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POUsing realloc to expand buffer while reading from file crashes
 

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    <p>I am writing some code that needs to read <a href="http://en.wikipedia.org/wiki/FASTA_format" rel="noreferrer">fasta files</a>, so part of my code (included below) is a fasta parser. As a single sequence can span multiple lines in the fasta format, I need to concatenate multiple successive lines read from the file into a single string. I do this, by realloc'ing the string buffer after reading every line, to be the current length of the sequence plus the length of the line read in. I do some other stuff, like stripping white space etc. All goes well for the first sequence, but fasta files can contain multiple sequences. So similarly, I have a dynamic array of structs with a two strings (title, and actual sequence), being "char *". Again, as I encounter a new title (introduced by a line beginning with '>') I increment the number of sequences, and realloc the sequence list buffer. The realloc segfaults on allocating space for the second sequence with</p> <pre><code>*** glibc detected *** ./stackoverflow: malloc(): memory corruption: 0x09fd9210 *** Aborted </code></pre> <p>For the life of me I can't see why. I've run it through gdb and everything seems to be working (i.e. everything is initialised, the values seems sane)... Here's the code:</p> <pre><code>#include &lt;stdio.h&gt; #include &lt;string.h&gt; #include &lt;stdlib.h&gt; #include &lt;ctype.h&gt; #include &lt;math.h&gt; #include &lt;errno.h&gt; //a struture to keep a record of sequences read in from file, and their titles typedef struct { char *title; char *sequence; } sequence_rec; //string convenience functions //checks whether a string consists entirely of white space int empty(const char *s) { int i; i = 0; while (s[i] != 0) { if (!isspace(s[i])) return 0; i++; } return 1; } //substr allocates and returns a new string which is a substring of s from i to //j exclusive, where i &lt; j; If i or j are negative they refer to distance from //the end of the s char *substr(const char *s, int i, int j) { char *ret; if (i &lt; 0) i = strlen(s)-i; if (j &lt; 0) j = strlen(s)-j; ret = malloc(j-i+1); strncpy(ret,s,j-i); return ret; } //strips white space from either end of the string void strip(char **s) { int i, j, len; char *tmp = *s; len = strlen(*s); i = 0; while ((isspace(*(*s+i)))&amp;&amp;(i &lt; len)) { i++; } j = strlen(*s)-1; while ((isspace(*(*s+j)))&amp;&amp;(j &gt; 0)) { j--; } *s = strndup(*s+i, j-i); free(tmp); } int main(int argc, char**argv) { sequence_rec *sequences = NULL; FILE *f = NULL; char *line = NULL; size_t linelen; int rcount; int numsequences = 0; f = fopen(argv[1], "r"); if (f == NULL) { fprintf(stderr, "Error opening %s: %s\n", argv[1], strerror(errno)); return EXIT_FAILURE; } rcount = getline(&amp;line, &amp;linelen, f); while (rcount != -1) { while (empty(line)) rcount = getline(&amp;line, &amp;linelen, f); if (line[0] != '&gt;') { fprintf(stderr,"Sequence input not in valid fasta format\n"); return EXIT_FAILURE; } numsequences++; sequences = realloc(sequences,sizeof(sequence_rec)*numsequences); sequences[numsequences-1].title = strdup(line+1); strip(&amp;sequences[numsequences-1].title); rcount = getline(&amp;line, &amp;linelen, f); sequences[numsequences-1].sequence = malloc(1); sequences[numsequences-1].sequence[0] = 0; while ((!empty(line))&amp;&amp;(line[0] != '&gt;')) { strip(&amp;line); sequences[numsequences-1].sequence = realloc(sequences[numsequences-1].sequence, strlen(sequences[numsequences-1].sequence)+strlen(line)+1); strcat(sequences[numsequences-1].sequence,line); rcount = getline(&amp;line, &amp;linelen, f); } } return EXIT_SUCCESS; } </code></pre>
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    1. COThanks for all the comments about the substring routine. I've fixed it in my code. I also noticed however that the way I dealt with negative indexes was wrong. I should add the negative index, not subtract it. That being said, I also realised that I copied the substr function in error, as I don't call it in the rest of the pasted code.
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    2. CO`strip()` is also buggy. It will do bad things with zero-length strings. It looks like you don't call it with such strings, but I think it would be a good thing to fix for when it's used elsewhere.
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      1. USMichael Burr
 

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