 /*==========================================================================
             RazerS - Fast Read Mapping with Controlled Loss Rate
                   http://www.seqan.de/projects/razers.html

 ============================================================================
  Copyright (C) 2008 by David Weese

  This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 3 of the License, or (at your options) any later version.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 ==========================================================================*/

#define SEQAN_PROFILE					// enable time measuring
//#define SEQAN_DEBUG_SWIFT				// test SWIFT correctness and print bucket parameters
//#define RAZERS_DEBUG					// print verification regions
#define RAZERS_PRUNE_QGRAM_INDEX		// ignore highly abundant q-grams
#define RAZERS_CONCATREADS				// use <ConcatDirect> StringSet to store reads
#define RAZERS_MEMOPT					// optimize memory consumption
#define RAZERS_MASK_READS				// remove matches with max-hits optimal hits on-the-fly
//#define NO_PARAM_CHOOSER				// disable loss-rate parameter choosing
#define RAZERS_MATEPAIRS				// enable paired-end matching
//#define RAZERS_DIRECT_MAQ_MAPPING
//#define SEQAN_USE_SSE2_WORDS			// use SSE2 128-bit integers for MyersBitVector
#define RAZERS_OPENADDRESSING
//#define RAZERS_SPLICED

#ifdef RAZERS_SPLICED
  #define RAZERS_MATEPAIRS
#endif

#include <cctype>

#include <seqan/platform.h>
#ifdef PLATFORM_WINDOWS
	#define SEQAN_DEFAULT_TMPDIR "C:\\TEMP\\"
#else
	#define SEQAN_DEFAULT_TMPDIR "./"
#endif

#include <seqan/arg_parse.h>
#include "razers.h"
#include "outputFormat.h"
#include "paramChooser.h"

#ifdef RAZERS_MATEPAIRS
#include "razers_matepairs.h"
#endif

#ifdef RAZERS_SPLICED
#include "razers_spliced.h"
#endif



#include <iostream>
#include <sstream>

using namespace std;
using namespace seqan;


//////////////////////////////////////////////////////////////////////////////
// Read a list of genome file names
template<typename TSpec>
int getGenomeFileNameList(CharString filename, StringSet<CharString> & genomeFileNames, RazerSOptions<TSpec> &options)
{
//IOREV
	ifstream file;
	file.open(toCString(filename),ios_base::in | ios_base::binary);
	if(!file.is_open())
		return RAZERS_GENOME_FAILED;

	clear(genomeFileNames);
	char c = _streamGet(file);
	if (c != '>' && c != '@')	//if file does not start with a fasta header --> list of multiple reference genome files
	{
		if(options._debugLevel >=1)
			cout << endl << "Reading multiple genome files:" <<endl;
		
/*		//locations of genome files are relative to list file's location
		string tempGenomeFile(filename);
		size_t lastPos = tempGenomeFile.find_last_of('/') + 1;
		if (lastPos == tempGenomeFile.npos) lastPos = tempGenomeFile.find_last_of('\\') + 1;
		if (lastPos == tempGenomeFile.npos) lastPos = 0;
		string filePrefix = tempGenomeFile.substr(0,lastPos);*/

		unsigned i = 1;
		while(!_streamEOF(file))
		{ 
			_parseSkipWhitespace(file, c);
			appendValue(genomeFileNames,_parseReadFilepath(file,c));
			//CharString currentGenomeFile(filePrefix);
			//append(currentGenomeFile,_parseReadFilepath(file,c));
			//appendValue(genomeFileNames,currentGenomeFile);
			if(options._debugLevel >=2)
				cout <<"Genome file #"<< i <<": " << genomeFileNames[length(genomeFileNames)-1] << endl;
			++i;
			_parseSkipWhitespace(file, c);
		}
		if(options._debugLevel >=1)
			cout << i-1 << " genome files total." <<endl;
	}
	else		//if file starts with a fasta header --> regular one-genome-file input
		appendValue(genomeFileNames, filename, Exact());
	file.close();
	return 0;

}

//////////////////////////////////////////////////////////////////////////////
// Main read mapper function
template <typename TSpec>
int mapReads(
	StringSet<CharString> & genomeFileNames,
	StringSet<CharString> & readFileNames,	// NULL terminated list of one/two read files (single/mate-pairs)
	CharString & errorPrbFileName,
	RazerSOptions<TSpec> &options)
{
	MultiFasta				genomeSet;
	TReadSet				readSet;
	StringSet<CharString>	genomeNames;	// genome names, taken from the Fasta file
	StringSet<CharString>	readNames;		// read names, taken from the Fasta file
	TMatches				matches;		// resulting forward/reverse matches
	String<String<unsigned short> > 	stats;		// needed for mapping quality calculation 

	// dump configuration in verbose mode
	if (options._debugLevel >= 1) 
	{
		CharString bitmap;
		Shape<Dna, GenericShape> shape;
		stringToShape(shape, options.shape);
		shapeToString(bitmap, shape);
		
		cerr << "___SETTINGS____________" << endl;
		cerr << "Genome file:                     \t" << genomeFileNames[0] << endl;
		if (length(readFileNames) > 1u && empty(readFileNames[1]))
			cerr << "Read file:                       \t" << readFileNames[0] << endl;
		else
		{
			cerr << "Read files:                      \t" << readFileNames[0] << endl;
			for (unsigned i = 1; i < length(readFileNames); ++i)
				cerr << "                                 \t" << readFileNames[i] << endl;
		}
		cerr << "Compute forward matches:         \t";
		if (options.forward)	cerr << "YES" << endl;
		else				cerr << "NO" << endl;
		cerr << "Compute reverse matches:         \t";
		if (options.reverse)		cerr << "YES" << endl;
		else				cerr << "NO" << endl;
		cerr << "Error rate:                      \t" << options.errorRate << endl;
		cerr << "Minimal threshold:               \t" << options.threshold << endl;
		cerr << "Shape:                           \t" << bitmap << endl;
		cerr << "Repeat threshold:                \t" << options.repeatLength << endl;
		cerr << "Overabundance threshold:         \t" << options.abundanceCut << endl;
		cerr << "Taboo length:                    \t" << options.tabooLength << endl;
		cerr << endl;
	}
	
	// circumvent numerical obstacles
	options.errorRate += 0.0000001;

	//////////////////////////////////////////////////////////////////////////////
	// Step 1: Load fasta files and determine genome file type
	SEQAN_PROTIMESTART(load_time);

#ifdef RAZERS_MATEPAIRS
	if (length(readFileNames) == 2)
	{
		if (!loadReads(readSet, readNames, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) {
		//if (!loadReads(readSet, readQualities, readNames, readFileNames[0], readFileNames[1], options)) {
			cerr << "Failed to load reads" << endl;
			return RAZERS_READS_FAILED;
		}
	}
	else
#endif
	{
		if (!loadReads(readSet, readNames, toCString(readFileNames[0]), options)) {
		//if (!loadReads(readSet, readQualities, readNames, readFileNames[0], readFileNames[1], options)) {
			cerr << "Failed to load reads" << endl;
			return RAZERS_READS_FAILED;
		}
	} 

	if (options._debugLevel >= 1) cerr << lengthSum(readSet) << " bps of " << length(readSet) << " reads loaded." << endl;
	options.timeLoadFiles = SEQAN_PROTIMEDIFF(load_time);

	if (options._debugLevel >= 1)
		cerr << "Loading reads took               \t" << options.timeLoadFiles << " seconds" << endl;

	if (length(genomeFileNames) == 1)
	{
		int result = getGenomeFileNameList(genomeFileNames[0], genomeFileNames, options);
		if (result == RAZERS_GENOME_FAILED)
		{
			cerr << "Failed to open genome file " << genomeFileNames[0] << endl;
			return result;
		}
	}

	//////////////////////////////////////////////////////////////////////////////
	// Step 2: Find matches using SWIFT
#ifdef RAZERS_PARALLEL
    typedef typename RazerSOptions<TSpec>::TMutex TMutex;
    options.patternMutex = new TMutex[length(readSet)];
#endif

	map<unsigned,pair< string,unsigned> > gnoToFileMap; //map to retrieve genome filename and sequence number within that file
	int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options);
	if (error != 0)
	{
		switch (error)
		{
			case RAZERS_GENOME_FAILED:
				cerr << "Failed to load genomes" << endl;
				break;
			
			case RAZERS_INVALID_SHAPE:
				cerr << "Invalid Shape" << endl;
				break;
		}
		return error;
	}

#ifdef RAZERS_PARALLEL
    delete[] options.patternMutex;
#endif

	//////////////////////////////////////////////////////////////////////////////
	// Step 3: Remove duplicates and output matches
	if (!options.spec.DONT_DUMP_RESULTS)
		dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options);

	return 0;
}

void setUpArgumentParser(ArgumentParser & parser, RazerSOptions<> const & options, ParamChooserOptions const & pm_options)
{
	string rev = "$Revision: 13764 $";
    string date = "$Date: 2013-03-15 11:17:10 +0100 (Fr, 15 Mär 2013) $";

    setAppName(parser, "razers");
    setShortDescription(parser, "Fast Read Mapping with Sensitivity Control");
    setCategory(parser, "Read Mapping");
    setVersion(parser, "1.2 [" + rev.substr(11, rev.size() - 13) + "]");
    setDate(parser, date.substr(7, _min((int)date.size() - 8, 10)));

    addArgument(parser, ArgParseArgument(ArgParseArgument::INPUTFILE));
    setValidValues(parser, 0, getFileFormatExtensions(seqan::AutoSeqFormat()));
    setHelpText(parser, 0, "A reference genome file.");
    addArgument(parser, ArgParseArgument(ArgParseArgument::INPUTFILE, "READS", true));
    setValidValues(parser, 1, getFileFormatExtensions(seqan::AutoSeqFormat()));
    setHelpText(parser, 1, "Either one (single-end) or two (paired-end) read files.");

    addUsageLine(parser, "[\\fIOPTIONS\\fP] <\\fIGENOME FILE\\fP> <\\fIREADS FILE\\fP>");
#ifdef RAZERS_MATEPAIRS
    addUsageLine(parser, "[\\fIOPTIONS\\fP] <\\fIGENOME FILE\\fP> <\\fIMP-READS FILE1\\fP> <\\fIMP-READS FILE2\\fP>");
#endif

    addDescription(parser, "RazerS is a versatile full-sensitive read mapper based on a k-mer counting filter. "
                           "It supports single and paired-end mapping, and optimally parametrizes "
                           "the filter based on a user-defined minimal sensitivity. "
                           "See \\fIhttp://www.seqan.de/projects/razers\\fP for more information.");

    addDescription(parser, "Input to RazerS is a reference genome file and either one file with single-end reads "
                           "or two files containing left or right mates of paired-end reads. ");

    addDescription(parser, "(c) Copyright 2009 by David Weese.");

    addSection(parser, "Main Options");
    addOption(parser, ArgParseOption("f", "forward", "Map reads only to forward strands."));
    addOption(parser, ArgParseOption("r", "reverse", "Map reads only to reverse strands."));
    addOption(parser, ArgParseOption("i", "percent-identity", "Percent identity threshold.", ArgParseOption::DOUBLE));
    setMinValue(parser, "percent-identity", "50");
    setMaxValue(parser, "percent-identity", "100");
    setDefaultValue(parser, "percent-identity", 100 - (100.0 * options.errorRate));
#ifndef NO_PARAM_CHOOSER
    addOption(parser, ArgParseOption("rr", "recognition-rate", "Percent recognition rate.", ArgParseOption::DOUBLE));
    setMinValue(parser, "recognition-rate", "80");
    setMaxValue(parser, "recognition-rate", "100");
    setDefaultValue(parser, "recognition-rate", 100 - (100.0 * pm_options.optionLossRate));
    addOption(parser, ArgParseOption("pd", "param-dir", "Read user-computed parameter files in the directory <\\fIDIR\\fP>.", ArgParseOption::STRING, "DIR"));
#endif
    addOption(parser, ArgParseOption("id", "indels", "Allow indels. Default: mismatches only."));
#ifdef RAZERS_MATEPAIRS
    addOption(parser, ArgParseOption("ll", "library-length", "Paired-end library length.", ArgParseOption::INTEGER));
    setMinValue(parser, "library-length", "1");
    setDefaultValue(parser, "library-length", options.libraryLength);
    addOption(parser, ArgParseOption("le", "library-error", "Paired-end library length tolerance.", ArgParseOption::INTEGER));
    setMinValue(parser, "library-error", "0");
    setDefaultValue(parser, "library-error", options.libraryError);
#endif
    addOption(parser, ArgParseOption("m", "max-hits", "Output only <\\fINUM\\fP> of the best hits.", ArgParseOption::INTEGER));
    setMinValue(parser, "max-hits", "1");
    setDefaultValue(parser, "max-hits", options.maxHits);
    addOption(parser, ArgParseOption("", "unique", "Output only unique best matches (-m 1 -dr 0 -pa)."));
    addOption(parser, ArgParseOption("tr", "trim-reads", "Trim reads to given length. Default: off.", ArgParseOption::INTEGER));
    setMinValue(parser, "trim-reads", "14");
    addOption(parser, ArgParseOption("o", "output", "Change output filename. Default: <\\fIREADS FILE\\fP>.razers.", ArgParseOption::OUTPUTFILE));
    setValidValues(parser, "output", "razers eland fa fasta gff");
    addOption(parser, ArgParseOption("v", "verbose", "Verbose mode."));
    addOption(parser, ArgParseOption("vv", "vverbose", "Very verbose mode."));

    addSection(parser, "Output Format Options");
    addOption(parser, ArgParseOption("a", "alignment", "Dump the alignment for each match (only \\fIrazer\\fP or \\fIfasta\\fP format)."));
    addOption(parser, ArgParseOption("pa", "purge-ambiguous", "Purge reads with more than <\\fImax-hits\\fP> best matches."));
    addOption(parser, ArgParseOption("dr", "distance-range", "Only consider matches with at most NUM more errors compared to the best. Default: output all.", ArgParseOption::INTEGER));
    addOption(parser, ArgParseOption("gn", "genome-naming", "Select how genomes are named (see Naming section below).", ArgParseOption::INTEGER));
    setMinValue(parser, "genome-naming", "0");
    setMaxValue(parser, "genome-naming", "1");
    setDefaultValue(parser, "genome-naming", options.genomeNaming);
    addOption(parser, ArgParseOption("rn", "read-naming", "Select how reads are named (see Naming section below).", ArgParseOption::INTEGER));
    setDefaultValue(parser, "read-naming", options.readNaming);
    setMinValue(parser, "read-naming", "0");
    setMaxValue(parser, "read-naming", "2");
    addOption(parser, ArgParseOption("so", "sort-order", "Select how matches are sorted (see Sorting section below).", ArgParseOption::INTEGER));
    setDefaultValue(parser, "sort-order", options.sortOrder);
    setMinValue(parser, "sort-order", "0");
    setMaxValue(parser, "sort-order", "1");
    addOption(parser, ArgParseOption("pf", "position-format", "Select begin/end position numbering (see Coordinate section below).", ArgParseOption::INTEGER));
    setMinValue(parser, "position-format", "0");
    setMaxValue(parser, "position-format", "1");
    setDefaultValue(parser, "position-format", options.sortOrder);

    addSection(parser, "Filtration Options");
    addOption(parser, ArgParseOption("s", "shape", "Manually set k-mer shape.", ArgParseOption::STRING, "BITSTRING"));
    setDefaultValue(parser, "shape", options.shape);
    addOption(parser, ArgParseOption("t", "threshold", "Manually set minimum k-mer count threshold.", ArgParseOption::INTEGER));
    setMinValue(parser, "threshold", "1");
    addOption(parser, ArgParseOption("oc", "overabundance-cut", "Set k-mer overabundance cut ratio.", ArgParseOption::INTEGER));
    setMinValue(parser, "overabundance-cut", "0");
    setMaxValue(parser, "overabundance-cut", "1");
    addOption(parser, ArgParseOption("rl", "repeat-length", "Skip simple-repeats of length <\\fINUM\\fP>.", ArgParseOption::INTEGER));
    setMinValue(parser, "repeat-length", "1");
    setDefaultValue(parser, "repeat-length", options.repeatLength);
    addOption(parser, ArgParseOption("tl", "taboo-length", "Set taboo length.", ArgParseOption::INTEGER));
    setMinValue(parser, "taboo-length", "1");
    setDefaultValue(parser, "taboo-length", options.tabooLength);

	addOption(parser, ArgParseOption("lm", "low-memory", "Decrease memory usage at the expense of runtime."));
#ifdef RAZERS_DIRECT_MAQ_MAPPING
	addSection(parser, "Mapping Quality Options:");
	addOption(parser, ArgParseOption("mq", "mapping-quality", "Switch on mapping quality mode."));
	addOption(parser, ArgParseOption("nbi", "no-below-id", "Do not report matches with seed identity < percent id."));
	addOption(parser, ArgParseOption("qsl", "mq-seed-length", "Set MAQ seed length." , ArgParseOption::INTEGER));
    setMinValue(parser, "mq-seed-length", "24");
    setDefaultValue(parser, "mq-seed-length", options.artSeedLength));
	addOption(parser, ArgParseOption("smq", "seed-mism-quality", "Set maximal mismatch-quality sum in the seed.", ArgParseOption::INTEGER));
    setMinValue(parser, "seed-mism-quality", "0");
    setDefaultValue(parser, "seed-mism-quality", options.maxMismatchQualSum));
	addOption(parser, ArgParseOption("tmq", "total-mism-quality", "Set total maximal mismatch-quality.", ArgParseOption::INTEGER));
    setMinValue(parser, "total-mism-quality", "0");
    setDefaultValue(parser, "total-mism-quality", options.absMaxQualSumErrors));
#endif

    addSection(parser, "Verification Options");
    addOption(parser, ArgParseOption("mN", "match-N", "N matches all other characters. Default: N matches nothing."));
    addOption(parser, ArgParseOption("ed", "error-distr", "Write error distribution to \\fIFILE\\fP.", ArgParseOption::STRING, "FILE"));

#ifdef RAZERS_SPLICED
	addOption(parser, ArgParseOption("sm", "spliced-mapping", "Set minimal match length for spliced mapping.", ArgParseOption::INTEGER));
    setMinValue(parser, "spliced-mapping", "6"));
    setDefaultValue(parser, "spliced-mapping", options.minMatchLen));
	addOption(parser, ArgParseOption("maxD", "max-distance", "Set maximal distance of prefix-suffix match.", ArgParseOption::INTEGER));
    setMinValue(parser, "max-distance", "0"));
    setDefaultValue(parser, "max-distance", options.maxDistance));
#endif
	
	addOption(parser, ArgParseOption("mcl", "min-clipped-len", "Set minimal read length for read clipping.", ArgParseOption::INTEGER));
    setMinValue(parser, "min-clipped-len", "0");
    setDefaultValue(parser, "min-clipped-len", options.minClippedLen);
	addOption(parser, ArgParseOption("qih", "quality-in-header", "Quality string in fasta header."));

//#ifdef RAZERS_SPLICED
//	addOption(parser, CommandLineOption("sm", "spliced-mapping",   "min. match length for prefix/suffix alignment strategy", OptionType::Int | OptionType::Label, options.minMatchLen));
//	addOption(parser, CommandLineOption("maxD", "max-distance",    "max distance of pref/suff match", OptionType::Int | OptionType::Label, options.maxDistance));
//#endif
//	
//	addOption(parser, CommandLineOption("mcl", "min-clipped-len",  "min. read length for read clipping", OptionType::Int | OptionType::Label, options.minClippedLen));
//	addOption(parser, CommandLineOption("qih", "quality-in-header","quality string in fasta header", OptionType::Boolean));
//

    addTextSection(parser, "Formats, Naming, Sorting, and Coordinate Schemes");

    addText(parser, "RazerS supports various output formats. The output format is detected automatically from the file name suffix.");
	addListItem(parser, ".razers", "Razer format");
	addListItem(parser, ".fa, .fasta", "Enhanced Fasta format");
	addListItem(parser, ".eland", "Eland format");
	addListItem(parser, ".gff", "GFF format");

    addText(parser, "");
    addText(parser, "By default, reads and contigs are referred by their Fasta ids given in the input files. "
                    "With the \\fB-gn\\fP and \\fB-rn\\fP options this behaviour can be changed:");
    addListItem(parser, "0", "Use Fasta id.");
    addListItem(parser, "1", "Enumerate beginning with 1.");
    addListItem(parser, "2", "Use the read sequence (only for short reads!).");

    addText(parser, "");
    addText(parser, "The way matches are sorted in the output file can be changed with the \\fB-so\\fP option for the following formats: "
                    "\\fBrazer\\fP, \\fBfasta\\fP, \\fBsam\\fP, and \\fBamos\\fP. Primary and secondary sort keys are:");
    addListItem(parser, "0", "1. read number, 2. genome position");
    addListItem(parser, "1", "1. genome position, 2. read number");

    addText(parser, "");
    addText(parser, "The coordinate space used for begin and end positions can be changed with the "
                    "\\fB-pf\\fP option for the \\fBrazer\\fP and \\fBfasta\\fP formats:");
    addListItem(parser, "0", "Gap space. Gaps between characters are counted from 0.");
    addListItem(parser, "1", "Position space. Characters are counted from 1.");

    addTextSection(parser, "Examples");
    addListItem(parser,
                "\\fBrazers\\fP \\fBexample/genome.fa\\fP \\fBexample/reads.fa\\fP \\fB-id\\fP \\fB-a\\fP \\fB-mN\\fP \\fB-v\\fP",
                "Map single-end reads with 4% error rate, indels, and output the alignments. Ns are considered to match everything.");
    addListItem(parser,
                "\\fBrazers\\fP \\fBexample/genome.fa\\fP \\fBexample/reads.fa\\fP \\fBexample/reads2.fa\\fP \\fB-id\\fP \\fB-mN\\fP",
                "Map paired-end reads with up to 4% errors, indels, and output concordantly mapped pairs within default library size. Ns are considered to match everything.");
}

ArgumentParser::ParseResult
extractOptions(
    StringSet<CharString> & genomeFileNames, StringSet<CharString> & readFileNames,
    RazerSOptions<> & options, ParamChooserOptions & pm_options, CharString &errorPrbFileName,
    ArgumentParser const & parser)
{
    //////////////////////////////////////////////////////////////////////////////
    // Extract options

    bool stop = false;
    getOptionValue(options.forward, parser, "forward");
    getOptionValue(options.reverse, parser, "reverse");
    getOptionValue(options.errorRate, parser, "percent-identity");
#ifndef NO_PARAM_CHOOSER
    getOptionValue(pm_options.optionLossRate, parser, "recognition-rate");
    getOptionValue(pm_options.paramFolder, parser, "param-dir");
    // append slash/backslash
    if (!empty(pm_options.paramFolder))
    {
        if (back(pm_options.paramFolder) != '/' && back(pm_options.paramFolder) != '\\')
        {
#ifdef PLATFORM_WINDOWS
            appendValue(pm_options.paramFolder, '\\');
#else
            appendValue(pm_options.paramFolder, '/');
#endif
        }
    }
#endif
	getOptionValue(options.hammingOnly, parser, "indels");
	options.hammingOnly = !options.hammingOnly;

#ifdef RAZERS_MATEPAIRS
    getOptionValue(options.libraryLength, parser, "library-length");
    getOptionValue(options.libraryError, parser, "library-error");
#endif
    getOptionValue(options.maxHits, parser, "max-hits");
    getOptionValue(options.purgeAmbiguous, parser, "purge-ambiguous");
    getOptionValue(options.distanceRange, parser, "distance-range");
    if (isSet(parser, "distance-range"))
        options.distanceRange++;
    getOptionValue(options.dumpAlignment, parser, "alignment");
    getOptionValue(options.sortOrder, parser, "sort-order");
    getOptionValue(options.genomeNaming, parser, "genome-naming");
    getOptionValue(options.readNaming, parser, "read-naming");
    getOptionValue(options.positionFormat, parser, "position-format");
    getOptionValue(options.shape, parser, "shape");
    getOptionValue(options.threshold, parser, "threshold");
    getOptionValue(options.abundanceCut, parser, "overabundance-cut");
    getOptionValue(options.repeatLength, parser, "repeat-length");

#ifdef RAZERS_DIRECT_MAQ_MAPPING
	getOptionValue(options.fastaIdQual, parser, "quality-in-header");
	getOptionValue(options.maqMapping, parser, "mapping-quality");
	getOptionValue(options.noBelowIdentity, parser, "no-below-id");
	getOptionValue(options.artSeedLength, parser, "mq-seed-length");
	getOptionValue(options.maxMismatchQualSum, parser, "seed-mism-quality");
	getOptionValue(options.absMaxQualSumErrors, parser, "total-mism-quality");
#endif
	getOptionValue(options.lowMemory, parser, "low-memory");
    getOptionValue(options.trimLength, parser, "trim-reads");
    getOptionValue(options.tabooLength, parser, "taboo-length");
    getOptionValue(options.matchN, parser, "match-N");
    getOptionValue(errorPrbFileName, parser, "error-distr");
#ifdef RAZERS_SPLICED
	getOptionValue(options.minMatchLen, parser, "spliced-mapping");
	getOptionValue(options.maxDistance, parser, "max-distance");
#endif
	getOptionValue(options.minClippedLen, parser, "min-clipped-len");
	getOptionValue(options.fastaIdQual, parser, "quality-in-header");
    if (isSet(parser, "verbose"))
        options._debugLevel = max(options._debugLevel, 1);
    if (isSet(parser, "vverbose"))
        options._debugLevel = max(options._debugLevel, 3);
    if (isSet(parser, "unique"))
    {
        options.maxHits = 1;
        options.distanceRange = 1;
        options.purgeAmbiguous = true;
    }
	if (!options.forward && !options.reverse)  // enable both per default
	{
		options.forward = true;
		options.reverse = true;
	}
#ifdef RAZERS_MATEPAIRS
    unsigned maxReadFiles = 2;
#else
    unsigned maxReadFiles = 1;
#endif
    resize(genomeFileNames, length(genomeFileNames) + 1);
    getArgumentValue(back(genomeFileNames), parser, 0);
    resize(readFileNames, _min(getArgumentValueCount(parser, 1), maxReadFiles), Exact());
    for (unsigned i = 0; i < length(readFileNames); ++i)
        getArgumentValue(readFileNames[i], parser, 1, i);

    // Get output file name from command line if set.  Otherwise, autogenerate from input file name.
    if (isSet(parser, "output"))
    {
        getOptionValue(options.output, parser, "output");
    }
    else
    {
        options.output = readFileNames[0];
        append(options.output, ".razers");
    }

    // Get lower case of the output file name.  File endings are accepted in both upper and lower case.
    CharString tmp = options.output;
    toLower(tmp);

    if (endsWith(tmp, ".razers"))
        options.outputFormat = 0;
    else if (endsWith(tmp, ".fa") || endsWith(tmp, ".fasta"))
        options.outputFormat = 1;
    else if (endsWith(tmp, ".eland"))
        options.outputFormat = 2;
    else if (endsWith(tmp, ".gff"))
        options.outputFormat = 3;

	if (isSet(parser, "shape"))
	{
		unsigned ones = 0;
		unsigned zeros = 0;
		for(unsigned i = 0; i < length(options.shape); ++i)
			switch (options.shape[i])
			{
				case '0':
					++zeros;
					break;
				case '1':
					++ones;
					break;
				default:
					cerr << "Shape must be a binary string" << endl;
					stop = true;
					i = length(options.shape);
			}
		if ((ones == 0 || ones > 31) && !stop) 
		{
			cerr << "Invalid Shape" << endl;
			stop = true;
		}
		unsigned maxOnes = 14;
#ifdef RAZERS_OPENADDRESSING
		maxOnes = 31;
#endif
		if ((ones < 7 || ones > maxOnes) && !stop)
			cerr << "Warning: Shape should contain at least 7 and at most " << maxOnes << " '1's" << endl;
	}
    if (getArgumentValueCount(parser, 1) == 1)
		options.libraryLength = -1;		// only 1 readset -> disable mate-pair mapping
    if ((getArgumentValueCount(parser, 1) > maxReadFiles) && (stop = true))
		cerr << "More than " << maxReadFiles << " read files specified." << endl;
    if ((getArgumentValueCount(parser, 1) == 0) && (stop = true))
        cerr << "No read files specified." << endl;
	if ((options.minClippedLen < 0) && (stop = true))
		cerr << "Min. clipped read length must be a value greater 0" << endl;

	options.errorRate = (100.0 - options.errorRate) / 100.0;
	pm_options.optionLossRate = (ParamChooserOptions::TFloat)(100.0 - pm_options.optionLossRate) / 100.0;

    return (stop) ? ArgumentParser::PARSE_ERROR : ArgumentParser::PARSE_OK;
}

//////////////////////////////////////////////////////////////////////////////
// Command line parsing and parameter choosing
int main(int argc, const char *argv[]) 
{
	RazerSOptions<>			options;
	ParamChooserOptions		pm_options;

	StringSet<CharString>	genomeFileNames;
	StringSet<CharString>	readFileNames;
	CharString				errorPrbFileName;

	// Change defaults
	options.forward = false;
	options.reverse = false;
	
    // Set up command line parser.
    ArgumentParser argParser;
    setUpArgumentParser(argParser, options, pm_options);

    // Parse command line.
    ArgumentParser::ParseResult res = parse(argParser, argc, argv);
    if (res != ArgumentParser::PARSE_OK)
    {
        if (res == ArgumentParser::PARSE_ERROR)
            cerr << "Exiting ..." << endl;
        return (res == ArgumentParser::PARSE_ERROR) ? RAZERS_INVALID_OPTIONS : 0;
    }
    // Extract options.
    res = extractOptions(genomeFileNames, readFileNames, options, pm_options, errorPrbFileName, argParser);
    if (res != ArgumentParser::PARSE_OK)
    {
        cerr << "Exiting ..." << endl;
        return RAZERS_INVALID_OPTIONS;
    }
	
	//////////////////////////////////////////////////////////////////////////////
	// get read length
	int readLength = estimateReadLength(toCString(readFileNames[0]));
	if (readLength == RAZERS_READS_FAILED)
	{
		cerr << "Failed to open reads file " << readFileNames[0] << endl;
		cerr << "Exiting ..." << endl;
		return RAZERS_READS_FAILED;
	}
	if (readLength == 0) {
		cerr << "Failed to read the first read sequence." << endl;
		cerr << "Exiting ..." << endl;
		return RAZERS_READS_FAILED;
	}

	if (options.trimLength > readLength)
		options.trimLength = readLength;
		
#ifndef NO_PARAM_CHOOSER
	if (!(isSet(argParser, "shape") || isSet(argParser, "threshold")))
	{
		if (options.lowMemory) pm_options.maxWeight = 13;
		pm_options.verbose = (options._debugLevel >= 1);
		pm_options.optionErrorRate = (ParamChooserOptions::TFloat)options.errorRate;
		if (options.hammingOnly)
		{
			pm_options.optionProbINSERT = (ParamChooserOptions::TFloat)0.0;
			pm_options.optionProbDELETE = (ParamChooserOptions::TFloat)0.0;
		}
		else
		{
			pm_options.optionProbINSERT = (ParamChooserOptions::TFloat)0.01;	//this number is basically without meaning, any value > 0 will lead to
			pm_options.optionProbDELETE = (ParamChooserOptions::TFloat)0.01;	//edit distance parameter choosing
		}

		if (options.trimLength > 0) readLength = options.trimLength;
		if (readLength > 0)
		{
/*			if(options.maqMapping && readLength != options.artSeedLength)
				pm_options.totalN = options.artSeedLength;
			else*/
				pm_options.totalN = readLength;
#ifdef RAZERS_SPLICED
			if(options.minMatchLen>0)
				pm_options.totalN = options.minMatchLen;
#endif
			if (options._debugLevel >= 1)
				cerr << "___PARAMETER_CHOOSING__" << endl;
			if (!chooseParams(options,pm_options))
			{
				if (pm_options.verbose) 
					cerr << "Couldn't find preprocessed parameter files. Please configure manually (options --shape and --threshold)." << endl;
				cerr << "Using default configurations (shape = " << options.shape << " and q-gram lemma)." << endl;
			}
			if (options._debugLevel >= 1) cerr << endl;
		} else
		{
			cerr << "Failed to load reads" << endl;
			cerr << "Exiting ..." << endl;
			return RAZERS_READS_FAILED;
		}
	}
#endif	

#ifdef RAZERS_PARALLEL
	tbb::task_scheduler_init scheduler;
#endif

	int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options);
	if (result != 0)
		cerr << "Exiting ..." << endl;
	return result;
}
