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Description: Some apps segfault when non-FASTA data is inputted, and this is flagged as a security
concern. I suspect there are still ways to segfault this app, but at least this fixes
an obvious crash.
Also fixes https://code.google.com/p/ampliconnoise/issues/detail?id=10
.
The package is orphaned upstream, hence not forwarded.
Forwarded: no
Author: Tim Booth
Last-Update: 2013-06-27
--- a/FastaUnique/FastaUnique.c
+++ b/FastaUnique/FastaUnique.c
@@ -39,6 +39,13 @@ void readData(t_Data *ptData, t_Params *
nPos = 0;
}
else{
+ //If there is no > on first line we're heading for a segfault.
+ if(! ptData->nSeq)
+ {
+ fprintf(stderr, "File %s does not appear to be in FASTA format.\n", ptParams->szInputFile);
+ exit(EXIT_FAILURE);
+ }
+
i = 0;
while(strrchr(szSequence,szLine[i]) != NULL){
i++;
@@ -46,6 +53,10 @@ void readData(t_Data *ptData, t_Params *
}
}
}
+ //Maybe the final sequence was the longest?
+ if(nPos > ptData->nMaxLen){
+ ptData->nMaxLen = nPos;
+ }
fclose(ifp);
}
--- a/NDist/NDist.c
+++ b/NDist/NDist.c
@@ -654,6 +654,13 @@ void readData(t_Data *ptData, t_Params *
nPos = 0;
}
else{
+ //If there is no > on first line we're heading for a segfault.
+ if(! ptData->nSeq)
+ {
+ fprintf(stderr, "File %s does not appear to be in FASTA format.\n", ptParams->szInputFile);
+ exit(EXIT_FAILURE);
+ }
+
i = 0;
while(strrchr(szSequence,szLine[i]) != NULL){
i++;
@@ -661,6 +668,10 @@ void readData(t_Data *ptData, t_Params *
}
}
}
+ //Maybe the final sequence was the longest?
+ if(nPos > ptData->nMaxLen){
+ ptData->nMaxLen = nPos;
+ }
fclose(ifp);
}
--- a/Perseus/Perseus.c
+++ b/Perseus/Perseus.c
@@ -793,6 +793,13 @@ void readData(char* szInputFile, t_Data
nPos = 0;
}
else{
+ //If there is no > on first line we're heading for a segfault.
+ if(! ptData->nSeq)
+ {
+ fprintf(stderr, "File %s does not appear to be in FASTA format.\n", szInputFile);
+ exit(EXIT_FAILURE);
+ }
+
i = 0;
while(strrchr(szSequence,szLine[i]) != NULL){
i++;
@@ -800,6 +807,10 @@ void readData(char* szInputFile, t_Data
}
}
}
+ //Maybe the final sequence was the longest?
+ if(nPos > ptData->nMaxLen){
+ ptData->nMaxLen = nPos;
+ }
fclose(ifp);
}
--- a/PerseusD/PerseusD.c
+++ b/PerseusD/PerseusD.c
@@ -844,6 +844,13 @@ void readData(char* szInputFile, t_Data
nPos = 0;
}
else{
+ //If there is no > on first line we're heading for a segfault.
+ if(! ptData->nSeq)
+ {
+ fprintf(stderr, "File %s does not appear to be in FASTA format.\n", szInputFile);
+ exit(EXIT_FAILURE);
+ }
+
i = 0;
while(strrchr(szSequence,szLine[i]) != NULL){
i++;
@@ -851,6 +858,10 @@ void readData(char* szInputFile, t_Data
}
}
}
+ //Maybe the final sequence was the longest?
+ if(nPos > ptData->nMaxLen){
+ ptData->nMaxLen = nPos;
+ }
fclose(ifp);
}
--- a/SeqDist/SeqDist.c
+++ b/SeqDist/SeqDist.c
@@ -799,6 +799,13 @@ void readData(t_Data *ptData, t_Params *
nPos = 0;
}
else{
+ //If there is no > on first line we're heading for a segfault.
+ if(! ptData->nSeq)
+ {
+ fprintf(stderr, "File %s does not appear to be in FASTA format.\n", ptParams->szInputFile);
+ exit(EXIT_FAILURE);
+ }
+
i = 0;
while(strrchr(szSequence,szLine[i]) != NULL){
i++;
@@ -806,6 +813,10 @@ void readData(t_Data *ptData, t_Params *
}
}
}
+ //Maybe the final sequence was the longest?
+ if(nPos > ptData->nMaxLen){
+ ptData->nMaxLen = nPos;
+ }
fclose(ifp);
}
--- a/SeqNoise/SeqNoise.c
+++ b/SeqNoise/SeqNoise.c
@@ -571,6 +571,13 @@ void readData(t_Data *ptData, t_Params *
nPos = 0;
}
else{
+ //If there is no > on first line we're heading for a segfault.
+ if(! ptData->nSeq)
+ {
+ fprintf(stderr, "File %s does not appear to be in FASTA format.\n", ptParams->szDataFile);
+ exit(EXIT_FAILURE);
+ }
+
i = 0;
while(strrchr(szSequence,szLine[i]) != NULL){
i++;
@@ -578,6 +585,10 @@ void readData(t_Data *ptData, t_Params *
}
}
}
+ //Maybe the final sequence was the longest?
+ if(nPos > ptData->nMaxLen){
+ ptData->nMaxLen = nPos;
+ }
fclose(ifp);
}
|
