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 "0.8.0"
+#define VERSION "1.0.1"
 
 
 /* ----------------------------------------------- */
@@ -80,7 +80,7 @@ static void PrintHelp()
         PP      "column 21 : sequence\n");
         PP      "column 22 : definition\n");
         PP      "------------------------------------------\n");
-        PP		" http://www.grenoble.prabi.fr/trac/ecoPCR/\n");
+        PP		" https://git.metabarcoding.org/obitools/ecopcr/wikis/home\n");
         PP      "------------------------------------------\n\n");        
         PP      "\n");
 
@@ -566,11 +566,11 @@ int main(int argc, char **argv)
 		        )
 		     {
 		
-				scname = taxonomy->taxons->taxon[seq->taxid].name;
+				//scname = taxonomy->taxons->taxon[seq->taxid].name;
-				strncpy(head,seq->SQ,10);
+				//strncpy(head,seq->SQ,10);
-				head[10]=0;
+				//head[10]=0;
-				strncpy(tail,seq->SQ+seq->SQ_length-10,10);
+				//strncpy(tail,seq->SQ+seq->SQ_length-10,10);
-				tail[10]=0;
+				//tail[10]=0;
 		
 				apatseq=ecoseq2apatseq(seq,apatseq,circular);
 				
@@ -610,18 +610,21 @@ int main(int argc, char **argv)
 									{
 										posj+=o2c->patlen;
 										// printf("coucou %d %d %d\n",posi,posj,apatseq->seqlen);
-										errj  =apatseq->hiterr[1]->val[j];
+										errj = apatseq->hiterr[1]->val[j];
 										length = 0;
 										if (posj > posi)
-											length=posj - posi  - o1->patlen - o2->patlen; 
+											length = posj - posi - o1->patlen - o2->patlen;
-										if (posj < posi)
+										else {
-											length= posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
+											if (circular > 0)
-										if (length &&
+												length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
+										}
+										if ((length>0) &&	// For when primers touch or overlap
 											(!lmin || (length >= lmin)) &&
 											(!lmax || (length <= lmax)))
+										{
 										    printRepeat(seq,oligo1,oligo2,&tparm,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
 											//printf("%s\tD\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o1Hits,o2cHits,posi,posj,scname);
-	
+										}
 									}
 								}
 							}
@@ -647,7 +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++)
 						{
@@ -666,13 +669,16 @@ int main(int argc, char **argv)
 
 										length = 0;
 										if (posj > posi)
-											length=posj - posi + 1  - o2->patlen - o1->patlen; /* - o1->patlen : suppress by <EC> */
+											length = posj - posi + 1  - o2->patlen - o1->patlen; /* - o1->patlen : deleted by <EC> (prior to the OBITools3) */
-										if (posj < posi)
+										else {
-											length= posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
+										if (circular > 0)
+											length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
+										}
 
-										if (length &&
+										if ((length>0) &&	// For when primers touch or overlap
 											(!lmin || (length >= lmin)) &&
 											(!lmax || (length <= lmax)))
+										{
 										    printRepeat(seq,oligo1,oligo2,&tparm,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
 											//printf("%s\tR\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o2Hits,o1cHits,posi,posj,scname);
 										}
@@ -680,6 +686,7 @@ int main(int argc, char **argv)
 								}
 							}
 						}
+				}	
 				
 		} /* End of taxonomic selection */
 		

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;
 	}