/** 
** Copyright (c) 2007-2010 Illumina, Inc. 
** 
** This software is covered by the "Illumina Genome Analyzer Software
** License Agreement" and the "Illumina Source Code License Agreement",
** and certain third party copyright/licenses, and any user of this
** source file is bound by the terms therein (see accompanying files
** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
** Illumina_Source_Code_License_Agreement.pdf and third party
** copyright/license notices).
** 
** This file is part of the Consensus Assessment of Sequence And VAriation 
** (CASAVA) software package. 
** 
** @file SmallAssemblerOptions.hh
** 
** @brief Stores default params for the SmallAssembler in Grouper.
** 
** @author Ole Schulz-Trieglaff
**/ 


#ifndef SMALLASSEMBLEROPTIONS_HH_
#define SMALLASSEMBLEROPTIONS_HH_


struct SmallAssemblerOptions {

    SmallAssemblerOptions() :
    // reasonable default values for 30x and 100bp reads
    wordLength(37), maxWordLength(65), minContigLength(15), minCoverage(1), maxError(0.2), minSeedReads(2), maxClusterReads(1000) {}
    //wordLength(37), maxWordLength(47), minContigLength(15), minCoverage(1), maxError(0.2), minSeedReads(2), maxClusterReads(1000) {}

    //  initial word (kmer) length
    unsigned wordLength; 
    // max word length
    unsigned maxWordLength;
    // min contig size
    unsigned minContigLength;
    // min. coverage required for contig extension
    unsigned minCoverage;
    // max error rates allowed during contig extension
    double  maxError;
    // min. number of reads required to start assembly
    unsigned minSeedReads;
    // max. accepted size of a read cluster
    unsigned maxClusterReads;
};

#endif