Actualiser src/libecoPCR/ecorank.c

the -c option was present or not.

src/ecopcr.c

@@ -614,8 +614,10 @@ int main(int argc, char **argv)
 										length = 0;
 										if (posj > posi)
 											length = posj - posi - o1->patlen - o2->patlen;
-										if (posj < posi)
-											length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
+										else {
+											if (circular > 0)
+												length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
+										}
 										if ((length>0) &&	// For when primers touch or overlap
 											(!lmin || (length >= lmin)) &&
 											(!lmax || (length <= lmax)))
@@ -648,7 +650,7 @@ int main(int argc, char **argv)
 					}	
 
 					o1cHits = ManberAll(apatseq,o1c,3,begin,length);
-					
+					// printf("circular=  %d\n",circular);
 					if (o1cHits)
 						for (i=0; i < o2Hits;i++)
 						{
@@ -668,8 +670,11 @@ int main(int argc, char **argv)
 										length = 0;
 										if (posj > posi)
 											length = posj - posi + 1  - o2->patlen - o1->patlen; /* - o1->patlen : deleted by <EC> (prior to the OBITools3) */
-										if (posj < posi)
+										else {
+										if (circular > 0)
 											length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
+										}
+
 										if ((length>0) &&	// For when primers touch or overlap
 											(!lmin || (length >= lmin)) &&
 											(!lmax || (length <= lmax)))

src/libecoPCR/ecorank.c

@@ -34,14 +34,11 @@ ecorankidx_t     *read_rankidx(const char *filename)
 int32_t rank_index(const char* label,ecorankidx_t* ranks)
 {
 	char **rep;
-	
+        fprintf(stderr,"Looking for rank -%s-... ",label);
 	rep = bsearch(label,ranks->label,ranks->count,sizeof(char*),compareRankLabel);
 
 	if (rep)
 		return rep-ranks->label;
-	else
-		ECOERROR(ECO_NOTFOUND_ERROR,"Rank label not found");
-		
 	return -1;
 }
 

src/libecoPCR/ecotax.c

@@ -341,6 +341,9 @@ ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,
 	if (taxonomy && tax!=taxonomy)
 	{
 		rankindex = rank_index("superkingdom",taxonomy->ranks);
+                if (rankindex < 0) {
+		   rankindex = rank_index("domain",taxonomy->ranks);
+                }
 		tax=taxonomy;
 	}