#!/usr/bin/perl
use Getopt::Long;
$|=1;
$script=$0;
$script=~s/^.+[\\\/]//;

$information="
 ================================ sRNAmapper ==================================
 VERSION 1.0.4                                    LAST MODIFIED: 22. March 2017

 Please cite:
 Rosenkranz D, Han CT, Roovers EF, Zischler H, Ketting RF. Piwi proteins and
 piRNAs in mammalian oocytes and early embryos: From sample to sequence.
 Genomics Data 2015 5:309-313.

 SCOPE:
 sRNAmapper is specifically designed to map small RNA sequences to genomes.
 To this end it uses a specialized mapping algorithm that requires a perfect
 5' seed match (default: 18nt) and optionally allows non-template 3' ends
 as well as internal mismatches in the part of the sequence that follows
 the seed region. Allowing non-template 3' ends will ensure the mapping of
 3' modified (adenylated/uridylated) small RNAs while allowing internal mis-
 matches can enhance sensitivity considering degressive read quality towards
 3' ends.
 
 ------------------------------------------------------------------------------
 
 EXEMPLARY ALIGNMENT OF VALID HIT USING DEFAULT PARAMETERS:
 
 genome  5'-TGCGTATTAGCTCGCATGACTCGCATAGCTACGTGGTAGC-3'
                  ||||||||||||||||||x||||||xx
 sRNA          5'-TTAGCTCGCATGACTCGCTTAGCTAAA-3'

 ------------------------------------------------------------------------------
 
 USAGE:
 perl $script -i input.fasta -g genome.fasta (-option [value])
 
 *You may also use FASTAQ-formatted files.

 ------------------------------------------------------------------------------

 OPTIONS:
 -f [value]
 -format [value]
             Specifies the output format. Valid values are <sam>, <eland> and
             <compact>. The default value is <eland>.
 -g [value]
 -genome [value]
             Name of the reference/genome file (FASTA). *REQUIRED
 -i [value]
 -input [value]
             Name of the input file (FASTA). Multiple input files are allowed.
             Input files will be processed in parallel. *REQUIRED
 -o [value]
 -output [value]
             Name of the output file. By default the output file will be named
             input.fasta.map (input file: input.fasta).
 -m [value]
 -mismatch [value]
             Defines the maximum internal mismatch in the part of the sequence
             that follows the seed region. The default value is <1>.
 -n [value]
 -nontemplates [value] 
             Defines the number of allowed non-template 3' nucleotides. The
             default value is <2> which means that the last 2 nucleotides do
             not need to match the reference to produce a valid hit.
 -a [value]
 -alignments [value]
             Strictness of the output. Valid values are <all> and <best>. <all>
             will output all hits while <best> will output only the best hits.
             Can be still more than one hit per sequence if the hits have equal
             quality. The default value is <all>.
 -s [value]
 -seedmatch [value]
             Defines the number of 5' nucleotides that must produce a perfect
             hit (seed match). The default value is <18>.
 -r [value]
 -replaceheads [value]
             Titles of the reference sequence (FASTA headers) can optionally be
             replaced by a consecutively numbering to reduce output size and
             save diskspace. Valid values are <0> (keep original names) and <1>
             (replace headers by numbers). The default value is <0>.
 -d [value]
 -direction [value]
             Defines if mapping is performed on plus strand only or on both
             strands. Valid values are <0> (search plus strand only) and <1>
             (search both strands). The default value is <1>.
 -v [value]
 -verbosity [value]
             Defines verbosity of the program during the mapping process. Valid
             values are <0> (silent), <1> (concise) and <2> (verbose). The
             default value is <2>.
 -h
 -help
             Will print this information.

 ------------------------------------------------------------------------------

 (c) David Rosenkranz
 Institute of Organismic and Molecular Evolutionary Biology
 Dept. Anthropology, small RNA group
 Johannes Gutenberg University Mainz, Germany
 Contact: rosenkranz\@uni-mainz.de
 Web: www.smallRNAgroup.uni-mainz.de
 
 ##############################################################################


";

$outfile="";
GetOptions
	(
	"h"=>\$print_info,
	"help"=>\$print_info,
	"i=s"=>\@input,
	"input=s"=>\@input,
	"o=s"=>\$outfile,
	"output=s"=>\$outfile,
	"g=s"=>\$genome_file,
	"genome=s"=>\$genome_file,
	"s=s"=>\$perfect_5p,
	"seedmatch=s"=>\$perfect_5p,
	"n=s"=>\$untemplate_3p,
	"nontemplates=s"=>\$untemplate_3p,
	"m=s"=>\$max_internal_mm,
	"mismatch=s"=>\$max_internal_mm,
	"d=s"=>\$search_both_strands,
	"direction=s"=>\$search_both_strands,
	"r=s"=>\$replace_titles_by_id,
	"replaceheads=s"=>\$replace_titles_by_id,
	"f=s"=>\$format,
	"format=s"=>\$format,
	"a=s"=>\$output_strictness,
	"alignments=s"=>\$output_strictness,
	"v=s"=>\$verbosity,
	"verbosity=s"=>\$verbosity,
	);

$format=lc$format;
if($print_info){print$information;exit;}
if($perfect_5p!~/^\d+$/){$perfect_5p=18;}
if($untemplate_3p!~/^\d+$/){$untemplate_3p=2;}
if($max_internal_mm!~/^\d+$/){$max_internal_mm=1;}
if($search_both_strands!~/^[01]$/){$search_both_strands=1;}
if($replace_titles_by_id!~/^[01]$/){$replace_titles_by_id=0;}
if($format ne'eland'&&$format ne'compact'&&$format ne'sam'){$format="eland";}
if($output_strictness ne 'all'&&$output_strictness ne 'best'){$output_strictness="all";}
if($verbosity!~/^[012]$/){$verbosity=2;}
if(@input==0){print"\n\n STOP: No probe/input file(s) specified.\n\n$information";exit;}
unless(-e$genome_file){print"\n\n STOP: No valid reference/genome file specified.\n\n$information";exit;}
if($search_both_strands==0){$info_strands="no";}else{$info_strands="yes";$search_both_strands=1;}
print"

             ------------------------------------------------
             sRNAmapper Version 1.0.4          22. March 2017
             ------------------------------------------------
             Starting sRNAmapper with the following settings:


             Seed size: ................ $perfect_5p
             Max. non-template 3' bases: $untemplate_3p
             Max. internal mismatch: ... $max_internal_mm
             Search both strands: ...... $info_strands
             Output format: ............ $format 
             Alignments: ............... $output_strictness
     
             (c) David Rosenkranz
             Institute of Organismic and Molecular
             Evolutionary Biology, Dept. Anthropology
             Johannes Gutenberg University Mainz, Germany
             Contact: rosenkranz\@uni-mainz.de
             ------------------------------------------------


";

@childs=();
foreach$probe(@input)
	{
	$pid=fork();
	if($pid) # parent
		{
		push(@childs,$pid);
		}
	elsif($pid==0) # child
		{
		# CHECK INPUT FILE FORMAT
		if($verbosity!=0)
			{
			print"\nChecking input file format...";
			}
		open(IN,$probe)||die print"\nCould not open input file $probe.\n$!\n\n";
		$i=0;
		$fasta_heads=0;
		$fastq_heads=0;
		while(<IN>)
			{
			$i++;
			last if($i==1000);
			if($_=~/^>/)
				{
				$fasta_heads++;
				}
			elsif($_=~/^@/||$_=~/^\+/)
				{
				$fastq_heads++;
				}
			}
		close IN;
		if($fasta_heads>$fastq_heads)
			{
			$iformat='FASTA';
			}
		elsif($fastq_heads>$fasta_heads)
			{
			$iformat='FASTQ';
			}
		else
			{
			die print"\nUnknown file format of input file $probe.\n\n";
			}
		if($verbosity!=0)
			{
			print" done. -> $iformat";
			}
		
		# INDEX PROBES (SENSE)
		$min_length=-1;
		$max_length=0;
		$n_probeseqs=0;
		%probes=();
		$t_start=time;
		open(PROBE,$probe)||die print"\nCould not open sequencefile $probe.\n$!\n\n";
		if($verbosity!=0)
			{
			print"\nIndexing sequences from $probe...";
			}
		$i=0;
		@seq_data=();
		while(<PROBE>)
			{
			$_=~s/\s*$//; # chomp depends on the operating system and can cause problems when processing files from different platforms (Unix vs. Windows)
			push(@seq_data,$_);
			if($iformat eq'FASTQ')
				{
				$i+=0.25;
				}
			elsif($iformat eq'FASTA')
				{
				$i+=0.5;
				}

			if($i==1)
				{
				if($seq_data[1]!~/^\s*$/&&substr($seq_data[1],0,$perfect_5p)!~/N/)
					{
					$n_probeseqs++;
					$seq_data[1]=~tr/atgc/ATGC/;
					
					# hash of arrays: key = 5p seq / array = all 3p seqs that belong to 5p seq
					push(@{$probes{substr($seq_data[1],0,$perfect_5p)}},substr($seq_data[1],$perfect_5p));	
					$seq_data[0]=~s/^[>\@]//;
					$probes_info{$seq_data[1]}=$seq_data[0];
					
					# check minimum and maximum sequence length
					if(length$seq_data[1]<$min_length||$min_length==-1)
						{
						$min_length=length$seq_data[1];
						}
					if(length$seq_data[1]>$max_length)
						{
						$max_length=length$seq_data[1];
						}
					}
				$i=0;
				@seq_data=();
				}
			}
		close PROBE;
		$n_indexes=keys%probes;
		print" done.\nCreated $n_indexes indexes for $n_probeseqs sequences ($min_length-$max_length nt)";
		
		# INDEX PROBES (FOR REVERSE STRAND SEARCH)
		if($search_both_strands==1)
			{
			open(PROBE,$probe)||die print"\nCould not open sequencefile $probe.\n$!\n\n";
			if($verbosity!=0)
				{
				print"\nIndexing sequences for reverse strand search...";
				}
			while(<PROBE>)
				{
				$_=~s/\s*$//;
				push(@seq_data,$_);
				if($iformat eq'FASTQ')
					{
					$i+=0.25;
					}
				elsif($iformat eq'FASTA')
					{
					$i+=0.5;
					}
				if($i==1)
					{
					if($seq_data[1]!~/^\s*$/&&substr($seq_data[1],0,$perfect_5p)!~/N/)
						{
						$seq_data[1]=~tr/atgc/ATGC/;
						$rc=$seq_data[1];
						$rc=~tr/ATGC/TACG/;
						$rc=reverse$rc;
						push(@{$probes_rc{substr($rc,-$perfect_5p)}},substr($rc,0,(length$rc)-$perfect_5p));
						$seq_data[0]=~s/^[>\@]//;
						$probes_rc_info{$rc}=$seq_data[0];
						}
					$i=0;
					@seq_data=();
					}
				}
			close PROBE;
			print" done.";
			}
		
		# READ GENOME, SAVE INFORMATION AND OPTIONALLY REPLACE FASTA TITLES BY IDs
		if($verbosity!=0)
			{
			print"\nRead genome file...";
			}
		open(GENOME,$genome_file)||die print"\nCould not open genome file $genome_file.\n$!\n\n";
		open(RAW,">$probe.raw");
		if($replace_titles_by_id==1)
			{
			print RAW"# original fasta header\t->\treplaced by ID\n";
			}
		
		$replace_id=0;
		$total_genome_size=0;
		@sam=();
		%sam=();
		while(<GENOME>)
			{
			$_=~s/\s*$//;
			if($_=~/>/)
				{
				$_=~s/^>//;
				$title=$_;
				push(@sam,$title);
				if($replace_titles_by_id==1)
					{
					$replace_id++;
					$replace_titles{$_}=$replace_id;
					print RAW"# $_\t->\t$replace_id\n";
					}
				}
			else
				{
				$sam{$title}+=length$_;
				$total_genome_size+=length$_;
				}
			}
		close GENOME;
		
		# START MAPPING
		if($verbosity!=0)
			{
			print" done. Total size: $total_genome_size"."bp"."\nStart mapping...";	
			}
		$chromosome="";
		$position=-1;
		$processed_bp=0;
		$raw_lines=0;
		$next_line="#";
		$stretch="##";
		$lagging_stretch="";
		%best_hit=();
		$t0=time;
		$t_start=time;
		open(GENOME,$genome_file)||die print"\nCould not open genome file $genome_file.\n$!\n\n";
		while(length$next_line>0)
			{
			# progress
			if($verbosity==2)
				{
				$t1=time;
				if($t1-$t0>=10)
					{
					$t0=time;
					$speed=int(($processed_bp/(time-$t_start))+0.5);
					$est_remaining="?";
					if($speed>0)
						{
						$est_remaining=int((($total_genome_size-$processed_bp)/$speed)+0.5);
						}
					print"\nPROBE:.. $probe\nREF:.... $chromosome\nPOS:.... $position\nScanned: $processed_bp bp\nSpeed:.. $speed bp/s\nEstimated remaining time: $est_remaining seconds\n";
					}	
				}
			
			if($concatenate_index==0)
				{
				sliding_window_increament();
				sub sliding_window_increament
					{
					# sliding window +1bp
					$stretch=~s/.//;
					$lagging_bp=$&;
					$position++;
					
					# save passed sequence for reverse strand search (extension of seed match)
					if($search_both_strands==1)
						{
						$lagging_stretch.=$lagging_bp;
						if(length$lagging_stretch>$max_length)
							{
							$lagging_stretch=~s/.//;
							}
						}
					}
				}
			
			if(length$stretch>=$max_length)
				{
				$concatenate_index=0;
				search_seed_matches();
				sub search_seed_matches
					{
					# check for seed match in sense orientation
					if($probes{substr($stretch,0,$perfect_5p)})
						{
						foreach$p3(@{$probes{substr($stretch,0,$perfect_5p)}})
							{
							$count_internal_mm=0;
							$count_untemplate_3p=0;
							foreach$pos(0..((length$p3)-$untemplate_3p)-1)
								{
								if(substr($stretch,$pos+$perfect_5p,1) ne substr($p3,$pos,1))
									{
									$count_internal_mm++;
									last if($count_internal_mm>$max_internal_mm);
									}
								}
							if($count_internal_mm<=$max_internal_mm)
								{
								$locus_seq=substr($stretch,0,$perfect_5p+length$p3);
								foreach$pos(0..$untemplate_3p-1)
									{
									if(substr($p3,-$untemplate_3p+$pos,1)=~/[ATGCN]/&&substr($p3,-$untemplate_3p+$pos,1) ne substr($locus_seq,-$untemplate_3p+$pos,1))
										{
										$count_untemplate_3p++;
										}
									}
								$hit_mm=$count_internal_mm+$count_untemplate_3p;
								$mapped_seq=substr($stretch,0,$perfect_5p).$p3;
								
								# do not output hit if output_strictness is 'best' and it is worse than a hit before
								unless(exists($best_hit{$mapped_seq}))
									{
									$best_hit{$mapped_seq}=$hit_mm;
									print RAW"$replace_titles{$chromosome}\t$position\t$locus_seq\t$probes_info{$mapped_seq}\t$mapped_seq\t$hit_mm\t+\n";
									$raw_lines++;
									}
								else
									{
									if($hit_mm<=$best_hit{$mapped_seq})
										{
										$best_hit{$mapped_seq}=$hit_mm;
										print RAW"$replace_titles{$chromosome}\t$position\t$locus_seq\t$probes_info{$mapped_seq}\t$mapped_seq\t$hit_mm\t+\n";
										$raw_lines++;
										}
									elsif($output_strictness eq'all')
										{
										print RAW"$replace_titles{$chromosome}\t$position\t$locus_seq\t$probes_info{$mapped_seq}\t$mapped_seq\t$hit_mm\t+\n";
										$raw_lines++;
										}
									}
								}
							}
						}
					
					if($search_both_strands==1)
						{
						# check for seed match in antisense orientation
						if($probes_rc{substr($stretch,0,$perfect_5p)})
							{
							foreach$p3(@{$probes_rc{substr($stretch,0,$perfect_5p)}})
								{
								$count_internal_mm=0;
								$count_untemplate_3p=0;
								foreach$pos(0..((length$p3)-$untemplate_3p)-1)
									{
									if(substr($lagging_stretch,-1-$pos,1) ne substr($p3,-1-$pos,1))
										{
										$count_internal_mm++;
										last if($count_internal_mm>$max_internal_mm);
										}
									}
									
								if($count_internal_mm<=$max_internal_mm)
									{
									$locus_seq=substr($stretch,0,$perfect_5p);
									if(length$p3>0)
										{
										$locus_seq=substr($lagging_stretch,-length$p3).$locus_seq;
										}
									$locus_seq=~tr/ATGC/TACG/;
									$locus_seq=reverse$locus_seq;
									
									$outside=0;
									foreach$pos(0..$untemplate_3p-1)
										{
										if(substr($lagging_stretch,-(length$p3)+$pos,1)eq'#') # check if 3' end of hit goes beyond start of the scaffold/chromosome sequence
											{
											$outside=1;
											last;
											}
										if(substr($p3,$pos,1)=~/[ATGCN]/&&substr($lagging_stretch,-(length$p3)+$pos,1) ne substr($p3,$pos,1))
											{
											$count_untemplate_3p++;
											}
										}
									next if($outside==1);
									$hit_mm=$count_internal_mm+$count_untemplate_3p;
									
									$mapped_seq=$p3.substr($stretch,0,$perfect_5p);
									$mapped_seq_rc=$mapped_seq;
									$mapped_seq=~tr/ATGC/TACG/;
									$mapped_seq=reverse$mapped_seq;
									$rc_position=($position-length$p3);
									
									# do not output hit if output_strictness is 'best' and it is worse than a hit before
									unless(exists($best_hit{$mapped_seq}))
										{
										$best_hit{$mapped_seq}=$hit_mm;
										print RAW"$replace_titles{$chromosome}\t$rc_position\t$locus_seq\t$probes_rc_info{$mapped_seq_rc}\t$mapped_seq\t$hit_mm\t-\n";
										$raw_lines++;
										}
									else
										{
										if($hit_mm<=$best_hit{$mapped_seq})
											{
											$best_hit{$mapped_seq}=$hit_mm;
											print RAW"$replace_titles{$chromosome}\t$rc_position\t$locus_seq\t$probes_rc_info{$mapped_seq_rc}\t$mapped_seq\t$hit_mm\t-\n";
											$raw_lines++;
											}
										elsif($output_strictness eq'all')
											{
											print RAW"$replace_titles{$chromosome}\t$rc_position\t$locus_seq\t$probes_rc_info{$mapped_seq_rc}\t$mapped_seq\t$hit_mm\t-\n";
											$raw_lines++;
											}
										}
									}
								}
							}
						}
					}
				}
			
			# elongate the sequence within the sliding windows
			else
				{
				$next_line=<GENOME>;
				$next_line=~s/\s*$//;
				if($next_line=~/^>/)
					{
					# finish processing previous reference sequence
					while(length$stretch>=$perfect_5p)
						{
						search_seed_matches();
						sliding_window_increament();
						}
					
					$chromosome=$next_line;
					$chromosome=~s/>//;
					if($replace_titles_by_id==0)
						{
						$replace_titles{$chromosome}=$chromosome;
						}
					$position=-1;
					$stretch="##";
					$lagging_stretch="";
					}
				else
					{
					$processed_bp+=length$next_line;
					$stretch.=uc$next_line;
					$concatenate_index=1;
					}
				}
			}
		$t_end=time;
		$time_used=$t_end-$t_start;
		if($verbosity==2)
			{
			print"\nPROBE:.. $probe\nREF:.... $chromosome\nPOS:.... $position\nScanned: $processed_bp bp\nSpeed:.. $speed bp/s\nEstimated remaining time: $est_remaining seconds.\n\nFiltering/Sorting raw file:\n\n0%                                50%                                100%\n|----------------------------------|----------------------------------|\n";
			}
		elsif($verbosity==1)
			{
			print" done.\nTime used for mapping: $time_used seconds.\n\nFiltering/Sorting raw file:\n\n0%                                50%                                100%\n|----------------------------------|----------------------------------|\n";
			}
		
		# FILTER AND/OR SORT
		$t_start=time;
		open(RAW,"$probe.raw")||die print"\nCould not open RAW file $probe.raw.\n$!\n\n";
		open(MAP,">$probe.map")||die print"\nCould not create MAP file $probe.map.\n$!\n\n";
		
		if($format eq 'sam')
			{
			%SAMstrand=("+"=>"0","-"=>"16");
			print MAP"\@HD VN: 1.5 SO:coordinate\n";
			foreach$rname(@sam)
				{
				print MAP"\@SQ SN:$rname LN:$sam{$rname}\n";
				}
			}
		
		@unsorted=();
		$buffer_max=100000;
		$buffer_release=90000;
		$prev_chromosome="#";
		$printed_dots=0;
		$processed_raw_lines=0;
		while(<RAW>)
			{
			# show progress
			if($verbosity!=0)
				{
				$processed_raw_lines++;
				if($processed_raw_lines>=$raw_lines/71)
					{
					print".";
					$printed_dots++;
					$processed_raw_lines=0;
					}
				}
			
			if($_=~/^#/&&$format ne 'sam')
				{
				print MAP$_;
				}
			else
				{
				@d=split("\t",$_);
				if($prev_chromosome ne "#"&&$d[0] ne $prev_chromosome)
					{
					sort_map();
					sub sort_map
						{
						@sorted=sort@unsorted;
						foreach$element(@sorted)
							{
							$element=~s/^.{13}//; # delete the index tag from entry (index tag is used for sorting only)
							print MAP$element;
							}
						undef@sorted;
						@sorted=();
						undef@unsorted;
						@unsorted=();
						}
					}
				elsif(@unsorted==$buffer_max)
					{
					@sorted=sort@unsorted;
					foreach$i(0..$buffer_release-1)
						{
						$sorted[$i]=~s/^.{13}//; # delete the index tag from entry (index tag is used for sorting only)
						print MAP$sorted[$i];
						}
					undef@unsorted;
					@unsorted=();
					foreach$i($buffer_release..$buffer_max-1)
						{
						push(@unsorted,$sorted[$i]);
						}
					undef@sorted;
					@sorted=();
					}
				
				if($d[5]==$best_hit{$d[4]}||$output_strictness eq'all')
					{
					$index="000000000000".$d[1];
					$index=substr($index,-12);
					if($format eq'compact') # chromosome | coordinate | strand | length | divergence | title
						{
						$length_hit=length$d[4];
						if($d[5]>0)
							{
							@gen_seq=split('',$d[2]);
							@hit_seq=split('',$d[4]);
							$seq_div="";
							foreach$pos(1..$length_hit)
								{
								if($gen_seq[$pos-1]ne$hit_seq[$pos-1])
									{
									$seq_div.="$pos$hit_seq[$pos-1]";
									}
								}
							}
						else
							{
							$seq_div="-";
							}
						$d[6]=~s/\s*$//;
						push(@unsorted,"$index\t$d[0]\t$d[1]\t$d[6]\t$length_hit\t$seq_div\t$d[3]\n");
						}
					elsif($format eq'eland')
						{
						push(@unsorted,"$index\t$d[0]\t$d[1]\t$d[2]\t$d[3]\t$d[4]\t$d[5]\t$d[6]");
						}
					elsif($format eq'sam')
						{
						# generate CIGAR string
						$cigar_pre="";
						$stretch=0;
						foreach$pos(0..(length$d[4])-1)
							{
							if(substr($d[2],$pos,1) eq substr($d[4],$pos,1))
								{
								$cigar_pre.="=";
								}
							else
								{
								$cigar_pre.="X";
								}
							}
						$cigar="";
						while(1)
							{
							if($cigar_pre=~s/^=+//)
								{
								$n=length$&;
								$cigar.="$n"."=";
								}
							elsif($cigar_pre=~s/^X+//)
								{
								$n=length$&;
								$cigar.="$n"."X";
								}
							else
								{
								last;
								}
							}

						if($d[6]=~/-/)
							{
							$d[4]=reverse$d[4];
							$d[4]=~tr/ATGC/TACG/;
							$strand=16;
							}
						else
							{
							$strand=0;
							}
						push(@unsorted,"$index\t$d[3]\t$strand\t$d[0]\t$d[1]\t255\t$cigar\t$d[3]\t*\t0\t0\t$d[4]\t*\n");
						}
					if($d[1]>$max_coordinate)
						{
						$max_coordinate=$d[1];
						}
					}
				$prev_chromosome=$d[0];
				}
			}
		sort_map();
		close RAW;
		close MAP;
		unlink"$probe.raw"||print"\nCould not remove RAW file $probe.raw.\n$!\n\n";
		$t_end=time;
		$time_used=$t_end-$t_start;
		if($verbosity!=0)
			{
			foreach($printed_dots..70)
				{
				print".";
				}
			print"\nTime used for filtering/sorting: $time_used seconds.\n";
			}
		if($outfile!~/^\s*$/)
			{
			rename("$probe.map","$outfile")||print"\nCould not rename MAP file '$probe.map' -> '$outfile'.\n$!\n\n";
			}
		exit 0;
		}
	else
		{
		die print"\nCould not fork mapping process: $!\n";
		}
	}
foreach(@childs)
	{
	$tmp=waitpid($_,0);
	}
exit;