C++ (Cpp) Genome::startPiece Examples

Example #1

File: Mutator.cpp Project: fnothaft/snap

    const Genome *
Mutator::mutate(const Genome &genome) const
{
  Genome *newGenome = new Genome(genome.getCountOfBases() + basesGained,genome.getCountOfBases() + basesGained);
    int nPieces = genome.getNumPieces();
    const Genome::Piece *pieces = genome.getPieces();
    for (int i = 0; i < nPieces; ++i) {
        const Genome::Piece &piece = pieces[i];
        unsigned start = piece.beginningOffset;
        unsigned end = i + 1 < nPieces ? pieces[i + 1].beginningOffset : genome.getCountOfBases();
        unsigned size = end - start;
        const Base *bases = genome.getSubstring(start, size);
        const char *name = piece.name;
        // printf("DEBUG: mutating %s of size %u, from %u to %u\n", name, size, start, end);
        newGenome->startPiece(name);
        getOrElse(chromMutators, string(name)).mutate(bases, bases + size, newGenome);
    }
    return newGenome;
}

Example #2

File: Genome.cpp Project: fnothaft/snap

//
// Makes a copy of a Genome, but with only one of the sex chromosomes.
//
// The fate of the mitochondrion is that of the X chromosome.
//
    Genome *
Genome::copy(bool copyX, bool copyY, bool copyM) const
{
    Genome *newCopy = new Genome(getCountOfBases(),getCountOfBases());

    if (NULL == newCopy) {
        fprintf(stderr,"Genome::copy: failed to allocate space for copy.\n");
        return NULL;
    }

    const Genome::Piece *currentPiece = NULL;
    const Genome::Piece *nextPiece = getPieceAtLocation(0);

    unsigned offsetInReference = 0;
    while (offsetInReference < getCountOfBases()) {
        if (NULL != nextPiece && offsetInReference >= nextPiece->beginningOffset) {
            //
            // Start of a new piece.  See if we want to skip it.
            //
            currentPiece = nextPiece;
            nextPiece = getNextPieceAfterLocation(offsetInReference + 1);
            if ((!copyX && !strcmp(currentPiece->name,"chrX")) ||
                (!copyY && !strcmp(currentPiece->name,"chrY")) ||
                (!copyM && !strcmp(currentPiece->name,"chrM"))) {
                //
                // Yes, skip over this piece.
                //
                nextPiece = getNextPieceAfterLocation(offsetInReference + 1);
                if (NULL == nextPiece) {
                    //
                    // The chromosome that we're skipping was the last one, so we're done.
                    //
                    break;
                } else {
                    offsetInReference = nextPiece->beginningOffset;
                    continue;
                }
            } // If skipping this chromosome

            newCopy->startPiece(currentPiece->name);
        } // If new piece beginning

        const size_t maxCopySize = 10000;
        char dataBuffer[maxCopySize + 1];

        unsigned amountToCopy = maxCopySize;
        if (nextPiece && nextPiece->beginningOffset < offsetInReference + amountToCopy) {
            amountToCopy = nextPiece->beginningOffset - offsetInReference;
        }

        if (getCountOfBases() < offsetInReference + amountToCopy) {
            amountToCopy = getCountOfBases() - offsetInReference;
        }

        memcpy(dataBuffer,getSubstring(offsetInReference,amountToCopy), amountToCopy);
        dataBuffer[amountToCopy] = '\0';

        newCopy->addData(dataBuffer);

        offsetInReference += amountToCopy;
    }

    return newCopy;
}