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Genome.cpp
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Genome.cpp
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/*++
Module Name:
geonome.cpp
Abstract:
Genome class for the SNAP sequencer
Authors:
Bill Bolosky, August, 2011
Environment:
User mode service.
Revision History:
Adapted from Matei Zaharia's Scala implementation.
--*/
#include "stdafx.h"
#include "Genome.h"
#include "Compat.h"
#include "BigAlloc.h"
Genome::Genome(unsigned i_maxBases, unsigned nBasesStored) : maxBases(i_maxBases), minOffset(0), maxOffset(i_maxBases)
{
bases = ((char *) BigAlloc(nBasesStored + 2 * N_PADDING)) + N_PADDING;
if (NULL == bases) {
fprintf(stderr,"Genome: unable to allocate memory for %llu bases\n",(_int64)maxBases);
exit(1);
}
// Add N's for the N_PADDING bases before and after the genome itself
memset(bases - N_PADDING, 'N', N_PADDING);
memset(bases + nBasesStored, 'N', N_PADDING);
nBases = 0;
maxPieces = 32; // A power of two that's bigger than the usual number of chromosomes, so we don't have to
// reallocate in practice.
nPieces = 0;
pieces = new Piece[maxPieces];
}
void
Genome::addData(const char *data, size_t len)
{
if ((size_t)nBases + len > maxBases) {
fprintf(stderr,"Tried to write beyond allocated genome size (or tried to write into a genome that was loaded from a file).\n");
fprintf(stderr,"Size = %lld\n",(_int64)maxBases);
exit(1);
}
memcpy(bases + nBases,data,len);
nBases += (unsigned)len;
}
void
Genome::addData(const char *data)
{
addData(data, strlen(data));
}
void
Genome::startPiece(const char *pieceName)
{
if (nPieces == maxPieces) {
//
// Reallocate (maybe we're sequencing a tree that's got lots of chromosomes).
//
int newMaxPieces = maxPieces * 2;
Piece *newPieces = new Piece[newMaxPieces];
if (NULL == newPieces) {
fprintf(stderr,"Genome: unable to reallocate piece array to size %d\n",newMaxPieces);
exit(1);
}
for (int i = 0; i < nPieces; i++) {
newPieces[i] = pieces[i];
}
delete [] pieces;
pieces = newPieces;
maxPieces = newMaxPieces;
}
pieces[nPieces].beginningOffset = nBases;
size_t len = strlen(pieceName) + 1;
pieces[nPieces].name = new char[len];
if (NULL == pieces[nPieces].name) {
fprintf(stderr,"Unable to allocate space for piece name\n");
exit(1);
}
strncpy(pieces[nPieces].name,pieceName,len);
pieces[nPieces].name[len-1] = '\0';
nPieces++;
}
Genome::~Genome()
{
BigDealloc(bases - N_PADDING);
for (int i = 0; i < nPieces; i++) {
delete [] pieces[i].name;
pieces[i].name = NULL;
}
delete [] pieces;
pieces = NULL;
}
bool
Genome::saveToFile(const char *fileName) const
{
//
// Save file format is (in binary) the number of bases, the number of pieces, followed by
// the pieces themselves, rounded up to 4K, followed by the bases.
//
FILE *saveFile = fopen(fileName,"wb");
if (saveFile == NULL) {
fprintf(stderr,"Genome::saveToFile: unable to open file '%s'\n",fileName);
return false;
}
fprintf(saveFile,"%d %d\n",nBases,nPieces);
char *curChar = NULL;
for (int i = 0; i < nPieces; i++) {
for (int n = 0; n < strlen(pieces[i].name); n++){
curChar = pieces[i].name + n;
if (*curChar == ' '){ *curChar = '_'; }
}
fprintf(saveFile,"%d %s\n",pieces[i].beginningOffset,pieces[i].name);
}
if (nBases != fwrite(bases,1,nBases,saveFile)) {
fprintf(stderr,"Genome::saveToFile: fwrite failed\n");
fclose(saveFile);
return false;
}
fclose(saveFile);
return true;
}
const Genome *
Genome::loadFromFile(const char *fileName, unsigned i_minOffset, unsigned length)
{
FILE *loadFile;
unsigned nBases,nPieces;
if (!openFileAndGetSizes(fileName,&loadFile,&nBases,&nPieces)) {
//
// It already printed an error. Just fail.
//
return NULL;
}
if (0 == length) {
length = nBases - i_minOffset;
} else {
//
// Don't let length go beyond nBases.
//
length = __min(length,nBases - i_minOffset);
}
Genome *genome = new Genome(nBases,length);
genome->nBases = nBases;
genome->nPieces = genome->maxPieces = nPieces;
genome->pieces = new Piece[nPieces];
genome->minOffset = i_minOffset;
if (i_minOffset >= nBases) {
fprintf(stderr,"Genome::loadFromFile: specified minOffset %u >= nBases %u\n",i_minOffset,nBases);
}
genome->maxOffset = i_minOffset + length;
static const unsigned pieceNameBufferSize = 512;
char pieceNameBuffer[pieceNameBufferSize];
unsigned n;
size_t pieceSize;
char *curName;
for (unsigned i = 0; i < nPieces; i++) {
if (NULL == fgets(pieceNameBuffer, pieceNameBufferSize, loadFile)){
fprintf(stderr,"Unable to read piece description\n");
delete genome;
return NULL;
}
for (n = 0; n < pieceNameBufferSize; n++){
if (pieceNameBuffer[n] == ' ') {
pieceNameBuffer[n] = '\0';
break;
}
}
genome->pieces[i].beginningOffset = atoi(pieceNameBuffer);
pieceNameBuffer[n] = ' ';
n++; // increment n so we start copying at the position after the space
pieceSize = strlen(pieceNameBuffer + n) - 1; //don't include the final \n
genome->pieces[i].name = new char[pieceSize + 1];
curName = genome->pieces[i].name;
for (unsigned pos = 0; pos < pieceSize; pos++) {
curName[pos] = pieceNameBuffer[pos + n];
}
curName[pieceSize] = '\0';
}
//
// Skip over the miserable \n that gets left in the file.
//
/* char newline;
if (1 != fread(&newline,1,1,loadFile)) {
fprintf(stderr,"Genome::loadFromFile: Unable to read expected newline\n");
delete genome;
return NULL;
}
if (newline != 10) {
fprintf(stderr,"Genome::loadFromFile: Expected newline to be 0x0a, got 0x%02x\n",newline);
delete genome;
return NULL;
}
*/
if (0 != _fseek64bit(loadFile,i_minOffset,SEEK_CUR)) {
fprintf(stderr,"Genome::loadFromFile: _fseek64bit failed\n");
exit(1);
}
if (length != fread(genome->bases,1,length,loadFile)) {
fprintf(stderr,"Genome::loadFromFile: fread of bases failed\n");
fclose(loadFile);
delete genome;
return NULL;
}
fclose(loadFile);
return genome;
}
bool
Genome::openFileAndGetSizes(const char *filename, FILE **file, unsigned *nBases, unsigned *nPieces)
{
*file = fopen(filename,"rb");
if (*file == NULL) {
fprintf(stderr,"Genome::openFileAndGetSizes: unable to open file '%s'\n",filename);
return false;
}
if (2 != fscanf(*file,"%d %d\n",nBases,nPieces)) {
fclose(*file);
*file = NULL;
fprintf(stderr,"Genome::openFileAndGetSizes: unable to read header\n");
return false;
}
return true;
}
bool
Genome::getSizeFromFile(const char *fileName, unsigned *nBases, unsigned *nPieces)
{
FILE *file;
unsigned localNBases, localNPieces;
if (!openFileAndGetSizes(fileName,&file,nBases ? nBases : &localNBases, nPieces ? nPieces : &localNPieces)) {
return false;
}
fclose(file);
return true;
}
bool
Genome::getOffsetOfPiece(const char *pieceName, unsigned *offset) const
{
for (int i = 0; i < nPieces; i++) {
if (!strcmp(pieceName,pieces[i].name)) {
if (NULL != offset) {
*offset = pieces[i].beginningOffset;
}
return true;
}
}
return false;
}
const Genome::Piece *
Genome::getPieceAtLocation(unsigned location) const
{
_ASSERT(location < nBases);
int low = 0;
int high = nPieces - 1;
while (low <= high) {
int mid = (low + high) / 2;
if (pieces[mid].beginningOffset <= location &&
(mid == nPieces-1 || pieces[mid+1].beginningOffset > location)) {
return &pieces[mid];
} else if (pieces[mid].beginningOffset <= location) {
low = mid + 1;
} else {
high = mid - 1;
}
}
return NULL; // Should not be reached
}
const Genome::Piece *
Genome::getNextPieceAfterLocation(unsigned location) const
{
_ASSERT(location < nBases);
int low = 0;
int high = nPieces - 1;
while (low <= high) {
int mid = (low + high) / 2;
if (pieces[mid].beginningOffset <= location &&
(mid == nPieces-1 || pieces[mid+1].beginningOffset > location)) {
if (mid >= nPieces - 1) {
//
// This location landed in the last piece, so return NULL for the next one.
//
return NULL;
} else {
return &pieces[mid+1];
}
} else if (pieces[mid].beginningOffset <= location) {
low = mid + 1;
} else {
high = mid - 1;
}
}
return NULL; // Should not be reached
}
//
// 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;
}
DiploidGenome *
DiploidGenome::Factory(const Genome *referenceGenome, bool isMale)
{
//
// This is just the special case where we use the same reference genome for both parents.
//
return Factory(referenceGenome, referenceGenome, isMale);
}
DiploidGenome *
DiploidGenome::Factory(const Genome *motherReference, const Genome *fatherReference, bool isMale)
{
//
// We have to create parent genomes that have the right set of chromosomes. Make ParentA as the mother (i.e., include chrX and not
// chrY).
//
Genome *mom = motherReference->copyGenomeOneSex(false, true); // Always get an X chromosome from mom
if (NULL == mom) {
fprintf(stderr,"DiploidGenome::Factory: Unable to allocate mom's genome.\n");
return NULL;
}
Genome *dad = fatherReference->copyGenomeOneSex(isMale, false); // Get dad's Y if this is a male, otherwise dad's X
if (NULL == dad) {
fprintf(stderr,"DiploidGenome::Factory: Unable to allocate dad's genome.\n");
delete mom;
return NULL;
}
DiploidGenome *diploidGenome = new DiploidGenome(mom, dad, true);
if (NULL == diploidGenome) {
fprintf(stderr,"DiploidGenome::Factory: Unable to allocate container.\n"); // Sometimes you write code that you just know will never execute.
delete mom;
delete dad;
return NULL;
}
return diploidGenome;
}
DiploidGenome *
DiploidGenome::Factory(const Genome *motherReference, const Genome *fatherReference)
{
return new DiploidGenome(motherReference, fatherReference, false);
}
DiploidGenome *
DiploidGenome::CopyingFactory(const Genome *motherReference, const Genome *fatherReference)
{
Genome *motherCopy = motherReference->copy();
if (NULL == motherCopy) {
fprintf(stderr,"DiploidGenome: unable to copy mother's genome\n");
return NULL;
}
Genome *fatherCopy = fatherReference->copy();
if (NULL == fatherCopy) {
fprintf(stderr,"DiploidGenome: unable to copy father's genome\n");
delete motherCopy;
return NULL;
}
DiploidGenome *diploidGenome = new DiploidGenome(motherCopy, fatherCopy, true);
if (NULL == diploidGenome) {
fprintf(stderr,"DiploidGenome: unable to allocate container.\n");
delete motherCopy;
delete fatherCopy;
return NULL;
}
return diploidGenome;
}
const char *
DiploidGenome::FilenameBase = "DiploidParent";
DiploidGenome *
DiploidGenome::loadFromDirectory(const char *directoryName)
{
size_t fileNameLen = strlen(directoryName) + 1 + strlen(FilenameBase) + 2; // +1 is PATH_SEP, +2 is A/B and \0
char *filename = new char[fileNameLen];
if (NULL == filename) {
fprintf(stderr,"DiploidGenome::loadFromDirectory: failed to allocate filename buffer.\n");
return NULL;
}
sprintf(filename,"%s%c%s%c",directoryName,PATH_SEP,FilenameBase,'A');
const Genome *motherGenome = Genome::loadFromFile(filename);
if (NULL == motherGenome) {
fprintf(stderr,"DiploidGenome::loadFromDirectory: failed to load mother's genome.\n");
delete [] filename;
return NULL;
}
sprintf(filename,"%s%c%s%c",directoryName,PATH_SEP,FilenameBase,'B');
const Genome *fatherGenome = Genome::loadFromFile(filename);
if (NULL == fatherGenome) {
fprintf(stderr,"DiploidGenome::loadFromDirectory: failed to load father's genome.\n");
delete motherGenome;
delete [] filename;
return NULL;
}
delete [] filename;
DiploidGenome *diploidGenome = new DiploidGenome(motherGenome, fatherGenome, true);
if (NULL == diploidGenome) {
fprintf(stderr,"DiploidGenome::loadFromDirectory: failed to allocate DiploidGenome container.\n");
delete motherGenome;
delete fatherGenome;
return NULL;
}
return diploidGenome;
}
bool
DiploidGenome::saveToDirectory(const char *directoryName) const
{
size_t fileNameLen = strlen(directoryName) + 1 + strlen(FilenameBase) + 2; // +1 is PATH_SEP, +2 is A/B and \0
char *filename = new char[fileNameLen];
if (NULL == filename) {
fprintf(stderr,"DiploidGenome::saveToDirectory: failed to allocate filename buffer.\n");
return false;
}
sprintf(filename,"%s%c%s%c",directoryName,PATH_SEP,FilenameBase,'A');
if (!motherGenome->saveToFile(filename)) {
fprintf(stderr,"DiploidGenome::saveToDirectory: failed to save mother's genome.\n");
delete [] filename;
return false;
}
sprintf(filename,"%s%c%s%c",directoryName,PATH_SEP,FilenameBase,'B');
if (!fatherGenome->saveToFile(filename)) {
fprintf(stderr,"DiploidGenome::saveToDirectory: failed to save father's genome.\n");
delete motherGenome;
delete [] filename;
return false;
}
delete [] filename;
return true;
}
const Genome *
DiploidGenome::getGenome(bool fromMother) const
{
if (fromMother) return motherGenome;
return fatherGenome;
}
DiploidGenome::~DiploidGenome()
{
if (ownsGenomes) {
delete motherGenome;
delete fatherGenome;
}
}