Method readPileUP

src/SNPinGenome.cpp:359–379

}

void SNPinGenome::readPileUP(FILE* stream, int minimalTotalLetterCountPerPosition, int minimalQualityPerPosition, GenomeCopyNumber* p_genomeCopyNumber) {
    string oldChr = "azeaze";
    int sNPpositionToProceed;
    int positionCount = 0;
    string line;
    int index=NA;
	char* line_buffer = NULL;
	char buffer[MAX_BUFFER];
	long normalCount = 0;
	long count = 0;

	while ((line_buffer = getLine(buffer, MAX_BUFFER, stream, line)) != NULL) {
	  normalCount += processPileUPLine(positionCount, line_buffer, oldChr, sNPpositionToProceed,minimalTotalLetterCountPerPosition,index,minimalQualityPerPosition, p_genomeCopyNumber);
	  count++;
	}

	if (p_genomeCopyNumber) {
	  p_genomeCopyNumber->finishCopyNumber(normalCount);
	}
	std::cout << count << " lines read\n";
}

void SNPinGenome::assignValues(std::string const& inFile, string inputFormat, int minimalTotalLetterCountPerPosition, int minimalQualityPerPosition, GenomeCopyNumber* p_genomeCopyNumber) {
//    vector <float> heterozygousBAFs;