Actualiser src/libecoPCR/ecorank.c

the -c option was present or not.

.gitignore

@@ -1,8 +1,12 @@
+/.gitignore
+/.cproject
+/.project
 
 # /src/
 /src/ecoPCR
 /src/ecofind
 /src/*.P
+/src/*.o
 /src/ecogrep
 
 # /src/libapat/
@@ -14,3 +18,4 @@
 
 # /src/libthermo/
 /src/libthermo/*.P
+

VERSION

@@ -1 +1 @@
-0.8.0
+1.0.0

src/ecopcr.c

@@ -6,7 +6,7 @@
 #include <getopt.h>
 
 
-#define VERSION "1.0.0"
+#define VERSION "1.0.1"
 
 
 /* ----------------------------------------------- */
@@ -614,9 +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;   // TODO
-											length = posi - posj - 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)))
@@ -649,7 +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++)
 						{
@@ -668,11 +669,12 @@ 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) */ TODO ????
-											length = posj - posi - o2->patlen - o1->patlen;
-										if (posj < posi)
-											//length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen; TODO ????
-											length = posi - posj - o2->patlen - o1->patlen;
+											length = posj - posi + 1  - o2->patlen - o1->patlen; /* - o1->patlen : deleted by <EC> (prior to the OBITools3) */
+										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;
 	}