Added Code to make sure that if -3 option is given then 3' end must match upto given number of base pairs

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@231 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/ecoprimer.c

@@ -777,7 +777,6 @@ int main(int argc, char **argv)
     pairs = buildPrimerPairs(seqdb, seqdbsize, primers, &options);
 
      printpairs (pairs, &options,taxonomy);
-    // closlibman ();
 
     return 0;
 }

src/libecoprimer/aproxpattern.c

@@ -97,8 +97,8 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
 
 	params.circular = options->circular;
 	params.maxerr   = options->error_max;
-	params.omask    = (1 << options->strict_three_prime) -1;
+//	params.omask    = (1 << options->strict_three_prime) -1;
-//	params.omask    = 0;
+	params.omask    = 0;
 	params.patlen   = options->primer_length;
 
 	positions.val=NULL;

src/libecoprimer/pairs.c

@@ -8,6 +8,7 @@
 #include  "ecoprimer.h"
 #include  <string.h>
 #include  <stdlib.h>
+#include "../libthermo/thermostats.h"
 
 static void buildPrimerPairsForOneSeq(uint32_t seqid,
 									  pecodnadb_t seqdb,
@@ -187,6 +188,9 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
 	bool_t             strand;
 	//char 			   prmr[50];
 	//float			   mtemp;
+	word_t 			   w1, w1a, omask = (0x1L << options->strict_three_prime) -1;;
+	word_t 			   w2, w2a, wtmp;
+	uint32_t   		   bp1,bp2;
 	
 	//prmr[options->primer_length] = '\0';
 	
@@ -292,6 +296,42 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
 		    		   current.asdirect2=bswp;
 		    	   }
 
+		    	   
+		    	   //Code to make sure that if -3 option is given then
+		    	   //3' end must match upto given number of base pairs
+		    	   if (options->strict_three_prime > 0)
+		    	   {
+		    		   w1 = current.p1->word;
+		    		   w2 = current.p2->word;
+		    		   if (!current.asdirect1) //make sure that word is from 5' to 3'
+		    			   w1=ecoComplementWord(w1,options->primer_length);
+
+		    		   if (!current.asdirect2) //make sure that word is from 5' to 3'
+		    			   w2=ecoComplementWord(w2,options->primer_length);
+		    		   //now both w1 and w2 are from 5' to 3' end
+		    		   bp1 = matches[i].position;
+		    		   bp2 = matches[j].position;
+		    		   if (!strand)
+		    		   {
+			    		   bp1 = matches[j].position;
+			    		   bp2 = matches[i].position;
+		    		   }
+		    		   //get word of first approximate repeat
+		    		   w1a = extractSite(seqdb[seqid]->SQ,bp1,options->primer_length,strand);
+		    		   //get word of second approximate repeat
+		    		   w2a = extractSite(seqdb[seqid]->SQ,bp2,options->primer_length,!strand);
+		    		   
+		    		   w1 = w1 & omask;   //keep only strict_three_prime bases on the right (3') end
+		    		   w2 = w2 & omask;   //keep only strict_three_prime bases on the right (3') end
+		    		   w1a = w1a & omask; //keep only strict_three_prime bases on the right (3') end
+		    		   w2a = w2a & omask; //keep only strict_three_prime bases on the right (3') end
+		    		   
+		    		   //now check that both words and primers of amplifia have same bases on 3' end
+		    		   if (w1 ^ w1a != 0) continue; 
+		    		   else if (w2 ^ w2a != 0) continue;
+		    	   }
+		    	   
+		    	   
 
 		    	   // Look for the new pair in already seen pairs
 

src/libthermo/thermostats.c

@@ -4,8 +4,7 @@
 #include <stdlib.h>
 #include "thermostats.h"
 
-static word_t extractSite(char* sequence,
+word_t extractSite(char* sequence, size_t begin, size_t length, bool_t strand)
-		                  size_t begin, size_t length, bool_t strand)
 {
 	char *c;
 	char *start;

src/libthermo/thermostats.h

@@ -4,5 +4,6 @@
 #include "../libecoprimer/ecoprimer.h"
 
 void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options);
+word_t extractSite(char* sequence, size_t begin, size_t length, bool_t strand);
 
 #endif