Segmentation Error - How!

Question

int Sequence::scoreDegeneracy() { cout << "Score Degeneracy" << name << seqLen << endl; int f = 0; if (degenComputed == false) { char _2foldTest = '*'; char _4foldTest = '*'; int aaseqLen = seqLen/3; int i = 0; for (i; i < aaseqLen; i++) { _4foldTest = is4FoldDegenerateSite(i); _2foldTest = is2FoldDegenerateSite(i,_4foldTest); degScores.totalCodons++ if (_2foldTest != '*') { degScores.totalCodons_2fold++; if (_2foldTest == 'A') { degScores.total_2fold_A++; } else if (_2foldTest == 'T') { degScores.total_2fold_T++; } else if (_2foldTest == 'G') { degScores.total_2fold_G++; } else { degScores.total_2fold_C++; } }else if (_4foldTest != '*') { degScores.totalCodons_4fold++; if (_4foldTest == 'A') { degScores.total_4fold_A++; } else if (_4foldTest == 'T') { degScores.total_4fold_T++; } else if (_4foldTest == 'C') { degScores.total_4fold_C++; } else { degScores.total_4fold_G++; } } cout << "Crashes right here when i = 0." << endl; } } degenComputed = true; return 1; } 

Driving me! SegFault happens right at the end of the first iteration of the for loop. Behaves EXACTLY, as expected, the first test returns the correct results. A segmentation error occurs before I even increase ....

What am I missing?

...

 char Sequence::is4FoldDegenerateSite(int codonIndex){ char aminoAcid = aaSeq[codonIndex]; //cout << "Amino acid of codon number " << codonIndex << " is: " << aminoAcid << endl; int loc = readingFrame + (codonIndex * 3) + 2; int locR = loc - 2; switch (aminoAcid){ case 'A': return seq[loc]; case 'T': return seq[loc]; case 'V': return seq[loc]; case 'G': return seq[loc]; case 'P': return seq[loc]; case 'S'://Can also be 2 fold degenerate if (seq[locR] == 'T'){ return seq[loc]; }else{ return '*'; } case 'R'://Can also be 2 fold degenerate if (seq[locR] == 'C'){ return seq[loc]; }else{ return '*'; } case 'L'://Can also be 2 fold degenerate if (seq[locR] == 'C'){ return seq[loc]; }else{ return '*'; } } return '*'; } char Sequence::is2FoldDegenerateSite(int codonIndex, char _4FoldResults){ char aminoAcid = aaSeq[codonIndex]; int loc = readingFrame + (codonIndex * 3) + 2; //char doubleDegeneracyTest = is4FoldDegenerateSite(codonIndex); //bool doubleDegeneracy = false; //if (doubleDegeneracyTest != '*') doubleDegeneracy = true; switch (aminoAcid){ case 'N': return seq[loc]; case 'D': return seq[loc]; case 'C': return seq[loc]; case 'Q': return seq[loc]; case 'E': return seq[loc]; case 'H': return seq[loc]; case 'K': return seq[loc]; case 'F': return seq[loc]; case 'Y': return seq[loc]; case 'X': return seq[loc]; case 'S'://Can also be 2 fold degenerate if (_4FoldResults == '*'){ return seq[loc]; }else{ return '*'; } case 'R'://Can also be 2 fold degenerate if (_4FoldResults == '*'){ return seq[loc]; }else{ return '*'; } case 'L'://Can also be 2 fold degenerate if (_4FoldResults == '*'){ return seq[loc]; }else{ return '*'; } } return '*'; } 

Valgrind Results:

 **17043** new/new[] failed and should throw an exception, but Valgrind ==17043== at 0x4024E35: VALGRIND_PRINTF_BACKTRACE (valgrind.h:3720) ==17043== by 0x40253C2: operator new(unsigned int) (vg_replace_malloc.c:214) ==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D70A7: std::string::_Rep::_M_clone(std::allocator<char> const&, unsigned int) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D7EDC: std::string::reserve(unsigned int) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D83AF: std::string::append(std::string const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x804BA7F: std::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) (basic_string.h:2168) ==17043== by 0x804ACDF: GenomeSeq::setup() (GenomeSeq.C:108) ==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52) ==17043== by 0x80496DF: main (Main2.C:143) **17043** cannot throw exceptions and so is aborting instead. Sorry. ==17043== at 0x4024E35: VALGRIND_PRINTF_BACKTRACE (valgrind.h:3720) ==17043== by 0x40253D0: operator new(unsigned int) (vg_replace_malloc.c:214) ==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D70A7: std::string::_Rep::_M_clone(std::allocator<char> const&, unsigned int) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D7EDC: std::string::reserve(unsigned int) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D83AF: std::string::append(std::string const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x804BA7F: std::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) (basic_string.h:2168) ==17043== by 0x804ACDF: GenomeSeq::setup() (GenomeSeq.C:108) ==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52) ==17043== by 0x80496DF: main (Main2.C:143) Loading sequence..==17043== ==17043== HEAP SUMMARY: ==17043== in use at exit: 2,749,679 bytes in 10 blocks ==17043== total heap usage: 39,043 allocs, 39,032 frees, 80,022,672,644 bytes allocated ==17043== ==17043== 27 bytes in 1 blocks are definitely lost in loss record 1 of 10 ==17043== at 0x4025390: operator new(unsigned int) (vg_replace_malloc.c:214) ==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D7340: ??? (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D7525: std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x804969E: main (Main2.C:143) ==17043== ==17043== 28 bytes in 1 blocks are definitely lost in loss record 2 of 10 ==17043== at 0x4025390: operator new(unsigned int) (vg_replace_malloc.c:214) ==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D7340: ??? (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D7525: std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x80496C3: main (Main2.C:143) ==17043== ==17043== 83 bytes in 1 blocks are definitely lost in loss record 3 of 10 ==17043== at 0x4025390: operator new(unsigned int) (vg_replace_malloc.c:214) ==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D70A7: std::string::_Rep::_M_clone(std::allocator<char> const&, unsigned int) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D7EDC: std::string::reserve(unsigned int) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D814A: std::string::append(char const*, unsigned int) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40B3F3E: std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, char) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40C9799: std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x804ACB5: GenomeSeq::setup() (GenomeSeq.C:106) ==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52) ==17043== by 0x80496DF: main (Main2.C:143) ==17043== ==17043== 100 bytes in 1 blocks are definitely lost in loss record 4 of 10 ==17043== at 0x4025390: operator new(unsigned int) (vg_replace_malloc.c:214) ==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D70A7: std::string::_Rep::_M_clone(std::allocator<char> const&, unsigned int) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D7EDC: std::string::reserve(unsigned int) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D814A: std::string::append(char const*, unsigned int) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40B3F3E: std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, char) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40C9799: std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x804AC07: GenomeSeq::setup() (GenomeSeq.C:101) ==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52) ==17043== by 0x80496DF: main (Main2.C:143) ==17043== ==17043== 100 bytes in 1 blocks are definitely lost in loss record 5 of 10 ==17043== at 0x4025390: operator new(unsigned int) (vg_replace_malloc.c:214) ==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D7340: ??? (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D75D1: std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D33C5: std::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >::basic_istringstream(std::string const&, std::_Ios_Openmode) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x804AC42: GenomeSeq::setup() (GenomeSeq.C:103) ==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52) ==17043== by 0x80496DF: main (Main2.C:143) ==17043== ==17043== 8,192 bytes in 1 blocks are definitely lost in loss record 8 of 10 ==17043== at 0x4025024: operator new[](unsigned int) (vg_replace_malloc.c:258) ==17043== by 0x40A2592: std::basic_filebuf<char, std::char_traits<char> >::_M_allocate_internal_buffer() (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40A65B1: std::basic_filebuf<char, std::char_traits<char> >::open(char const*, std::_Ios_Openmode) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40A7EAF: std::basic_ifstream<char, std::char_traits<char> >::basic_ifstream(char const*, std::_Ios_Openmode) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x804ABBF: GenomeSeq::setup() (GenomeSeq.C:97) ==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52) ==17043== by 0x80496DF: main (Main2.C:143) ==17043== ==17043== 8,192 bytes in 1 blocks are definitely lost in loss record 9 of 10 ==17043== at 0x4025024: operator new[](unsigned int) (vg_replace_malloc.c:258) ==17043== by 0x40A2592: std::basic_filebuf<char, std::char_traits<char> >::_M_allocate_internal_buffer() (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40A65B1: std::basic_filebuf<char, std::char_traits<char> >::open(char const*, std::_Ios_Openmode) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40A7EAF: std::basic_ifstream<char, std::char_traits<char> >::basic_ifstream(char const*, std::_Ios_Openmode) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x804AC9D: GenomeSeq::setup() (GenomeSeq.C:105) ==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52) ==17043== by 0x80496DF: main (Main2.C:143) ==17043== ==17043== 2,732,253 bytes in 1 blocks are definitely lost in loss record 10 of 10 ==17043== at 0x4025390: operator new(unsigned int) (vg_replace_malloc.c:214) ==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D70A7: std::string::_Rep::_M_clone(std::allocator<char> const&, unsigned int) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D7EDC: std::string::reserve(unsigned int) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x40D83AF: std::string::append(std::string const&) (in /usr/lib/libstdc++.so.6.0.13) ==17043== by 0x804BA7F: std::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) (basic_string.h:2168) ==17043== by 0x804ACDF: GenomeSeq::setup() (GenomeSeq.C:108) ==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52) ==17043== by 0x80496DF: main (Main2.C:143) ==17043== ==17043== LEAK SUMMARY: ==17043== definitely lost: 2,748,975 bytes in 8 blocks ==17043== indirectly lost: 0 bytes in 0 blocks ==17043== possibly lost: 0 bytes in 0 blocks ==17043== still reachable: 704 bytes in 2 blocks ==17043== suppressed: 0 bytes in 0 blocks ==17043== Reachable blocks (those to which a pointer was found) are not shown. ==17043== To see them, rerun with: --leak-check=full --show-reachable=yes ==17043== ==17043== For counts of detected and suppressed errors, rerun with: -v ==17043== ERROR SUMMARY: 8 errors from 8 contexts (suppressed: 19 from 8) 

Sequence.h:

 #ifndef SEQUENCE_H #define SEQUENCE_H using namespace std; #include <iostream> #include <fstream> #include <cstring> #include <sstream> #include <string> class GeneSeqs; class Sequence{ public: Sequence(); Sequence(char * seqStart,char * aaSeqStart, int length);//Constructor ~Sequence();//Destructor -- for the transprof //void setup();//Setups up variables. char &operator[](int); char * getSeq(){return seq;}//returns the address of sequence string getAASeq(){return aaSeq;}//returns address of aaSeq int getLength(){return seqLen;} bool isPositive(){return positiveStrand;} /** * Setters */ void setRevC(char * sequ){revC = sequ;} void setSeq(char * sequ){ seq = sequ; } void setAASeq(char * a){aaSeq = a;} void setLength(int len){seqLen = len;} void setAALength(int len){aaSeqLen = len;} void setPositivity(bool trufal){ positiveStrand = trufal; if (trufal == false){ buildRevC(); } } // int getTCount(){return count.T;} int getACount(){return count.A;} int getCCount(){return count.C;} int getGCount(){return count.G;} //void setAASeq(int * a){aaSeq = a;} string get_aaSeq(){return aaSeq;} bool get_aaSeqExhists(){return aaSeqTranslated;} int get_aaSeqLen(){return aaSeqLen;} void print(); void printAA(); char getAA(int i){return aaSeq[i];} int getAALoc(char aa){return AAchar2num(aa);} float getMIMScore(){return MIMScore;} void setMIM(float MIM){MIMScore = MIM;} void translateToAA(int code); void computeCrudeCompositions(); int scoreDegeneracy(); void degeneracyReport(); void setName(string n){name = n;} float distanceMeasure(Sequence * target); bool degeneracyIsScored(){return degenComputed;} float distanceMeasure(GeneSeqs * target); float distanceMeasureA(GeneSeqs * target, int point, float runningSum); int getDegenData(int code); void setStartConstant(int i){start = i;} void printInfo(); private: struct nucleotideCounts{ int T; int C; int A; int G; }count; struct degeneracyScores{ int totalCodons; int totalCodons_4fold; int totalCodons_2fold; int total_4fold_A; int total_4fold_T; int total_4fold_C; int total_4fold_G; int total_2fold_A; int total_2fold_T; int total_2fold_G; int total_2fold_C; }degScores; string name; char is4FoldDegenerateSite(int codonIndex); char is2FoldDegenerateSite(int codonIndex, char _4FoldResults); bool degenComputed; float MIMScore; void buildRevC(); string revC; char nucleoRevC(char c); char * seq; int readingFrame;//zero till used... int aaSeqLen; bool aaSeqTranslated; int start; int seqLen; //Number of nucleotides in sequence bool positiveStrand; //Positive strand = true, negative = false; //bool hasY; //Genetic sequence in numerical Amino Acide representation; string aaSeq; void geneSegments2AASeq(); void computeAATransProf(); int AAchar2num(char x); char AAnum2char(int x); char codon2AA(int codonIndex); char codon2AA(char * codon); char codon2AA(int * codon); int Int(string num); int Int(char num); char num2nucleo(int a); void codonSeq2AASeq(); int char2nucleo2(char a); string String(int num); }; #endif 

Answer 1

 total heap usage: 39,043 allocs, 39,032 frees, 80,022,672,644 bytes allocated 

80GB ?? I think you have a memory leak somewhere ...

I would vote for how you treat "seq" as char *, and use std: string in other places. It looks like an accident awaiting his ministry.

Answer 2

Are you using unix or linux? If so, Valgrind is a great tool to solve these problems.

Answer 3

Either is4FoldDegenerateSite or is2FoldDegenerateSite your stack, and then when the program tries to return to the beginning of the input, the stack is disabled, so you go into bad memory.

Take a look at these two functions and make sure they clear their memory correctly. Do you have code from any of those functions that you could place?

EDIT: You overload the [] operator. Maybe this is a good place to view? The code is pretty complicated for others to debug remotely.

Answer 4

Start deleting things in parts (block comments are helpful) to find out what affects your failure. The correctness of this troubleshooting method does not matter. If you delete something, it probably looks at something systemic.

The sad fact is that your problem is not local to crashsite, so sending bits and parts around the crash site is not enough for us to detect your error.

Answer 5

I seriously doubt how you handle the seq variable in the Sequence class. At the moment, I suggest you add

 bool Sequence::isValid (int loc){ if ((seq != NULL) && (loc < strlen(seq))) { return true; } // optimize it later else { return false; } } 

and updating is4FoldDegenerateSite () && & is2FoldDegenerateSite () with the following,

 int loc = readingFrame + (codonIndex * 3) + 2; int locR = loc - 2; if (isValid(loc) == false) return '*'; // also validate locR before using it. 

In my opinion, you should also add exception handling; update setSeq (char * sequ) and setLength (int len) to throw exceptions in case of invalid input.

Hth