fixed segmentation fault reported by Pierre.

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@289 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/libecoprimer/strictprimers.c

@@ -132,7 +132,7 @@ pwordcount_t lookforStrictPrimer(pecodnadb_t database, uint32_t seqdbsize,
 	double seconde;
 	char   *logfilename;
 	FILE   *logfile;
-	uint32_t i;
+	uint32_t i, j;
 	bool_t first=TRUE;
 	pwordcount_t strictprimers=NULL;
 	uint64_t totallength=0;
@@ -232,6 +232,36 @@ pwordcount_t lookforStrictPrimer(pecodnadb_t database, uint32_t seqdbsize,
     if (neededWords)
     	ECOFREE(neededWords,"Clean needed word table");
 
+	//TR: Somehow for some primers strictcount value is extremely large hence invalid
+	//we need to remove these primers from the list
+	j = strictprimers->size+1;
+	for (i=0; i<strictprimers->size; i++)
+	{
+		if (strictprimers->strictcount[i] > seqdbsize)
+		{
+			if (j == (strictprimers->size+1))
+				j = i;
+		}
+		
+		if (j < i && strictprimers->strictcount[i] <= seqdbsize)
+		{
+			strictprimers->words[j] = strictprimers->words[i];
+			strictprimers->strictcount[j] = strictprimers->strictcount[i];
+			j++;
+		}
+	}
+	
+	if (j < strictprimers->size)
+	{
+		strictprimers->size = j;
+		strictprimers->strictcount = ECOREALLOC(strictprimers->strictcount,
+												sizeof(uint32_t)*strictprimers->size,
+												"Cannot reallocate strict primer count table");
+		strictprimers->words   = ECOREALLOC(strictprimers->words,
+											sizeof(word_t)*strictprimers->size,
+											"Cannot reallocate strict primer table");		
+	}
+	
 	return strictprimers;
 }
 

src/libecoprimer/taxstats.c

@@ -126,7 +126,7 @@ float taxonomycoverage(ppair_t pair, poptions_t options)
 	return pair->bc;
 }
 
-
+/*
 static int cmpamp(const void *ampf1, const void* ampf2)
 {
 	int i;
@@ -170,6 +170,55 @@ static int cmpamp(const void *ampf1, const void* ampf2)
 	if (pampf1->length > pampf2->length) return chd ? -1: 1;
 	if (pampf2->length > pampf1->length) return chd ? 1: -1;
 
+	return 0;
+}*/
+
+static int cmpamp(const void *ampf1, const void* ampf2)
+{
+	int i;
+	char cd1;
+	char cd2;
+	int len = 0;
+	char *ch1;
+	char *ch2;
+	int incr1;
+	int incr2;
+	
+	pamptotaxon_t pampf1 = (pamptotaxon_t) ampf1;
+	pamptotaxon_t pampf2 = (pamptotaxon_t) ampf2;
+	
+	ch1 = pampf1->amplifia;
+	ch2 = pampf2->amplifia;
+	
+	incr1 = 1;
+	incr2 = 1;
+	
+	if (!pampf1->strand)
+		incr1 = -1;
+	if (!pampf2->strand)
+		incr2 = -1;
+	
+	len = (pampf1->length <= pampf2->length)? pampf1->length: pampf2->length;
+	for (i = 0; i < len; i++)
+	{
+		cd1 = *ch1;
+		if (incr1 == -1)
+			cd1 = ecoComplementChar(*ch1);
+		
+		cd2 = *ch2;
+		if (incr2 == -1)
+			cd2 = ecoComplementChar(*ch2);
+		
+		if (cd1 < cd2) return -1;
+		if (cd2 < cd1) return 1;
+		
+		ch1 += incr1;
+		ch2 += incr2;
+	}
+	
+	if (pampf1->length > pampf2->length) return 1;
+	if (pampf2->length > pampf1->length) return -1;
+	
 	return 0;
 }