diff options
Diffstat (limited to 'sci-biology/mrfast/files/mrfast-2.1.0.3-disc_buffer_overflow.patch')
| -rw-r--r-- | sci-biology/mrfast/files/mrfast-2.1.0.3-disc_buffer_overflow.patch | 52 |
1 files changed, 0 insertions, 52 deletions
diff --git a/sci-biology/mrfast/files/mrfast-2.1.0.3-disc_buffer_overflow.patch b/sci-biology/mrfast/files/mrfast-2.1.0.3-disc_buffer_overflow.patch deleted file mode 100644 index bdf5cbb91..000000000 --- a/sci-biology/mrfast/files/mrfast-2.1.0.3-disc_buffer_overflow.patch +++ /dev/null @@ -1,52 +0,0 @@ -diff -durr mrfast-2.1.0.3.orig/MrFAST.c mrfast-2.1.0.3/MrFAST.c ---- mrfast-2.1.0.3.orig/MrFAST.c 2011-12-18 17:48:16.431973604 -0500 -+++ mrfast-2.1.0.3/MrFAST.c 2011-12-18 17:55:11.400723582 -0500 -@@ -7358,6 +7358,7 @@ - char fname1[FILE_NAME_LENGTH]; - char fname2[FILE_NAME_LENGTH]; - char l; -+ int l_int; - int loc1, loc2; - int err1, err2; - char dir1, dir2; -@@ -7399,28 +7400,28 @@ - - //tmp = fwrite (&(mi2[k].cigarSize), sizeof(int), 1, out); - -- tmp = fread(&l, sizeof(int), 1, in); -- tmp = fread(cigar1, sizeof(char), l, in); -- cigar1[(int)l]='\0'; -+ tmp = fread(&l_int, sizeof(int), 1, in); -+ tmp = fread(cigar1, sizeof(char), l_int, in); -+ cigar1[l_int]='\0'; - //tmp = fwrite ((mi2[k].cigar), sizeof(char), mi2[k].cigarSize, out); - - //tmp = fwrite (&(mi2[k].mdSize), sizeof(int), 1, out); -- tmp = fread(&l, sizeof(int), 1, in); -- tmp = fread(editString1, sizeof(char), l, in); -- editString1[(int)l]='\0'; -+ tmp = fread(&l_int, sizeof(int), 1, in); -+ tmp = fread(editString1, sizeof(char), l_int, in); -+ editString1[l_int]='\0'; - //tmp = fwrite ((mi2[k].md), sizeof(char), mi2[k].mdSize, out); - - tmp = fread(&loc2, sizeof(int), 1, in); - tmp = fread(&err2, sizeof(int), 1, in); - tmp = fread(&sc2, sizeof(float), 1, in); - -- tmp = fread(&l, sizeof(int), 1, in); -- tmp = fread(cigar2, sizeof(char), l, in); -- cigar2[(int)l]='\0'; -+ tmp = fread(&l_int, sizeof(int), 1, in); -+ tmp = fread(cigar2, sizeof(char), l_int, in); -+ cigar2[l_int]='\0'; - /* FARHAD: l is of type char; and you fread into it with sizeof(char) above; but as sizeof(int) here; are you sure? 1 byte vs. 4 bytes */ -- tmp = fread(&l, sizeof(int), 1, in); -- tmp = fread(editString2, sizeof(char), l, in); -- editString2[(int)l]='\0'; -+ tmp = fread(&l_int, sizeof(int), 1, in); -+ tmp = fread(editString2, sizeof(char), l_int, in); -+ editString2[l_int]='\0'; - - convertMDCigarToMatrix(cigar1, strlen(cigar1), editString1, strlen(editString1), tmp_matrix1); - convertMDCigarToMatrix(cigar2, strlen(cigar2), editString2, strlen(editString2), tmp_matrix2); |