Method init

src/fastqreader.cpp:169–209

}

void FastqReader::init(){
	if (ends_with(mFilename, ".gz")){
		mFile = fopen(mFilename.c_str(), "rb");
		if(mFile == NULL) {
			error_exit("Failed to open file: " + mFilename);
		}

		// Check for BGZF format — use parallel decompression if detected
		if (isBgzf(mFile)) {
			fseek(mFile, 0, SEEK_SET);
			mBgzfReader = new BgzfMtReader(mFile, mBgzfThreadBudget);
			mZipped = true;
			readToBuf();
			return;
		}

		isal_gzip_header_init(&mGzipHeader);
		isal_inflate_init(&mGzipState);
		mGzipState.crc_flag = ISAL_GZIP_NO_HDR_VER;
		mGzipState.next_in = mGzipInputBuffer;
		mGzipState.avail_in = fread(mGzipState.next_in, 1, mGzipInputBufferSize, mFile);
		mGzipInputUsedBytes += mGzipState.avail_in;
		int ret = isal_read_gzip_header(&mGzipState, &mGzipHeader);
		if (ret != ISAL_DECOMP_OK) {
			error_exit("igzip: Error invalid gzip header found: "  + mFilename);
		}
		mZipped = true;
	}
	else {
		if(mFilename == "/dev/stdin") {
			mFile = stdin;
		}
		else
			mFile = fopen(mFilename.c_str(), "rb");
		if(mFile == NULL) {
			error_exit("Failed to open file: " + mFilename);
		}
		mZipped = false;
	}
	readToBuf();
}

void FastqReader::getBytes(size_t& bytesRead, size_t& bytesTotal) {
	if(mZipped) {