Question

我一直在努力解决这个问题，但无济于事。在下面的代码中，我使用了一个char指针（all_seq），但是当我释放它时，在代码的末尾，有时它会出现段错误。我有时说，因为它显然取决于输入文件。使用小输入文件，它很好。有一个大的，它也没关系。对于中等大小的文件，它是段错误的。我只是无法弄清楚为什么......

任何想法都将不胜感激。感谢。

/* SeqProb (Sequence Probability) - 2012/03/13 */
/* Given a series of aligned sequences -in one file, one per line- this program calculates the probability of having, in each location, the letter in the first sequence. */

#include <stdio.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>

FILE *input_file;
FILE *output_file;

///////////////////////////////
// DECLARATION OF FUNCTIONS: //
///////////////////////////////
int GetSize(FILE *file, int *length, int *lines);
double CalcProb(char *one_seq);

//////////////////////////////////////////////////////////////////
// ************************************************************ //
// **************        START MAIN BLOCK        ************** //
// ************************************************************ //
//////////////////////////////////////////////////////////////////

int main( int argc, char *argv[] )  // We expect three command-line arguments: 1)program name, 2)file to read and 3)file to write.
{
   int i=0,j=0;
   int length, lines, size;
   double prob=0;
   char *all_seq, *one_seq;

////////////////////////////
// CHECK INPUT ARGUMENTS: //
////////////////////////////
// Check if arguments in command line are right and if file can be opened for reading:

   if ( argc != 3 ) {   // There should be 3 arguments for correct execution
      printf("\n Usage: %s <input file> <output file>\n\n ", argv[0]);  // We print argv[0] assuming it is the program name
      exit(1);
   }

   if (!(input_file=fopen(argv[1],"r"))){
      printf("\n Error: can't open input file \n\n");
      exit(2);
   }

   if (!(output_file=fopen(argv[2],"w"))){
      printf("\n Error: can't open output file \n\n");
      exit(3);
   }

/////////////////////////////////////////
// GET LENGTH AND NUMBER OF SEQUENCES: //
/////////////////////////////////////////
   GetSize(input_file,&length,&lines);
   size=length*lines;
   printf("\n length of sequences = %d\n",length);
   printf(" number of sequences = %d\n",lines);

//////////////////////////////////////////////////////
// ALLOCATE MEMORY FOR all_seq AND one_seq VECTORS: //
//////////////////////////////////////////////////////
   all_seq = (char *) malloc((length*lines+10)*sizeof(char));
   one_seq = (char *) malloc((lines+10)*sizeof(char));
   if (all_seq == NULL){    // In case of memory allocation failure, exit.
      printf ("Error: Can't allocate memory \n");
      exit(4);
   }
   if (one_seq == NULL){    // In case of memory allocation failure, exit.
      printf ("Error: Can't allocate memory \n");
      exit(5);
   }

/////////////////////////////////////////////
// INITIALIZE VECTORS all_seq and one_seq: //
/////////////////////////////////////////////
   for (i=0;i<=size;i++) {
      all_seq[i]=0;
   }
   for (i=0;i<=length;i++) {
      one_seq[i]=0;
   }

///////////////////////////////////////////////////////
// LOAD SEQUENCES FROM INPUT FILE IN VECTOR all_seq: //
///////////////////////////////////////////////////////
// Read input file, containing sequences, and put every letter into the all_seq vector, one sequence right after the other (we'll also include the escape character (\n) at the end of each line).
// Note that, in this way, the letter at location (row,col) in the input file will be given by all_seq[(length+1)*row+col]:
   printf("\n Processing file: %s\n\n", argv[1]);
   rewind(input_file);
   for ( i=0; i<=size; ++i) {
      fscanf(input_file,"%c",&all_seq[i]);
//      printf("%d: %c\n",i, all_seq[i]);
   }
//   printf("%c",all_seq[2]);

///////////////////////////////////////////////////////////////
// CALCUALTE PROBABILITIES OF EACH LETTER IN FIRST SEQUENCE: //
///////////////////////////////////////////////////////////////
// Read one column at a time, write it to the one_seq vetor, and calculate the probability of occurrance of the first letter in that column; repeat for all columns:
   for ( j=0; j<length; j++) {
      for ( i=0; i<lines; i++) {
         one_seq[i]=all_seq[(length+1)*i+j];
      }
      prob = CalcProb(one_seq);
//      printf("col=%d: prob=%f \n\n",j,prob);
// Write output file: the first column is just an enumeration, from 1 to the length of the sequences, and the second column gives the probability for finding the first letter in the column, anywhere along the column (a measure of its conservation). 
      fprintf(output_file,"%d     %f\n",j+1,prob);
   }

////////////////////////////////////
/// CLOSE FILES AND FREE MEMORY: ///
////////////////////////////////////
   fclose(input_file);
   fclose(output_file);
   free( all_seq );
   free( one_seq );
   return(0);
}
//////////////////////////////////////////////////////////////////
// ************************************************************ //
// ***************        END MAIN BLOCK        *************** //
// ************************************************************ //
//////////////////////////////////////////////////////////////////

//////////////////////////////////////////////////////
// FUNCTION GetSize: LENGTH AND NUMBER OF SEQUENCES //
//////////////////////////////////////////////////////
int GetSize(FILE *file, int *length, int *lines)
{    
   char c;
   int i=0;
   int *len;
//  Count how many characters in first line:
   while ((c=fgetc(file)) != '\n') {
     ++i;
   }
   *length=i;
   *lines=0;
   *len=0;

// Now count many lines, and check that all lines have same length:
   i=0;
   rewind(file);
   while ( (c=fgetc(file)) != EOF ) {
      ++i;
      if (c=='\n') {
         *lines=*lines+1;
         *len=i-1;
         i=0;
//       printf("length=%d\n",*len);
         if ( *len != *length && *len != 0) {
            printf("ERROR: not all lines in input file have the same length.\n");
            exit(6);
         }
         if ( *len == 0) {
            *lines=*lines-1;
         }
      }
   }

//   printf("lines=%d\n",*lines);
   return(0);
}

///////////////////////////////////////////////////////////////////////////////
// FUNCTION CalcProb: PROBABILITY OF THE FIRST CHARACTER IN THE GIVEN VECTOR //
///////////////////////////////////////////////////////////////////////////////
double CalcProb(char *one_seq)
{
   int i=0;
   double count=0, prob=0;
   while ( one_seq[i] != '\0' ) {
//     printf("one_seq[%d]= %d\n",i,one_seq[i]);
     if ( toupper(one_seq[i]) == toupper(one_seq[0]) ) {
       count=count+1;
     }
     i=i+1;
   }
   prob=count/i;
//   printf("count=%f, i=%d, prob=%f: \n",count,i,prob);
   return(prob);
}

Answer 1

释放内存中的错误通常是由于释放相同的指针两次（此处不太可能），释放无效指针，或先前的缓冲区欠载（同一块）或溢出（前面的块）导致管理数据变得腐败。既然你说它是以大文件作为输入而不是小的，你很可能会超越缓冲区。

当你只分配length个元素时，看起来你通过在0和lines之间迭代来超越one_seq []。

另请注意，您应该可以删除+10安全区，并且还应将for循环修复为<最后一个索引，而不是<=。

由于释放内存导致的分段错误

1 个答案: