV == 3;

# perform some standard subroutines 
$fh = open_file($library);

$offset = tell($fh);

my $ofile = $ARGV[1];
unless (open(OFILE, ">$ofile")){
	print "Cannot open output file \"$ofile\"\n\n";
    exit;
}


# header line for output files
#print OFILE "# small indels summary, parsed from MAF 3-way alignment file, coords are translated from (-) to (+) if necessary\n";
print OFILE "#block\tindel_type\tindel_length\tingroup1\tingroup1_start\tingroup1_end\tingroup1_alignSize\tingroup1_orient\tingroup2\tingroup2_start\tingroup2_end\tingroup2_alignSize\tingroup2_orient\toutgroup\toutgroup_start\toutgroup_end\toutgroup_alignSize\toutgroup_orient\n";

# main body of program
while ($record = get_next_record($fh) ){
	if ($record=~ m/\s*##maf(.*)\s*# maf/s){
		next;
	}
   
	my @sequences = get_sequences_within_block($record);
	my @seq_info = get_indels_within_block(@sequences);
	
	get_indels_lengths(@seq_info);	
	$offset = tell($fh);
    $count++;
        
}

get_starts_only(@seq1_insert);
get_starts_only(@seq1_delete);
get_starts_only(@seq2_insert);
get_starts_only(@seq2_delete);
get_starts_only(@seq3_insert);
get_starts_only(@seq3_delete);

# print some things to keep track of progress
#print "# $library\n";
#print "# number of records = $count\n";
#print "# number of sequence \"s\" lines = $count2\n";

if ($count3 != 0){
	print "Skipped $count3 blocks with only 2 seqs;\n";
}
#print "# number of records with only h-m = $count4\n\n";

print "Ingroup1 = $ingroup1; Ingroup2 = $ingroup2; Outgroup = $outgroup;\n";
print "# of ingroup1 inserts = $count_seq1insert;\n";
print "# of ingroup1 deletes = $count_seq1delete;\n";
print "# of ingroup2 inserts = $count_seq2insert;\n";
print "# of ingroup2 deletes = $count_seq2delete;\n";
print "# of outgroup3 inserts = $count_seq3insert;\n";
print "# of outgroup3 deletes = $count_seq3delete\n";


#close OFILE;

if ($count == $count3){
	print STDERR "Skipped all blocks since none of them contain 3-way alignments.\n";
  	exit -1;
}

###################SUBROUTINES#####################################

# subroutine to open file
sub open_file {
        my($filename) = @_;
        my $fh;

        unless (open($fh, $filename)){
                print "Cannot open file $filename\n";
                exit;
        }
        return $fh;
}

# get next record
sub get_next_record {
        my ($fh) = @_;
        my ($offset);
        my ($record) = "";
        my ($save_input_separator) = $/;
	
	    $/ = "a score";

        $record = <$fh>;

        $/ = $save_input_separator;
        
        return $record;
}

# get header info
sub get_sequences_within_block{
	my (@alignment) = @_;
	my @lines = ();
	
	my @sequences = ();
		
	@lines = split ("\n", $record);
	foreach (@lines){
		chomp($_);
		if (m/^\s*$/){
			next;
		}
		elsif (m/^\s*=(\d+\.*\d*)/){

		}elsif (m/^\s*s(.*)$/){
			$count2++;
			
			push (@sequences,$_);
		}
	}
	
	return @sequences;
}

#get the indels within the blocks	
sub get_indels_within_block{
	my (@sequences) = @_;	
	my $line1 = my $line2 = my $line3 = "";
    my @line1 = my @line2 = my @line3 = ();
	my $score = 0;
        my $start1 = my $align_length1 = my $end1 = my $seq_length1 = 0;
        my $start2 = my $align_length2 = my $end2 = my $seq_length2 = 0;
        my $start3 = my $align_length3 = my $end3 = my $seq_length3 = 0;
        my $seq1 = my $orient1 = "";
        my $seq2 = my $orient2 = "";
        my $seq3 = my $orient3 = "";
        my $start1_plus = my $end1_plus = 0;
        my $start2_plus = my $end2_plus = 0;
        my $start3_plus = my $end3_plus = 0;
   	my @test = ();
        my $test = "";
        my $header = "";
        my @header = ();
        my $sequence1 = my $sequence2 = my $sequence3 ="";
	my @array_return = ();	
	my $test1 = 0;
	my $line1_stat = my $line2_stat = my $line3_stat = "";
    
	# process 3-way blocks only
	if (scalar(@sequences) == 3){
		$line1 = $sequences[0]; 
		chomp ($line1);
		$line2 = $sequences[1]; 
		chomp ($line2);
		$line3 = $sequences[2];	
		chomp ($line3);
		
		# check order of sequences and assign uniformly seq1= human, seq2 = chimp, seq3 = macaque
		if ($line1 =~ m/$outgroup/){
			$line1_stat = "out";
			$line2=~ s/^\s*//;
            $line2 =~ s/\s+/\t/g;
            @line2 = split(/\t/, $line2);
			if (($ingroup1 eq "") || ($line2[1] =~ m/$ingroup1/)){
			 	$line2_stat = "in1";
			 	$line3_stat = "in2";
			 }
			 else{
             	$line3_stat = "in1";
             	$line2_stat = "in2";              
			 }
			}
		elsif ($line2 =~ m/$outgroup/){
			$line2_stat = "out";
			$line1=~ s/^\s*//;
            $line1 =~ s/\s+/\t/g;
            @line1 = split(/\t/, $line1);
            if (($ingroup1 eq "") || ($line1[1] =~ m/$ingroup1/)){
             	$line1_stat = "in1";
             	$line3_stat = "in2";
             }
             else{
             	$line3_stat = "in1";
             	$line1_stat = "in2";              
             }
            }
		elsif ($line3 =~ m/$outgroup/){
			$line3_stat = "out";
			$line1=~ s/^\s*//;
            $line1 =~ s/\s+/\t/g;
            @line1 = split(/\t/, $line1);
            if (($ingroup1 eq "") || ($line1[1] =~ m/$ingroup1/)){
             	$line1_stat = "in1";
             	$line2_stat = "in2";
             }
             else{
             	$line2_stat = "in1";
             	$line1_stat = "in2";              
             }
		}

		#print "# l1 = $line1_stat\n";
		#print "# l2 = $line2_stat\n";
		#print "# l3 = $line3_stat\n";
		
		my $linei1 = my $linei2 = my $lineo = "";
		my @linei1 = my @linei2 = my @lineo = ();
		
        if ($line1_stat eq "out"){
            $lineo = $line1;
        }
        elsif ($line1_stat eq "in1"){
            $linei1 = $line1;
        }
        else{
            $linei2 = $line1;
        }
        
        if ($line2_stat eq "out"){
            $lineo = $line2;
        }
        elsif ($line2_stat eq "in1"){
            $linei1 = $line2;
        }
        else{
            $linei2 = $line2;
        }
        
        if ($line3_stat eq "out"){
            $lineo = $line3;
        }
        elsif ($line3_stat eq "in1"){
            $linei1 = $line3;
        }
        else{
            $linei2 = $line3;
        }
        
        $linei1=~ s/^\s*//;
        $linei1 =~ s/\s+/\t/g;
        @linei1 = split(/\t/, $linei1);
        $end1 =($linei1[2]+$linei1[3]-1);
        $seq1 = $linei1[1].":".$linei1[3];
        $ingroup1 = (split(/\./, $seq1))[0];
        $start1 = $linei1[2];
        $align_length1 = $linei1[3];
        $orient1 = $linei1[4];
        $seq_length1 = $linei1[5];
        $sequence1 = $linei1[6];
        $test1 = length($sequence1);
        my $total_length1 = $test1+$start1;
        my @array1 = ($start1,$end1,$orient1,$seq_length1);
        ($start1_plus, $end1_plus) =  convert_coords(@array1);
           
        $linei2=~ s/^\s*//;
        $linei2 =~ s/\s+/\t/g;
        @linei2 = split(/\t/, $linei2);
        $end2 =($linei2[2]+$linei2[3]-1);               
        $seq2 = $linei2[1].":".$linei2[3];
        $ingroup2 = (split(/\./, $seq2))[0];
        $start2 = $linei2[2];
        $align_length2 = $linei2[3];
        $orient2 = $linei2[4];
        $seq_length2 = $linei2[5];
        $sequence2 = $linei2[6];
        my $test2 = length($sequence2);
        my $total_length2 = $test2+$start2;
        my @array2 = ($start2,$end2,$orient2,$seq_length2);
        ($start2_plus, $end2_plus) = convert_coords(@array2); 
            
        $lineo=~ s/^\s*//;
        $lineo =~ s/\s+/\t/g;
        @lineo = split(/\t/, $lineo);
        $end3 =($lineo[2]+$lineo[3]-1);
        $seq3 = $lineo[1].":".$lineo[3];
        $start3 = $lineo[2];
        $align_length3 = $lineo[3];
        $orient3 = $lineo[4];
        $seq_length3 = $lineo[5];
        $sequence3 = $lineo[6];
        my $test3 = length($sequence3);
        my $total_length3 = $test3+$start3;
        my @array3 = ($start3,$end3,$orient3,$seq_length3);
        ($start3_plus, $end3_plus) = convert_coords(@array3);
        
        #print "# l1 = $ingroup1\n";
		#print "# l2 = $ingroup2\n";
		#print "# l3 = $outgroup\n";
	
		my $ABC = "";
		my $coord1 = my $coord2 = my $coord3 = 0;
                $coord1 = $start1_plus;
                $coord2 = $start2_plus;
                $coord3 = $start3_plus;
		
		#variables to store the lengths of gaps in each sequence
		my $gapLenth = my $gapLenth1 = my $gapLenth2 = my $gapLenth3 = 0;
				
		#variables to store the index of the start of a gap in each sequence
		my $gapStartPos = my $gapStartPos1 = my $gapStartPos2 = my $gapStartPos3 = 0;	
		my $gapEndPos = 0;
		
		#variable to determine if there is a valid gap
		my $getValidGap = 0;
		
		#scan the block from left to right looking for gaps
		for (my $position = 0; $position < $test1; $position++) {
			my $indelType = "";
			my $indel_line = "";
	
			#print($position ." position\n");
			#print($sequence1 ." sequence1\n");
			#print($sequence2 ." sequence2\n");
			#print($sequence3 ." sequence3\n");
			#if ($position > 2 && $position < ($test1 - 3)){
				#print(substr($sequence1,$position - 3, 3) . " before " . substr($sequence1, $position + 1, 3) . " after\n");
				#print(substr($sequence2,$position - 3, 3) . " before " . substr($sequence2, $position + 1, 3) . " after\n");
				#print(substr($sequence3,$position - 3, 3) . " before " . substr($sequence3, $position + 1, 3) . " after\n");
			#}
					
			#if the current position is the start of a gap, look for any overlapping gaps in the other two sequences 
			if (substr($sequence1,$position,1) eq "-" || substr($sequence2,$position,1) eq "-" || substr($sequence3,$position,1) eq "-"){
				
				#print($gapStartPos . " gapStartPos\n");
				#print("starting a gap\n");
				
				#reset all gap related variables to 0
				$gapLenth = $gapLenth1 = $gapLenth2 = $gapLenth3 = 0;
				$gapStartPos = $gapStartPos1 = $gapStartPos2 = $gapStartPos3 = 0;
				$gapEndPos = 0;
				$getValidGap = 0;

				#if($position > 2 && $position < $test1 - 3){
					#print(substr($sequence1,$position - 3, 3) . " before " . substr($sequence1, $position + 1, 3) . " after\n");
					#print(substr($sequence2,$position - 3, 3) . " before " . substr($sequence2, $position + 1, 3) . " after\n");
					#print(substr($sequence3,$position - 3, 3) . " before " . substr($sequence3, $position + 1, 3) . " after\n");
				#}
				
				#check if this position is the start of a gap
				if ($gapStartPos == 0){
					
					#the variables $gapStartPos and $gapEndPos are initialized with the current position value $position
					$gapStartPos = $gapEndPos = $position;
					
					#iterate till the end of the gap and/or the end of any overlapping gap, whichever is greater
					while (substr($sequence1, $gapEndPos, 1) eq "-" || substr($sequence2, $gapEndPos, 1) eq "-" || substr($sequence3,$gapEndPos,1) eq "-"){
						
						#check if the current single gap is in sequence1
						if(substr($sequence1, $gapEndPos, 1) eq "-" && $gapEndPos < $test1){
							$gapLenth1++;
							if ($gapLenth1 == 1){
								$gapStartPos1 = $gapEndPos;
							}	
						}
						
						#check if the current single gap is in sequence2
						if(substr($sequence2, $gapEndPos, 1) eq "-" && $gapEndPos < $test1){
							$gapLenth2++;
							if ($gapLenth2 == 1){
								$gapStartPos2 = $gapEndPos;
							}	
						}
						
						#check if the current single gap is in sequence3
						if(substr($sequence3, $gapEndPos, 1) eq "-" && $gapEndPos < $test1){
							$gapLenth3++;
							if ($gapLenth3 == 1){
								$gapStartPos3 = $gapEndPos;
							}	
						}
						$gapEndPos++;
					}
					
					#readjust the value of $gapStartPos to represent the index of the end of the gap 
					#and/or the end of any overlapping gaps, whichever is greater
					$gapEndPos--;
					
					#print($gapStartPos . " - " . $gapEndPos . " gapStartPos - gapEndPos\n");
					#print($gapStartPos1 . " - " . $gapLenth1 . " gapStartPos1 - gapLenth1\n");
					#print($gapStartPos2 . " - " . $gapLenth2 . " gapStartPos2 - gapLenth2\n");
					#print($gapStartPos3 . " - " . $gapLenth3 . " gapStartPos3 - gapLenth3\n");
			        
			        #variable $gapLength stores the length of the max gap among the three gaps if any 
			        if ($gapLenth < $gapLenth1){
			        	$gapLenth = $gapLenth1;
			        }
			        if ($gapLenth < $gapLenth2){
			        	$gapLenth = $gapLenth2;
			        }
			        if ($gapLenth < $gapLenth3){
			        	$gapLenth = $gapLenth3;
			        }
				        
			        #print("The length of the longest gap is: " . $gapLenth . "\n");
			        
			        #check if there are two overlapping gaps from sequence1 and sequence2 but not from sequence3
			        if ($gapLenth1 > 0 && $gapLenth2 > 0 && $gapLenth3 == 0){
		        		if ($gapLenth1 != $gapLenth2 || $gapStartPos1 != $gapStartPos2){
		        			
		        			#print("Invalid case: gaps are overlapping starting at position: " . $position . "\n");
		        			
		        			# readjust the value of the variable $gapLenth to include all unequal-lenght gaps
		        			$gapLenth = $gapEndPos - $position + 1;
		        			
		        			# readjust the value of the variable $position to the next non-gap character
		        			$position = $position + $gapLenth - 1;
		        			
		        			#print("The total length of the overlapping gaps is: " . $gapLenth . "\n");	
		        			
		        			#add as many characters "N" as the length of $gapLenth to the sequence $ABC as if there is no gap
		        			while($gapLenth > 0){
								$ABC = join("",($ABC,"N"));
								$coord1++; $coord2++; $coord3++;
								$gapLenth--;
							}
		        		}
			        }
	        		else{   #check if there are two overlapping gaps from sequence1 and sequence3 but not from sequence2
	        			if ($gapLenth1 > 0 && $gapLenth3 > 0 && $gapLenth2 == 0){
	        				
		        			if ($gapLenth1 != $gapLenth3 || $gapStartPos1 != $gapStartPos3){
		        				
		        				#print("Invalid case: gaps are overlapping starting at position: " . $position . "\n");
		        				
		        				# readjust the value of the variable $gapLenth to include all unequal-lenght gaps
	        					$gapLenth = $gapEndPos - $position + 1;
	        			
		        				# readjust the value of the variable $position to the next non-gap character
		        				$position = $position + $gapLenth - 1;
		        				
		        				#print("The total length of the overlapping gaps is: " . $gapLenth . "\n");
		        				
		        				#add as many characters "N" as the length of $gapLenth to the sequence $ABC as if there is no gap
		        				while($gapLenth > 0){
									$ABC = join("",($ABC,"N"));
									$coord1++; $coord2++; $coord3++;
									$gapLenth--;
								}
		        			}
		        		}
		        		else{    #check if there are two overlapping gaps from sequence2 and sequence3 but not from sequence1
		        			if ($gapLenth2 > 0 && $gapLenth3 > 0 && $gapLenth1 == 0){
			        			if ($gapLenth2 != $gapLenth3 || $gapStartPos2 != $gapStartPos3){
			        				
			        				#print("Invalid case: gaps are overlapping starting at position: " . $position . "\n");
			        				
			        				# readjust the value of the variable $gapLenth to include all unequal-lenght gaps
	        						$gapLenth = $gapEndPos - $position + 1;
	        						
			        				# readjust the value of the variable $position to the next non-gap character
			        				$position = $position + $gapLenth - 1;
			        				
			        				#print("The total length of the overlapping gaps is: " . $gapLenth . "\n");
							
			        				#add as many characters "N" as the length of $gapLenth to the sequence $ABC as if there is no gap
			        				while($gapLenth > 0){
										$ABC = join("",($ABC,"N"));
										$coord1++; $coord2++; $coord3++;
										$gapLenth--;
									}
			        			}
			        		}
			        		else{ #check if there are three overlapping gaps from the three sequences
			        			if ($gapLenth1 > 0 && $gapLenth2 > 0 && $gapLenth3 > 0){
				        			if ($gapLenth1 != $gapLenth2 || $gapLenth1 != $gapLenth3 ||  $gapLenth2 != $gapLenth3 
				        			    || $gapStartPos1 != $gapStartPos2 || $gapStartPos1 != $gapStartPos3
				        			    || $gapStartPos2 != $gapStartPos3){
				        			    
				        			    #print("Invalid case: gaps are overlapping starting at position: " . $position . "\n");
				        			    
				        			    # readjust the value of the variable $gapLenth to include all unequal-lenght gaps
	        							$gapLenth = $gapEndPos - $position + 1;
	        			
				        			    # readjust the value of the variable $position to the next non-gap character
				        			    $position = $position + $gapLenth - 1;
				        			    
				        			    #print("The total length of the overlapping gaps is: " . $gapLenth . "\n"); 						
							
				        			    #add as many characters "N" as the length of $gapLenth to the sequence $ABC as if there is no gap
				        				while($gapLenth > 0){
											$ABC = join("",($ABC,"N"));
											$coord1++; $coord2++; $coord3++;
											$gapLenth--;
										}
				        			}
				        		}
			        		}
		        		}
	        		}
	        		
	        		#check if the gaps are overlapping
	        		if ($gapLenth == 0){
	        				
	        			#check if the overlapping gaps are also within less than three base from either end of the block 
						if ($gapStartPos <= 2 || $gapEndPos >= ($test1 - 3)){
							if ($gapStartPos <= 2){
								#print("Invalid case: at least one of the overlapping gaps is within less than 3 bases from the left end of the block starting at position: " . $gapStartPos . "\n");
							}
							elsif ($gapEndPos >= $test1 - 3){
									#print("Invalid case: at least one of the overlapping gaps is within less than 3 bases from the right end of the block starting at position: " . $gapStartPos . "\n");
							}
							elsif ($gapStartPos <= 2 && $gapEndPos >= ($test1 - 3)){
								#print("Invalid case: at least one of the overlapping gaps is within less than 3 bases from each end of the block starting at position: " . $gapStartPos . "\n");
							}
						}
						
						#check if the gap starts at position located within three bases from the start of the block
						my $preSubSeqLength = 0;
						if ($gapStartPos - 3 < 0){
							$preSubSeqLength = $gapStartPos;
						}
						else{
							$preSubSeqLength = 3;
						}
						
						#check if the there is a masked character among the three bases on at least one side of the gap
				    	if ((substr($sequence1, $gapStartPos - $preSubSeqLength, $preSubSeqLength)     =~ m/[-\#$?^@]/)
					         || (substr($sequence2, $gapStartPos - $preSubSeqLength, $preSubSeqLength) =~ m/[-\#$?^@]/)
					         || (substr($sequence3, $gapStartPos - $preSubSeqLength, $preSubSeqLength) =~ m/[-\#$?^@]/)
					         || (substr($sequence1, $gapEndPos + 1, 3) =~ m/[-\#$?^@]/)
					         || (substr($sequence2, $gapEndPos + 1, 3) =~ m/[-\#$?^@]/)
					         || (substr($sequence3, $gapEndPos + 1, 3) =~ m/[-\#$?^@]/)){
							
							#print("Invalid case: at least one masked character is within 3 bases from at least one of overlapping gaps starting at position: " . $gapStartPos . "\n");
						}
						
						#check if there is at least one base with low score (maskd) within the gap interval	
						if((substr($sequence1, $gapStartPos, $gapEndPos - $gapStartPos + 1)    =~ m/[\#$?^@]/)
						    || (substr($sequence2, $gapStartPos, $gapEndPos - $gapStartPos + 1) =~ m/[\#$?^@]/)
						    || (substr($sequence3, $gapStartPos, $gapEndPos - $gapStartPos + 1) =~ m/[\#$?^@]/)){
   
						    #print("Invalid case: at least one masked character is within the gap interval starting at position: " . $gapStartPos . "\n");
						}	
						
						#print($sequence1 ." sequence1\n");
						#print($sequence2 ." sequence2\n");
						#print($sequence3 ." sequence3\n");		
	        		    #print("________________________________________________________________\n");
	        		}    	    
	        		
					
					#if $gapLenth > 0, then there is no overlapping gaps, which means that either there is only one gap 
					# or two gaps that have equal lengths and start at the same position 
					if ($gapLenth > 0){  
	
						#variable indicating if the gap is within less than three bases from the end of the blocks
						my $blockEndGap = 0; 
						#variable indicating if the gap is within less than three bases from the end of the blocks
						my $maskedCharWithinGap = 0; 			
						#variable indicating if there is any masked character among the three bases flanking the gap from each side 
						my $maskedCharNearGap = 0;
						
						#check if there are at least there bases on each side of the gap 				
						if ($position > 2 && ($position + $gapLenth - 1) < ($test1 - 3)){
							$blockEndGap = 0;
						}
						else{   #the gap is within less than 3 bases from the end of the block
	
							$blockEndGap = 1;
						}
						
						#variable $preSubSeqLength stores the number of bases available on the left side of the gap 
						my $preSubSeqLength = 0;
						#variable $leftStartCheckingPosition stores the index of the base at which 
						#we start checking the number of bases available on the left side of the gap 
						my $leftStartCheckingPosition = 0;
						
						if ($gapStartPos - 3 < 0){
							$preSubSeqLength = $gapStartPos;
						}
						else{
							$preSubSeqLength = 3;
							$leftStartCheckingPosition = $position - 3;
						}
						#check if all the three bases on each side of the gap have high scores (unmasked)
						if ((substr($sequence1, $leftStartCheckingPosition, $preSubSeqLength) !~ m/[-\#$?^@]/)
						     && (substr($sequence2, $leftStartCheckingPosition, $preSubSeqLength) !~ m/[-\#$?^@]/)
						     && (substr($sequence3, $leftStartCheckingPosition, $preSubSeqLength) !~ m/[-\#$?^@]/)
						     && (substr($sequence1, $position + $gapLenth, 3) !~ m/[-\#$?^@]/)
						     && (substr($sequence2, $position + $gapLenth, 3) !~ m/[-\#$?^@]/)
						     && (substr($sequence3, $position + $gapLenth, 3) !~ m/[-\#$?^@]/)){
	     	
							#there are three bases with high scores (unmasked) on each side of the gap
							$maskedCharNearGap = 0;
						}
						else{   #three is a masked character among the three bases on at least one side of the gap
							$maskedCharNearGap = 1;
						}
						    
						#check if there is at least one base with low score (maskd) within the gap interval	
						if((substr($sequence1, $position, $gapLenth)     !~ m/[\#$?^@]/)
						    && (substr($sequence2, $position, $gapLenth) !~ m/[\#$?^@]/)
						    && (substr($sequence3, $position, $gapLenth) !~ m/[\#$?^@]/)){
    
						    #there is no base with low score (unmasked) within the gap interval   	
							$maskedCharWithinGap = 0;
						}
						else{   #there is at least one base with low score (maskd) within the gap interval	
							$maskedCharWithinGap = 1;
						}
				        
				        #check if the gap is, valid which means:
				        #check if the gap is within at least 3 bases from each end of the block,
						#and that all the three bases on each side of the block have high scores (unmasked),
						#and that there is no base with low score (masked) within the gap interval at the same time
				        if ($blockEndGap == 0 && $maskedCharNearGap == 0 && $maskedCharWithinGap == 0){
				        	
				        	#print("The gap is valid and will be treated accordingly\n");
				        	$getValidGap = 1
				        }
				        
				        #the gap is not valid, which means:
				        #the gap is not valid, so check if the gap is within less than 3 bases from the end of the block,
						#and that there is a masked character among the three bases on at least one side of the gap,
						#and that there is a masked character within the gap interval at the same time
						elsif ($blockEndGap == 1 && $maskedCharNearGap == 1 && $maskedCharWithinGap == 1){
							#print("Invalid case: the gap is within less than 3 bases from the end of the block starting at position: " . $position . "\n");
							#print("Invalid case: at least one masked character is within 3 bases from the gap starting at position: " . $position . "\n");
							#print("Invalid case: at least one masked character is within the gap interval starting at position: " . $position . "\n");
							#print("The total length of the overlapping gaps is: " . $gapLenth . "\n");
						}
						#check if the gap is within less than 3 bases from the end of the block, and
						#that there is a masked character among the three bases on at least one side of the gap at the same time
						elsif ($blockEndGap == 1 && $maskedCharNearGap == 1){
							#print("Invalid case: the gap is within less than 3 bases from the end of the block starting at position: " . $position . "\n");
							#print("Invalid case: at least one masked character is within 3 bases from the gap starting at position: " . $position . "\n");
							#print("The total length of the overlapping gaps is: " . $gapLenth . "\n");
						}
						#check if the gap is within less than 3 bases from the end of the block and
						#and that there is a masked character within the gap interval at the same time
						elsif ($blockEndGap == 1 && $maskedCharWithinGap == 1){
							#print("Invalid case: the gap is within less than 3 bases from the end of the block starting at position: " . $position . "\n");
							#print("Invalid case: at least one masked character is within the gap interval starting at position: " . $position . "\n");
							#print("The total length of the overlapping gaps is: " . $gapLenth . "\n");
						}
						#check if there is a masked character among the three bases on at least one side of the gap
						#and that there is a masked character within the gap interval at the same time
						elsif ($maskedCharNearGap == 1 && $maskedCharWithinGap == 1){
							#print("Invalid case: at least one masked character is within 3 bases from the gap starting at position: " . $position . "\n");
							#print("Invalid case: at least one masked character is within the gap interval starting at position: " . $position . "\n");
							#print("The total length of the overlapping gaps is: " . $gapLenth . "\n");
						}
						#check if the gap is within less than 3 bases from the end of the block
						elsif ($blockEndGap == 1){
								#print("Invalid case: the gap is within less than 3 bases from the end of the block starting at position: " . $position . "\n");
								#print("The total length of the overlapping gaps is: " . $gapLenth . "\n");
						}
						#check if there is a masked character within 3 bases on each side of the gap
						elsif ($maskedCharNearGap == 1){
							#print("Invalid case: at least one masked character is within 3 bases from the gap starting at position: " . $position . "\n");
							#print("The total length of the overlapping gaps is: " . $gapLenth . "\n");
						}
						#check if there is a masked character within the gap interval
						elsif ($maskedCharWithinGap == 1){
							#print("Invalid case: at least one masked character is within the gap interval starting at position: " . $position . "\n");
							#print("The total length of the overlapping gaps is: " . $gapLenth . "\n");
						}
						
						#check if the gap is not valid in order to readjust the $position value and increment coordinates varaibles
						if ($getValidGap == 0){	
							#print($sequence1 . " sequence1\n");
							#print($sequence2 . " sequence2\n");
							#print($sequence3 . " sequence3\n");
							#print("________________________________________________________________\n");
						
							# readjust the value of the variable $position to the next non-gap character
							$position = $position + $gapLenth - 1;
				
							#add as many characters "N" as the length of $gapLenth to the sequence $ABC as if there is no gap
							while($gapLenth > 0){
								$ABC = join("",($ABC,"N"));
								$coord1++; $coord2++; $coord3++;
								$gapLenth--;
							}
						}					
					}
				}			
			}
			else{   #there is no gap at this position
				#if ($position <= 2){
					#print("invalid case\n");
					#print(substr($sequence1, 0, $position) ." before\n");
					#print(substr($sequence2, 0, $position) ." before\n");
					#print(substr($sequence3, 0, $position) ." before\n");
				#}
				#if ($position >= ($test1 - 3)){
					#print("invalid case\n");
					#print(substr($sequence1, $position - $test1) . " after\n");
					#print(substr($sequence2, $position - $test1) . " after\n");
					#print(substr($sequence3, $position - $test1) . " after\n");
				#}
				
				#add as many characters "N" as the length of $gapLenth to the sequence $ABC becasue there is no gap
				$ABC = join("",($ABC,"N"));
				$coord1++; $coord2++; $coord3++;
				
				# reset the value of the variable $gapStartPos to 0
				if ($gapStartPos > 0){
					$gapStartPos = 0;
				}
				
				# reset the value of the variable $getValidGap to 0
				if ($getValidGap > 0){
					$getValidGap = 0;
				}
			}  
	
			#The gap is valid and will be treated accordingly
			if ($getValidGap > 0){
		
				my $localGap = $gapLenth;
				
				# seq1 deletes
				 if ((substr($sequence1,$position,1) eq "-") 
			    		&& (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/)
		       			&& (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){
		       			
		       			while($gapLenth > 0){
							$ABC = join("",($ABC,"X"));
							my @s = split(/:/, $seq1);
							$indelType = $s[0]."_delete";
		
							#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";	
							$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
							push (@indels,$indel_line);
							push (@seq1_delete,$indel_line);
				 			$coord2++; 
				 			$coord3++;
				 			
				 			$gapLenth--;
		       			}
		       		}	
				# seq2 deletes
				elsif ((substr($sequence1,$position,1) !~ m/[-*\#$?^@]/)
					&& (substr($sequence2,$position,1) eq "-")
					&& (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){
						
						while($gapLenth > 0){
							$ABC = join("",($ABC,"Y"));
							my @s = split(/:/, $seq2);
							$indelType = $s[0]."_delete";
							
							#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
							$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
		                    push (@indels,$indel_line);
							push (@seq2_delete,$indel_line);
							$coord1++;
							$coord3++;
							
							$gapLenth--;
						}
				}
				# seq1 inserts
				elsif ((substr($sequence1,$position,1) !~ m/[-*\#$?^@]/)
					&& (substr($sequence2,$position,1) eq "-")
					&& (substr($sequence3,$position,1) eq "-")){
						
						while($gapLenth > 0){
							$ABC = join("",($ABC,"Z"));
							my @s = split(/:/, $seq1);
							$indelType = $s[0]."_insert";
							
							#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
							$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
							push (@indels,$indel_line);
							push (@seq1_insert,$indel_line);
							$coord1++;
							
							$gapLenth--;
						}
				}
				# seq2 inserts	
				elsif ((substr($sequence1,$position,1) eq "-")
					&& (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/)
					&& (substr($sequence3,$position,1) eq "-")){
						
						while($gapLenth > 0){
							$ABC = join("",($ABC,"W"));
							my @s = split(/:/, $seq2);
							$indelType = $s[0]."_insert";
							
							#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
							$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
							push (@indels,$indel_line);
							push (@seq2_insert,$indel_line);
							$coord2++;
							
							$gapLenth--;
						}
				}
				# seq3 deletes
				elsif ((substr($sequence1,$position,1) !~ m/[-*\#$?^@]/)
					&& (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/)
					&& (substr($sequence3,$position,1) eq "-")){
						
						while($gapLenth > 0){
							$ABC = join("",($ABC,"S"));
							my @s = split(/:/, $seq3);
							$indelType = $s[0]."_delete";
							
							#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
							$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
							push (@indels,$indel_line);
							push (@seq3_delete,$indel_line);
							$coord1++; 
							$coord2++;
							
							$gapLenth--;
						}
				}
				# seq3 inserts
				elsif ((substr($sequence1,$position,1) eq "-")
					&& (substr($sequence2,$position,1) eq "-")
					&& (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){
						
						while($gapLenth > 0){
							$ABC = join("",($ABC,"T"));
							my @s = split(/:/, $seq3);
							$indelType = $s[0]."_insert";
							
							#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
							$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
							push (@indels,$indel_line);
							push (@seq3_insert,$indel_line);
							$coord3++;
							
							$gapLenth--;
						}
				}else{
					while($gapLenth > 0){
						$ABC = join("",($ABC,"N"));
						$coord1++; $coord2++; $coord3++;
						
						$gapLenth--;
					}
				}
				
				# readjust the value of the variable $position to indicate the last character of the gap
				$position = $position + $localGap - 1;
			}
			
		}
		@array_return=($seq1,$seq2,$seq3,$ABC);
		return (@array_return); 

	}
	# ignore pairwise cases for now, just count the number of blocks
	elsif (scalar(@sequences) == 2){
		my $ABC = "";
		my $coord1 = my $coord2 = my $coord3 = 0;
		$count3++;

		$line1 = $sequences[0];
		$line2 = $sequences[1];
		chomp ($line1);
		chomp ($line2);

		if ($line2 !~ m/$ingroup2/){
			$count4++;
		}
	}
}

		
sub get_indels_lengths{
	my (@array) = @_;
	if (scalar(@array) == 4){
		my $seq1 = $array[0]; my $seq2 = $array[1]; my $seq3 = $array[2]; my $ABC = $array[3];

		while ($ABC =~ m/(X+)/g) {
			push (@seq1_delete_lengths,length($1));
			$count_seq1delete++;
		}
		
		while ($ABC =~ m/(Y+)/g) {
			push (@seq2_delete_lengths,length($1));
			$count_seq2delete++;
		}
		while ($ABC =~ m/(S+)/g) {
			push (@seq3_delete_lengths,length($1));
			$count_seq3delete++;
		}
		while ($ABC =~ m/(Z+)/g) {	
			push (@seq1_insert_lengths,length($1));
			$count_seq1insert++;
		}
		while ($ABC =~ m/(W+)/g) {
			push(@seq2_insert_lengths,length($1));
			$count_seq2insert++;
		}
		while ($ABC =~ m/(T+)/g) {
			push (@seq3_insert_lengths,length($1));
			$count_seq3insert++;
		}
	}
	elsif (scalar(@array) == 0){
		next;
	}
		
}
# convert to coordinates to + strand if align orient = -
sub convert_coords{
	my (@array) = @_;
	my $s = $array[0];
	my $e = $array[1];
	my $o = $array[2];
	my $l = $array[3];
	my $start_plus = my $end_plus = 0;

	if ($o eq "-"){
		$start_plus = ($l - $e);
		$end_plus = ($l - $s);
	}elsif ($o eq "+"){
		$start_plus = $s;
		$end_plus = $e;
	}

	return ($start_plus, $end_plus);
}

# get first line only for each event
sub get_starts_only{
	my (@test) = @_;
    my $seq1 = my $seq2 = my $seq3 = my $indelType = my $old_seq1 = my $old_seq2 = my $old_seq3 = my $old_indelType = my $old_line = "";
    my $coord1 = my $coord2 = my $coord3 = my $old_coord1 = my $old_coord2 = my $old_coord3 = 0;

    my @matches = ();
    my @seq1_insert = my @seq1_delete = my @seq2_insert = my @seq2_delete = my @seq3_insert = my @seq3_delete = ();
				
	
    foreach my $line (@test){
    	chomp($line);
        $line =~ s/^\s*//;
        $line =~ s/\s+/\t/g;
		my @line1 = split(/\t/, $line);
        $seq1 = $line1[1];
        $coord1 = $line1[2];
        $seq2 = $line1[4];
        $coord2 = $line1[5];
        $seq3 = $line1[7];
        $coord3 = $line1[8];
        $indelType = $line1[10];
               
        if ($indelType =~ m/$ingroup1/ && $indelType =~ m/insert/){
        	if ($coord1 != $old_coord1+1 || ($coord2 != $old_coord2 || $coord3 != $old_coord3)){
	       		$start1++;
                push (@seq1_insert_startOnly,$line);
            }
	    }
        elsif ($indelType =~ m/$ingroup1/ && $indelType =~ m/delete/){
			if ($coord1 != $old_coord1 || ($coord2 != $old_coord2+1 || $coord3 != $old_coord3+1)){
		        $start2++;
		        push(@seq1_delete_startOnly,$line);
		    }
		}
        elsif ($indelType =~ m/$ingroup2/ && $indelType =~ m/insert/){
	    	if ($coord2 != $old_coord2+1 || ($coord1 != $old_coord1 || $coord3 != $old_coord3)){
		    	$start3++;
		        push(@seq2_insert_startOnly,$line);
		    }
		}
        elsif ($indelType =~ m/$ingroup2/ && $indelType =~ m/delete/){
        	if ($coord2 != $old_coord2 || ($coord1 != $old_coord1+1 || $coord3 != $old_coord3+1)){
            	$start4++;
                push(@seq2_delete_startOnly,$line);
            }
        }
        elsif ($indelType =~ m/$outgroup/ && $indelType =~ m/insert/){
            if ($coord3 != $old_coord3+1 || ($coord1 != $old_coord1 || $coord2 != $old_coord2)){
                $start5++;
                 push(@seq3_insert_startOnly,$line);
            }
        }
        elsif ($indelType =~ m/$outgroup/ && $indelType =~ m/delete/){
        	if ($coord3 != $old_coord3 || ($coord1 != $old_coord1+1 ||$coord2 != $old_coord2+1)){
            	$start6++;
                push(@seq3_delete_startOnly,$line);
            }
        }
        
        $old_indelType = $indelType;
        $old_seq1 = $seq1;
        $old_coord1 = $coord1;
        $old_seq2 = $seq2;
        $old_coord2 = $coord2;
        $old_seq3 = $seq3;
        $old_coord3 = $coord3;
        $old_line = $line;
	}
}
# append lengths to each event start line
my $counter1; my $counter2; my $counter3; my $counter4; my $counter5; my $counter6; 
my @final1 = my @final2 = my @final3 = my @final4 = my @final5 = my @final6 = ();
my $final_line1 = my $final_line2 = my $final_line3 = my $final_line4 = my $final_line5 = my $final_line6 = "";


for ($counter1 = 0; $counter1 < @seq3_insert_startOnly; $counter1++){
	$final_line1 = join("\t",($seq3_insert_startOnly[$counter1],$seq3_insert_lengths[$counter1]));
	push (@final1,$final_line1);
}

for ($counter2 = 0; $counter2 < @seq3_delete_startOnly; $counter2++){
    $final_line2 =  join("\t",($seq3_delete_startOnly[$counter2],$seq3_delete_lengths[$counter2]));
    push(@final2,$final_line2);
}

for ($counter3 = 0; $counter3 < @seq2_insert_startOnly; $counter3++){
    $final_line3 =  join("\t",($seq2_insert_startOnly[$counter3],$seq2_insert_lengths[$counter3]));
	push(@final3,$final_line3);
}

for ($counter4 = 0; $counter4 < @seq2_delete_startOnly; $counter4++){
    $final_line4 =  join("\t",($seq2_delete_startOnly[$counter4],$seq2_delete_lengths[$counter4]));
    push(@final4,$final_line4);
}
		
for ($counter5 = 0; $counter5 < @seq1_insert_startOnly; $counter5++){
    $final_line5 =  join("\t",($seq1_insert_startOnly[$counter5],$seq1_insert_lengths[$counter5]));
    push(@final5,$final_line5);
}

for ($counter6 = 0; $counter6 < @seq1_delete_startOnly; $counter6++){
    $final_line6 =  join("\t",($seq1_delete_startOnly[$counter6],$seq1_delete_lengths[$counter6]));
    push(@final6,$final_line6);
}       

# format final output
# # if inserts, increase coords for the sequence inserted, other sequences give coords for 5' and 3' bases flanking the gap
# # for deletes, increase coords for other 2 sequences and the one deleted give coords for 5' and 3' bases flanking the gap

get_final_format(@final5);
get_final_format(@final6);
get_final_format(@final3);
get_final_format(@final4);
get_final_format(@final1);
get_final_format(@final2);

sub get_final_format{
	my (@final) = @_;
	foreach (@final){
		my $event_line = $_;
		my @events = split(/\t/, $event_line);
		my $event_type = $events[10];
		my @name_align1 = split(/:/, $events[1]);
		my @name_align2 = split(/:/, $events[4]);
		my @name_align3 = split(/:/, $events[7]);
		my $seq1_event_start = my $seq1_event_end = my $seq2_event_start = my $seq2_event_end = my $seq3_event_start = my $seq3_event_end = 0;
		my $final_event_line = "";	
		# seq1_insert
		if ($event_type =~ m/$ingroup1/ && $event_type =~ m/insert/){
			# only increase coord for human
			# remember that other two sequnences, the gap spans (coord - 1) --> coord
			$seq1_event_start = ($events[2]);
			$seq1_event_end = ($events[2]+$events[11]-1);
			$seq2_event_start = ($events[5]-1);
			$seq2_event_end = ($events[5]);
			$seq3_event_start = ($events[8]-1);
			$seq3_event_end = ($events[8]);
			$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
		}
		# seq1_delete
		elsif ($event_type =~ m/$ingroup1/ && $event_type =~ m/delete/){
			# only increase coords for seq2 and seq3
			# remember for seq1, the gap spans (coord - 1) --> coord
			$seq1_event_start = ($events[2]-1);
			$seq1_event_end = ($events[2]);
            $seq2_event_start = ($events[5]);
            $seq2_event_end = ($events[5]+$events[11]-1);
            $seq3_event_start = ($events[8]);
            $seq3_event_end = ($events[8]+$events[11]-1);
			$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
		}
		# seq2_insert
		elsif ($event_type =~ m/$ingroup2/ && $event_type =~ m/insert/){	
			# only increase coords for seq2 
			# remember that other two sequnences, the gap spans (coord - 1) --> coord
            $seq1_event_start = ($events[2]-1);
            $seq1_event_end = ($events[2]);
			$seq2_event_start = ($events[5]);
            $seq2_event_end = ($events[5]+$events[11]-1);
            $seq3_event_start = ($events[8]-1);
			$seq3_event_end = ($events[8]);			
			$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
		}
		# seq2_delete
		elsif ($event_type =~ m/$ingroup2/ && $event_type =~ m/delete/){
			# only increase coords for seq1 and seq3
			# remember for seq2, the gap spans (coord - 1) --> coord
            $seq1_event_start = ($events[2]);
			$seq1_event_end = ($events[2]+$events[11]-1);	
            $seq2_event_start = ($events[5]-1);
	        $seq2_event_end = ($events[5]);
            $seq3_event_start = ($events[8]);
            $seq3_event_end = ($events[8]+$events[11]-1);
			$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
		}	
		# start testing w/seq3_insert
		elsif ($event_type =~ m/$outgroup/ && $event_type =~ m/insert/){
			# only increase coord for rheMac
			# remember that other two sequnences, the gap spans (coord - 1) --> coord
			$seq1_event_start = ($events[2]-1);
			$seq1_event_end = ($events[2]);
			$seq2_event_start = ($events[5]-1);
			$seq2_event_end = ($events[5]);
			$seq3_event_start = ($events[8]);
			$seq3_event_end = ($events[8]+$events[11]-1);
			$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
		}
		# seq3_delete
		elsif ($event_type =~ m/$outgroup/ && $event_type =~ m/delete/){
			# only increase coords for seq1 and seq2
			# remember for seq3, the gap spans (coord - 1) --> coord
			$seq1_event_start = ($events[2]);
			$seq1_event_end = ($events[2]+$events[11]-1);
			$seq2_event_start = ($events[5]);
			$seq2_event_end = ($events[5]+$events[11]-1);
			$seq3_event_start = ($events[8]-1);
			$seq3_event_end = ($events[8]);
			$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));

		}
		
		print OFILE "$final_event_line\n";
	}
}
close OFILE;