//
// 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(), chromosomePadding);
if (NULL == newCopy) {
WriteErrorMessage("Genome::copy: failed to allocate space for copy.\n");
return NULL;
}
const Genome::Contig *currentContig = NULL;
const Genome::Contig *nextContig = getContigAtLocation(0);
unsigned offsetInReference = 0;
while (offsetInReference < getCountOfBases()) {
if (NULL != nextContig && offsetInReference >= nextContig->beginningOffset) {
//
// Start of a new contig. See if we want to skip it.
//
currentContig = nextContig;
nextContig = getNextContigAfterLocation(offsetInReference + 1);
if ((!copyX && !strcmp(currentContig->name,"chrX")) ||
(!copyY && !strcmp(currentContig->name,"chrY")) ||
(!copyM && !strcmp(currentContig->name,"chrM"))) {
//
// Yes, skip over this contig.
//
nextContig = getNextContigAfterLocation(offsetInReference + 1);
if (NULL == nextContig) {
//
// The chromosome that we're skipping was the last one, so we're done.
//
break;
} else {
offsetInReference = nextContig->beginningOffset;
continue;
}
} // If skipping this chromosome
newCopy->startContig(currentContig->name);
} // If new contig beginning
const size_t maxCopySize = 10000;
char dataBuffer[maxCopySize + 1];
unsigned amountToCopy = maxCopySize;
if (nextContig && nextContig->beginningOffset < offsetInReference + amountToCopy) {
amountToCopy = nextContig->beginningOffset - offsetInReference;
}
if (getCountOfBases() < offsetInReference + amountToCopy) {
amountToCopy = getCountOfBases() - offsetInReference;
}
memcpy(dataBuffer,getSubstring(offsetInReference,amountToCopy), amountToCopy);
dataBuffer[amountToCopy] = '\0';
newCopy->addData(dataBuffer);
offsetInReference += amountToCopy;
}
newCopy->fillInContigLengths();
newCopy->sortContigsByName();
return newCopy;
}
//
// 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;
}
