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Segment fault for C++ program when return vector

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# 1  
Old 10-28-2014
Segment fault for C++ program when return vector
I am trying to reverse complement DNA sequence (string) with a short c++ code using boost library. Code was compiled without any warning/error, but ran into Segmentation fault.
My guess is the function to return a vector, but not sure.
Code:
#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include <boost/assign.hpp>

using namespace std;
using namespace boost::assign;

vector <char> revcomp(string str) 
{
vector <char> str_rc;
map <char, char> m = map_list_of('A','T')('T','A')('G','C')('C','G');

for (unsigned i = str.size(); i >= 0 ; --i)
{
str_rc.push_back(m[str[i]]);        //get all the chars except str[0]
}
str_rc.push_back(m[str[0]]);        //get the first char 

return str_rc;
}

int main()
{
vector <char> str2;
string str1 = "ATCGTTTCCC";
str2 = revcomp(str1);

vector<char>::iterator itr2;
for (itr2 = str2.begin(); itr2 != str2.end(); ++itr2)
{
cout << *itr2;
}
cout << endl;

return 0;
}

Code:
$ g++ -Wall revcomp.cpp 
$ ./a.out
Segmentation fault

Can anyone look into it? Thanks a lot!
# 2  
Old 10-28-2014
This is the error:

Code:
for (unsigned i = str.size()-1; i >= 0 ; --i)

An unsigned number is never going to be less than zero, making this an infinite loop. Some compilers will warn you about this.

That said, this code looks suspect in a number of ways. Why are you using strings as the input and vector as the output -- why not vector or string for both? Why return giant vectors since it means it'll be copying them again and again and again and again and again? Pass one in as a reference.

Above all, why use boost? You will be chained to that depleted uranium lawn gnome forever. There's plenty of ways to initialize a map.

Code:
const char *i[]={"AG", "TC"};
for(int n=0; i[0][n]; n++)  { m[i[0][n]]=m[i[1][n]]; m[i[1][n]]=m[i[0][n]]; }

Or don't even use a map at all:

Code:
#include <stdio.h>
#include <string.h>
#include <stdlib.h>

static const unsigned char map[256]={
        ['A']='T',      ['T']='A',      ['G']='C',      ['C']='G'       };

int main(int argc, char *argv[])
{
        int n;
        const char *input="ATCGTTTCCC";
        char *output=strdup(input);

        for(n=0; input[n]; n++) output[n]=map[input[n]];

        printf("%s = %s\n", input, output);
}

Vectors and maps have made this problem more difficult, not less.
Last edited by Corona688; 10-28-2014 at 02:49 PM..
This User Gave Thanks to Corona688 For This Post:
yifangt
# 3  
Old 10-28-2014
Quote:
Originally Posted by Corona688
...

Above all, why use boost? You will be chained to that depleted uranium lawn gnome forever. There's plenty of ways to initialize a map.

...
LOL
# 4  
Old 10-28-2014
Above all, why use boost?
1) It's simply a learning trial by "copy-paste" and still at stage of "try and error" to understand more, hopefully;
2) The purpose is to make a function which will be combined to other .cpp code. Modified from a snippet online as was told "ultra-fast"!
Code:
// http://www.bashthat.com/2014/09/30/reverse-complement-response.html
#include <boost/assign.hpp>

using namespace std;
using namespace boost::assign;

//compile with g++                                                          

int main( int argc,const char *argv[] )
{
  string str = argv[1];
  map<char, char> m = map_list_of ('A', 'T') ('T', 'A') ('G', 'C') ('C', 'G');

  string::iterator it;
  for ( it = str.begin() ; it != str.end(); ++it )
  {
    cout <<  m[*it] ;
  }
  cout << endl;
}

Am I stubborn and offending if I insist C++, as I need modify your code to reverse the output and then integrate it into other .cpp code?
Thanks a lot in any way!
Last edited by yifangt; 10-28-2014 at 03:24 PM..
# 5  
Old 10-28-2014
Quote:
Originally Posted by yifangt
Above all, why use boost?
1) It's simply a learning trial by "copy-paste" and still at stage of "try and error" to understand more, hopefully;
2) The purpose is to make a function which will be combined to other .cpp code. Modified from a snippet online as was told "ultra-fast"!
You are learning from suspicious sources. It is not "fast" to create and initialize a new map every time you call that function. It is especially not fast to return a vector by value.
Quote:
Am I stubborn and offending if I insist C++
Frankly?

My "pure C" code is one cout away from being "pure C++" code. That it looks so mysterious means you've skipped learning big, important chunks of both. It's like trying to avoid using variables of type 'int', or doing everything by calling system("this"); system("that");

Learning how arrays, strings, structures, and pointers actually work will explain almost everything that's baffling you right now. Then you'll be equipped enough to actually troubleshoot your problems and learn more, and take proper advantage of the standard template library -- most of its design imitates them, after all. Maps and vectors imitate arrays, map[index]. Iterators imitate pointers to arrays(and crash all the same ways as them): iterator->content, iterator++... If you don't understand those, you'll never know what you're looking at.

And STL strings imitate real strings (which are themselves, arrays). Notice how little really changes when I substitute one for the other.

Code:
#include <iostream>
#include <string>

using namespace std;

unsigned char m[256];

int main() {
        int n;
        string input="ATCGTTTCCC";
        string output=input;
        m['A']='T';     m['T']='A';     m['G']='C';     m['C']='G';

        for(n=0; n<input.length(); n++) output[n]=m[input[n]];

        cout << input << " " << output << "\n";
        return(0);
}

Last edited by Corona688; 10-28-2014 at 04:22 PM..
This User Gave Thanks to Corona688 For This Post:
yifangt
# 6  
Old 10-28-2014
Learning how arrays, strings, structures, and pointers actually work will explain almost everything that's baffling you right now.
I am very aware of that, which reminds me of my early posts in this forum. Learning by "practice" related to real problem is better, like this one and the strtok() function......
Am I stubborn and offending if I insist C++
As I have the same feeling like most of the beginners that sometimes C++ is easier to catch than C, and I am not able to mix C with C++ code together in one program at this moment. Neither do I want get lost when trying to solve one problem, so that I asked for C++.
OK, here is a modified version of the code, and I hope it is a improved version from "professional views"
Code:
#include <iostream>
#include <string>
#include <algorithm>

using namespace std;
string revcomp(string);

int main(int argc, char *argv[]) 
{
string str = argv[1];
string str2 = revcomp(str);

cout << str << " = " << str2 << endl;

 return 0;
}

string revcomp(string input)
{
unsigned char m[256];
int n;
string output = input;

m['A'] = 'T'; m['T'] = 'A'; m['C'] = 'G'; m['G'] = 'C';
m['a'] = 'T'; m['t'] = 'A'; m['c'] = 'G'; m['g'] = 'C';

for (n = 0; n < input.length(); n++)
{
output[n] = m[input[n]];
}
string result = output;
reverse(result.begin(), result.end());

return result;
}

Code:
$ g++ -Wall test.cpp 
$ ./a.out aCTGCTACCC
aCTGCTACCC = GGGTAGCAGT

Which is what I need.
Thank you so much again!
# 7  
Old 10-28-2014
Quote:
Originally Posted by yifangt
Learning how arrays, strings, structures, and pointers actually work will explain almost everything that's baffling you right now.
I am very aware of that, which reminds me of my early posts in this forum. Learning by "practice" related to real problem is better, like this one and the strtok() function.
You have learned one way to avoid your blind spots, but your blind spots are still there.
Quote:
Am I stubborn and offending if I insist C++
As I have the same feeling like most of the beginners that sometimes C++ is easier to catch than C
Would you say you could program Perl if you just had line after line of system("echo hello world"), system("mv file1 file2"), system("echo $variable") ?

You understand integers and for-loops, and that's about all. Everything else you've just "shelled out" to an external library. Your programming comfort zone is very, very small.

If you don't recognize something, that doesn't make it "C". You've thrown out big parts of both languages along the way.
Quote:
I am not able to mix C with C++ code together in one program at this moment.
Labeling everything you don't understand as "C" and therefore "out of the curriculum" is part of the problem. You've found one C++ library you like and decided that must be what the language is all about. It's not. You've overlooked something important.

I seriously think you should try and program without STL vector, string, and map for a while.
Last edited by Corona688; 10-28-2014 at 06:26 PM..
This User Gave Thanks to Corona688 For This Post:
yifangt
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