int GenericFile_stdio::advance(long long offset)
{
return _fseek64bit(_file, offset, SEEK_CUR);
}
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;
}
