How to implement a stream that can be splitted by newline - c++

Question

The following code works, but is about twice as inefficient compared to when I use a (linux) pipe that gives unzipped data to the (modified) program. I need a steady stream within the program which I can keep splitting by \n. Is there a way to do this using a (string?) stream or any other trick?
int main(int argc, char *argv[]) {
static const int unzipBufferSize = 8192;
long long int counter = 0;
int i = 0, p = 0, n = 0;
int offset = 0;
char *end = NULL;
char *begin = NULL;
unsigned char unzipBuffer[unzipBufferSize];
unsigned int unzippedBytes;
char * inFileName = argv[1];
char buffer[200];
buffer[0] = '\0';
bool breaker = false;
char pch[4][200];
Read *aRead = new Read;
gzFile inFileZ;
inFileZ = gzopen(inFileName, "rb");
while (true) {
unzippedBytes = gzread(inFileZ, unzipBuffer, unzipBufferSize);
if (unzippedBytes > 0) {
unzipBuffer[unzippedBytes] = '\0'; //put a 0-char after the total buffer
begin = (char*) &unzipBuffer[0]; // point to the address of the first char
do {
end = strchr(begin,(int)'\n'); //find the end of line
if (end != NULL) *(end) = '\0'; // put 0-char to use it as a c-string
pch[p][0] = '\0'; \\ put a 0-char to be able to strcat
if (strlen(buffer) > 0) { // if buffer from previous iteration contains something
strcat(pch[p], buffer); // cat it to the p-th pch
buffer[0] = '\0'; \\ set buffer to null-string or ""
}
strcat(pch[p], begin); // put begin (or rest of line in case there was a buffer into p-th pch
if (end != NULL) { // see if it already points to something
begin = end+1; // if so, advance begin to old end+1
p++;
}
if(p>3) { // a 'read' contains 4 lines, so if p>3
strcat(aRead->bases,pch[1]); // we use line 2 and 4 as
strcat(aRead->scores,pch[3]); // bases and scores
//do things with the reads
aRead->bases[0] = '\0'; //put them back to 0-char
aRead->scores[0] = '\0';
p = 0; // start counting next 4 lines
}
}
while (end != NULL );
strcat(buffer,pch[p]); //move the left-over of unzipBuffer to buffer
}
else {
break; // when no unzippedBytes, exit the loop
}
}

Answer 1

Your main problem is probably the standard C string library.
With using strxxx() funcions, you are iterating through the complete buffer multiple times each call, first for strchr(), then for strlen(), then for each of the strcat() calls.
Using the standard library is a nice thing, but here, it's just plain inefficient.
Try if you could come up with something simpler that touches each character only once like (code just to show the principle, do not expect it working):
do
{
do
{
*tp++ = *sp++;
} while (sp < buffer_end && *sp != '\n');
/* new line, do whatever it requires */
...
/* reset tp to beginning of buffer */
} while (sp < buffer_end);

Answer 2

I am trying to get this to work, but all it does is giving a Segmentation Fault at runtime:
do {
unzippedBytes = gzread(inFileZ, unzipBuffer, unzipBufferSize);
if (unzippedBytes > 0) {
while (*unzipBuffer < unzippedBytes) {
*pch = *unzipBuffer++;
cout << pch;
i++;
}
i=0;
}
else break;
} while (true);
What am I doing wrong here?