Function init

parseIt.cpp:54–72

map<int, READ_INT_TYPE>::iterator iter;

void init(const char* imdName, const char* alignF) {
	parser = new SamParser(alignF, aux, transcripts, imdName);

	memset(cat, 0, sizeof(cat));
	memset(readOutFs, 0, sizeof(readOutFs));

	int tmp_n_os = -1;

	for (int i = 0; i < 3; i++) {
		genReadFileNames(imdName, i, read_type, n_os, readOutFs[i]);

		assert(tmp_n_os < 0 || tmp_n_os == n_os); tmp_n_os = n_os;

		for (int j = 0; j < n_os; j++)
			cat[i][j] = new ofstream(readOutFs[i][j]);
	}

	counter.clear();
}

//Do not allow duplicate for unalignable reads and supressed reads in SAM input
template<class ReadType, class HitType>