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}
else
{
        print "Unknown option for -R\n";
        exit;
}

####################################
# Processing tiling output         #
####################################
if ($debug) {
  print "Do tiling...\n";
}

#-------------------------------- 

##################
#Do Tiling
#-------------------------------------------
doTiling ($mummer_tiling, $path_toPass, $path_dir,$reference, $query_file, $choice, $prefix,$mlfas, $fasta_bin, $avoid_Ns, $ref_len, $gaps_2file, $ref_inline, $add_bin_2ps, $pick_primer, $flank, $chk_uniq, $tbx,$numNs);





############################################## SUB ROUTINES for CONTIG ORDERING and PRIMER DESIGN ##########################################################
# Put in one file for ease of downloading. They could be placed in separate packages.
#----------------------------------------------------------------------------------------------------------
#################################Contig ordering ##########################################################
######## 

sub help
{

die <<EOF 

***********************************************************************************
* ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences           *
*                                                                                 *
*                                                                                 *
*   Copyright (C) 2008-11 The Wellcome Trust Sanger Institute, Cambridge, UK.     *
*   All Rights Reserved.                                                          *
*                                                                                 *
***********************************************************************************

USAGE
abacas.pl -r <reference file: single fasta> -q <query sequence file: fasta> -p <nucmer/promer>  [OPTIONS]

	-r	reference sequence in a single fasta file
	-q	contigs in multi-fasta format
	-p	MUMmer program to use: 'nucmer' or 'promer'
OR
abacas.pl -r <reference file: single fasta>  -q <pseudomolecule/ordered sequence file: fasta> -e 
OPTIONS
        -h              print usage
	-d		use default nucmer/promer parameters 
	-s	int	minimum length of exact matching word (nucmer default = 12, promer default = 4)
	-m		print ordered contigs to file in multifasta format 
	-b		print contigs in bin to file 
	-N		print a pseudomolecule without "N"s 
	-i 	int 	mimimum percent identity [default 40]
	-v	int	mimimum contig coverage [default 40]
	-V	int	minimum contig coverage difference [default 1]
	-l	int	minimum contig length [default 1]
	-t		run tblastx on contigs that are not mapped 
	-g 	string (file name)	print uncovered regions (gaps) on reference to file name
	-n	int	insert n Ns between overlapping contigs [default 100]
	-a		append contigs in bin to the pseudomolecule
	-o	prefix  output files will have this prefix
	-P		pick primer sets to close gaps
	-f	int	number of flanking bases on either side of a gap for primer design (default 350)
        -R      int     Run mummer [default 1, use -R 0 to avoid running mummer]
	-e 		Escape contig ordering i.e. go to primer design
	-c 		Reference sequence is circular

EOF
}
########
sub usage
{

die <<EOF 
---------------------------------------------------------------------------------------------------

ABACAS.$version
visit www.abacas.sourceforge.net for more information.
--------------------------------
Please report bugs to:sa4 (at)sanger.ac.uk  and tdo (at) sanger.ac.uk
----------------------------------------------------------------------------------------------------

USAGE
abacas.pl -r <reference file: single fasta> -q <query sequence file: fasta> -p <nucmer/promer>  [OPTIONS]
	-r	reference sequence in a single fasta file
	-q	contigs in multi-fasta format
	-p	MUMmer program to use: 'nucmer' or 'promer'
for contig ordering and  primer design

OR
abacas.pl -r <reference file: single fasta>  -q <pseudomolecule/ordered sequence file: fasta> -e 
to escape contig ordering and go directly to primer design

OR
abacas.pl -h  for help

EOF
}
########
##################
sub print_header
{
    print "
***********************************************************************************
* ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences           *
*                                                                                 *
*                                                                                 *
*   Copyright (C) 2008-11 The Wellcome Trust Sanger Institute, Cambridge, UK.     *
*   All Rights Reserved.                                                          *
*                                                                                 *
***********************************************************************************
\n";
}