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main_fmIndex.cpp

// ==========================================================================
//                                mini_bowtie
// ==========================================================================
// Copyright (c) 2006-2012, Knut Reinert, FU Berlin
// All rights reserved.

#include <iostream>
#include <time.h>
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/file.h>
#include <seqan/index.h>
#include <seqan/index/index_fm.h>
#include <seqan/store.h>

using namespace seqan;





int main(int argc, char *argv[])
{
    clock_t indexing_time = clock();
    
	// type definitions
    typedef Dna5String TString;
    typedef StringSet<TString> TStringSet;
    typedef Index<TStringSet, FMIndex<> > TIndex;
    typedef Iterator<TIndex, TopDown<ParentLinks<> > >::Type TIter;
    
    
    
      
    // reading the command line arguments
    if (argc < 2) {
        std::cerr << "Invalid number of arguments." << std::endl
                  << "USAGE: fmIndex GENOME.fasta" << std::endl;
        return 1;
    }
    




    // declaration and initialization of the fragment store
    FragmentStore<> fragStore;
	// loading the contigs
    if (!loadContigs(fragStore, argv[1])) {
		std::cerr << "Loading GENOME failed" << std::endl;
		return 1;
	}
    
    // copy the contigs to the string set "mySeq"
    TStringSet mySeq;
    for (unsigned i = 0; i < length(fragStore.contigStore); ++i) {
        appendValue(mySeq, fragStore.contigStore[i].seq);
        std::cout << "Sequence " << i << " has " << length(mySeq[i]) << " nucleotides" << std::endl;
	}
	//std::cout << mySeq[0] << std::endl;
	
	// clear contigs to free memory
	clearContigs(fragStore);





////////////////////////////////////////////////////////////////////////
	// REVERSE the ref genome !!! REVERSE !!! REVERSE !!!
    reverse(mySeq);
////////////////////////////////////////////////////////////////////////    






    // FM INDEXING
    TIndex fmIndex(mySeq); // the index is not created yet
    TIter it(fmIndex); // the index is created after this line
    
    char indexFile[100];
    strcpy(indexFile, argv[1]);
    strcat(indexFile, ".index");
    if (save(fmIndex, indexFile)) {
		std::cout << "Index saved!" << std::endl;
	}
	else {
		std::cout << "Failed to save index" << std::endl;
		return 1; 
	}






    indexing_time = clock() - indexing_time;
    std::cout << "Total indexing time: " << ((double)indexing_time)/CLOCKS_PER_SEC << " seconds" << std::endl;
    
    return 0;
}

main_fmIndex2.cpp

// ==========================================================================
//                                mini_bowtie
// ==========================================================================
// Copyright (c) 2006-2012, Knut Reinert, FU Berlin
// All rights reserved.

#include <iostream>
#include <time.h>
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/file.h>
#include <seqan/index.h>
#include <seqan/index/index_fm.h>
#include <seqan/store.h>

using namespace seqan;





int main(int argc, char *argv[])
{
    clock_t indexing_time = clock();
    
	// type definitions
    typedef Dna5String TString;
    typedef StringSet<TString> TStringSet;
    typedef Index<TStringSet, FMIndex<> > TIndex;
    typedef Iterator<TIndex, TopDown<ParentLinks<> > >::Type TIter;
    
    
    
      
    // reading the command line arguments
    if (argc < 2) {
        std::cerr << "Invalid number of arguments." << std::endl
                  << "USAGE: fmIndex GENOME.fasta" << std::endl;
        return 1;
    }
    




    // declaration and initialization of the fragment store
    FragmentStore<> fragStore;
	// loading the contigs
    if (!loadContigs(fragStore, argv[1])) {
		std::cerr << "Loading GENOME failed" << std::endl;
		return 1;
	}
    
    // copy the contigs to the string set "mySeq"
    TStringSet mySeq;
    for (unsigned i = 0; i < length(fragStore.contigStore); ++i) {
        appendValue(mySeq, fragStore.contigStore[i].seq);
        std::cout << "Sequence " << i << " has " << length(mySeq[i]) << " nucleotides" << std::endl;
	}
	//std::cout << mySeq[0] << std::endl;
	
	// clear contigs to free memory
	clearContigs(fragStore);





////////////////////////////////////////////////////////////////////////
	// REVERSE the ref genome !!! REVERSE !!! REVERSE !!!
    reverse(mySeq);
////////////////////////////////////////////////////////////////////////    






    // FM INDEXING
    TIndex fmIndex(mySeq); // the index is not created yet
    TIter it(fmIndex); // the index is created after this line
    
    char indexFile[100];
    strcpy(indexFile, argv[1]);
    strcat(indexFile, ".index");
    if (save(fmIndex, indexFile)) {
		std::cout << "Index saved!" << std::endl;
	}
	else {
		std::cout << "Failed to save index" << std::endl;
		return 1; 
	}






    indexing_time = clock() - indexing_time;
    std::cout << "Total indexing time: " << ((double)indexing_time)/CLOCKS_PER_SEC << " seconds" << std::endl;
    
    return 0;
}

main_fmIndex3.cpp

// ==========================================================================
//                                mini_bowtie
// ==========================================================================
// Copyright (c) 2006-2012, Knut Reinert, FU Berlin
// All rights reserved.

#include <iostream>
#include <time.h>
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/file.h>
#include <seqan/index.h>
#include <seqan/index/index_fm.h>
#include <seqan/store.h>

using namespace seqan;





int main(int argc, char *argv[])
{
    clock_t indexing_time = clock();
    
	// type definitions
    typedef Dna5String TString;
    typedef StringSet<TString> TStringSet;
    typedef Index<TStringSet, FMIndex<> > TIndex;
    typedef Iterator<TIndex, TopDown<ParentLinks<> > >::Type TIter;
    
    
    
      
    // reading the command line arguments
    if (argc < 2) {
        std::cerr << "Invalid number of arguments." << std::endl
                  << "USAGE: fmIndex GENOME.fasta" << std::endl;
        return 1;
    }
    




    // declaration and initialization of the fragment store
    FragmentStore<> fragStore;
	// loading the contigs
    if (!loadContigs(fragStore, argv[1])) {
		std::cerr << "Loading GENOME failed" << std::endl;
		return 1;
	}
    
    // copy the contigs to the string set "mySeq"
    TStringSet mySeq;
    for (unsigned i = 0; i < length(fragStore.contigStore); ++i) {
        appendValue(mySeq, fragStore.contigStore[i].seq);
        std::cout << "Sequence " << i << " has " << length(mySeq[i]) << " nucleotides" << std::endl;
	}
	//std::cout << mySeq[0] << std::endl;
	
	// clear contigs to free memory
	clearContigs(fragStore);





////////////////////////////////////////////////////////////////////////
	// REVERSE the ref genome !!! REVERSE !!! REVERSE !!!
    reverse(mySeq);
////////////////////////////////////////////////////////////////////////    






    // FM INDEXING
    TIndex fmIndex(mySeq); // the index is not created yet
    TIter it(fmIndex); // the index is created after this line
    
    char indexFile[100];
    strcpy(indexFile, argv[1]);
    strcat(indexFile, ".index");
    if (save(fmIndex, indexFile)) {
		std::cout << "Index saved!" << std::endl;
	}
	else {
		std::cout << "Failed to save index" << std::endl;
		return 1; 
	}






    indexing_time = clock() - indexing_time;
    std::cout << "Total indexing time: " << ((double)indexing_time)/CLOCKS_PER_SEC << " seconds" << std::endl;
    
    return 0;
}