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Author: Andreas Tille <tille@debian.org>
Last-Update: 2015-12-18
Bug-Debian: https://bugs.debian.org/715593
https://bugs.debian.org/715594
Description: Fix Mayhem issues by making reading fasta files more robust
The package is orphaned upstream, hence not forwarded.
Forwarded: no
--- a/Perseus/Perseus.c
+++ b/Perseus/Perseus.c
@@ -839,6 +839,11 @@ void readData(char* szInputFile, t_Data
}
szBrk = strpbrk(szLine, " \n");
+ if(! szBrk)
+ {
+ fprintf(stderr, "File %s does not appear to be in FASTA format.\n", szInputFile);
+ exit(EXIT_FAILURE);
+ }
(*szBrk) = '\0';
ptData->aszID[nSequences] = strdup(szLine + 1);
ptData->adFreq[nSequences] = getWeight(ptData->aszID[nSequences]);
--- a/PerseusD/PerseusD.c
+++ b/PerseusD/PerseusD.c
@@ -891,6 +891,11 @@ void readData(char* szInputFile, t_Data
}
szBrk = strpbrk(szLine, " \n");
+ if(! szBrk)
+ {
+ fprintf(stderr, "File %s does not appear to be in FASTA format.\n", szInputFile);
+ exit(EXIT_FAILURE);
+ }
(*szBrk) = '\0';
ptData->aszID[nSequences] = strdup(szLine + 1);
ptData->anFreq[nSequences] = getWeight(ptData->aszID[nSequences]);
--- a/SeqNoise/SeqNoise.c
+++ b/SeqNoise/SeqNoise.c
@@ -634,6 +634,11 @@ void readData(t_Data *ptData, t_Params *
}
szBrk = strpbrk(szLine, " \n");
+ if(! szBrk)
+ {
+ fprintf(stderr, "File %s does not appear to be in FASTA format.\n", ptParams->szDataFile);
+ exit(EXIT_FAILURE);
+ }
(*szBrk) = '\0';
ptData->aszID[nSequences] = strdup(szLine + 1);
ptData->adW[nSequences] = getWeight(ptData->aszID[nSequences]);
@@ -2454,6 +2459,11 @@ void readDistanceMatrix(char *szDistFile
szBrk = strpbrk(szLine, "\n");
+ if(! szBrk)
+ {
+ fprintf(stderr, "File %s does not appear to be in FASTA format.\n", szDistFile);
+ exit(EXIT_FAILURE);
+ }
(*szBrk) = '\0';
nTest = strtol(szLine, &pcError, 10);
@@ -2478,6 +2488,11 @@ void readDistanceMatrix(char *szDistFile
fgets(szLine, MAX_LINE_LENGTH, ifp);
szBrk = strpbrk(szLine, "\n");
+ if(! szBrk)
+ {
+ fprintf(stderr, "File %s does not appear to be in FASTA format.\n", szDistFile);
+ exit(EXIT_FAILURE);
+ }
(*szBrk) = '\0';
afDist[i*nN + j] = (float) strtod(szLine, &pcError);
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