My complete changes on my laptop, with specificity bug fix + ahocorasick + sets

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@393 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/libecoprimer/filtering.c

@@ -114,6 +114,8 @@ static	int32_t *ecoFilteringHashSequence(int32_t *dest,
 		error<<= 1;
 		error&=ERRORMASK(FWORDSIZE);
 
+		//code = -1;
+		//if((*base) >= 'A' && (*base) <= 'Z')
 		code = encoder[(*base) - 'A'];
 		if (code <0)
 		{
@@ -154,7 +156,7 @@ int32_t *filteringSeq(pecodnadb_t database, uint32_t seqdbsize,
 
 	for (i=0;i<seqdbsize;i++)
     {
-    	if (database[i]->isexample)
+    	if (database[i]->isexample && database[i]->SQ_length > options->primer_length)
     	{
     		j++;
     		wordscount=ecoFilteringHashSequence(wordscount,