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Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 10 Dec 2018 07:36:57 +0100
Description: Enhance print buffer to avoid:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 36 and 3418 bytes into a destination of size 1000
Finally this patch is not fully working since the enhanced buffers
make sprint assume that even larger buffers are needed.
--- a/src/ali2gff/ali2gff.c
+++ b/src/ali2gff/ali2gff.c
@@ -234,7 +234,7 @@ void processGFFfile() {
unsigned long int yseqLen_4 = LONG_MAX;
float score;
- char scores[MAXSTRING];
+ char scores[2*MAXSTRING];
char strand1;
char strand2;
@@ -426,8 +426,8 @@ void processMumfile() {
time_t now;
char nowString[100];
- char nextMUM[MAXSTRING] = "";
- char nextGAP[MAXSTRING] = "";
+ char nextMUM[5*MAXSTRING] = "";
+ char nextGAP[3*MAXSTRING] = "";
char seq1[MAX_SEQUENCE_LENGTH];
@@ -974,7 +974,7 @@ void processSimfile() {
FILE *simfile;
char line[MAXSTRING]; /*----- read line -----*/
- char seqboundsline[MAXSTRING];
+ char seqboundsline[2*MAXSTRING];
char *ptr; /*----- pointer to line -----*/
char waste[MAXSTRING];
@@ -1000,7 +1000,7 @@ void processSimfile() {
unsigned long int yrev; /* start position + end position of y sequence --- this term is used to calculate positions of rev. compl. fragments on forward strand */
unsigned short int aliPrinted = 0;
- char aliPrintString[MAXSTRING];
+ char aliPrintString[4*MAXSTRING];
/*----- open alignment file -----*/
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