Segmentation fault - can't find it

I have a function that compresses string and one function reading textfiles to strings. There's some issue that I can't nail. The idea is to read a textfile line by line and put each line into a string vector. When I dump the vector each line seems to be propper but when I try to use the vector in an function I get segmentation fault. Adding to my confusion - if I hard code the strings insterad of using file2string str2comp works.

The two functions are as follows.

Code:

string str2comp(std::string str, int offset = 0){

........string compstr;
........string::iterator it;
........int index = offset;

..for ( it = str.begin() ; it < str.end(); ++it){
................if (index%4 == 0){
.. ..................compstr += (char)map.find(str.substr(index,4))->second;
.... ........}
....................index++;
.... }

........return compstr;
}

Code:

string file2String(const string &fileName){
....ifstream ifs(fileName.c_str(), ios::in | ios::binary | ios::ate);
....if(!ifs)
.... ..{
.... .. ..cerr << "Error : file2String() could not open file: " << fileName << endl;
.... .. ..exit(1);
.... ..} else {
.... ..ifstream::pos_type fileSize = ifs.tellg();
.... ..ifs.seekg(0, ios::beg);
.... ..vector<char> bytes(fileSize);
.... ..ifs.read(&bytes[0], fileSize);
.... ..ifs.close();
.... ..return string(&bytes[0], fileSize);
....}
}

I'm kind of green when it comes to C++ and I would really appreciate feedback or help.

Have you tried running your program through your debugger? The debugger should be able to tell you exactly where the problem is detected. Plus you should be able to view the variables at the time of the crash. Without a complete program, finding a segmentation fault is very difficult.

Jim

You are aware we're not mind readers?

Without some representative code that calls those functions, and exhibits your problem, you rely on us having mindreading skills.

Try creating a SMALL but COMPLETE sample of code that exhibits the symptoms. In the process of producing that sample, you might have an "aha!" moment. If not, you can post the code, and mere mortals might have a chance of helping you.

Sure...

Code:

string = file2String("filename");
compstr = string2comp(string,0);

How about properly indenting your code, rather than filling it with useless dots.

The next thing, run the program in the debugger, and it will point you at the line of code causing the fault, and give you the chance to look around and find out why it's crashing.

Originally Posted by Salem

How about properly indenting your code, rather than filling it with useless dots.

The next thing, run the program in the debugger, and it will point you at the line of code causing the fault, and give you the chance to look around and find out why it's crashing.

About that debugging, any names or links to the software?

Originally Posted by überfuzz

Sure...

Code:

string = file2String("filename");
compstr = string2comp(string,0);

How does the above relate to a SMALL but COMPLETE program?

About that debugging, any names or links to the software?

What compiler are you using?

Jim

I write:..make Aligner && ./Aligner in the bash window..

Edit, I'm trying to help some biologist, one being my girlfriend, with some analysis on their cluster. I'm not really used to C++ and I thought my errors would, or hoped they would be quite evident. That's why I only posted the functions messing things up.

If you're using a modern IDE then it should have a debugger already built-in.

As for the file2String function there are easier/shorter ways of reading the entire content of a file into a string container (if I judge your intent with that function correctly) by way of using a stringstream container as an intermediate storage object:

Code:

std::ifstream file("your_file_name_goes_here");
std::stringstream sstr;
std::string data;
 
sstr << file.rdbuf();  // Get whole file into stringstream object sstr
data = sstr.str();  // Convert into string, data now contains entire file's content

Originally Posted by jimblumberg

How does the above relate to a SMALL but COMPLETE program?

It doesn't.

The str2comp() function is also referring to a map, which is not declared, let alone defined in any code provided by the OP.

The map:

Code:

void buildmap(){


         map["AAAA"]=0;
         map["AAAT"]=1;
..        etc...
         map["CCCC"]=255;
         
}

Some reading material for you here.

Originally Posted by hk_mp5kpdw

If you're using a modern IDE then it should have a debugger already built-in.

I'm sitting by an old unix system, I have no permissions nor do I have an insight on what softwares available. Thanks anyway!

As for the file2String function there are easier/shorter ways of reading the entire content of a file into a string container (if I judge your intent with that function correctly) by way of using a stringstream container as an intermediate storage object:

Code:

std::ifstream file("your_file_name_goes_here");
std::stringstream sstr;
std::string data;
..
sstr << file.rdbuf(); ..// Get whole file into stringstream object sstr
data = sstr.str(); ..// Convert into string, data now contains entire file's content

Cheers!

As already posted in the other thread: map.find(str.substr(index,4))->second may crash, if map.find(...) returns map.end(). You should compare it to that before you dereference the iterator.


Do you have gdb?

A tutorial (one of many, this is just google's lucky hit)
gdb Tutorial