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Buffer overflow while storing .alt file using bwa mem #232

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Buffer overflow while storing .alt file using bwa mem #232

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24 changes: 22 additions & 2 deletions bntseq.c
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Original file line number Diff line number Diff line change
Expand Up @@ -177,7 +177,26 @@ bntseq_t *bns_restore(const char *prefix)
bns = bns_restore_core(ann_filename, amb_filename, pac_filename);
if (bns == 0) return 0;
if ((fp = fopen(strcat(strcpy(alt_filename, prefix), ".alt"), "r")) != 0) { // read .alt file if present
char str[1024];
// Seek to end of regular, non-binary, file
off_t alt_file_size;
if (fseeko(fp, 0, SEEK_END) != 0) {
return 0;
}

// Get file size
alt_file_size = ftello(fp);
if (alt_file_size == -1) {
return 0;
}

// Allocate adequate memory to store .alt file
char *str = (char*)calloc(alt_file_size, sizeof(char));
if (str == NULL) {
return 0;
}
// Seek back to beginning of file to be read
fseeko(fp, 0, SEEK_SET);

khash_t(str) *h;
int c, i, absent;
khint_t k;
Expand All @@ -197,10 +216,11 @@ bntseq_t *bns_restore(const char *prefix)
}
while (c != '\n' && c != EOF) c = fgetc(fp);
i = 0;
} else str[i++] = c; // FIXME: potential segfault here
} else str[i++] = c;
}
kh_destroy(str, h);
fclose(fp);
free(str);
}
return bns;
}
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