Changelog

+1.0.8: 12/04/18 O. Sallou
+   - bug fix when searching with errors, some branches in tree were not analysed
+1.0.7: 11/12/17 O. Sallou
+   - bug fix, last character was not indexed
+1.0.6: 26/10/17 O. Sallou
+   - Fix search with tree reduction, closes #1
 1.0.5: 18/11/16 O. Sallou
    - bug fix in search with reduction
 1.0.4: 08/04/16 O. Sallou

debian/changelog

+cassiopee (1.0.8-1) unstable; urgency=medium
+
+  * New upstream release (bug fixes)
+
+ -- Olivier Sallou <osallou@debian.org>  Thu, 12 Apr 2018 11:32:39 +0000
+
 cassiopee (1.0.5-2) unstable; urgency=medium
 
   * Team upload.

src/cassiopee.cxx

@@ -215,12 +215,11 @@ void CassieSearch::search(string suffix, bool clear) {
 
 bool CassieSearch::searchAtreduction(const string suffix, const tree<TreeNode>::iterator sib, long counter, long tree_reducted_pos, int nbSubst, int nbIn, int nbDel, int nbN) {
 
-	//LOG(INFO) << "SEARCH AT REDUCTION";
 	char tree_char;
 	char suffix_char;
 	bool isequal = true;
 	while(counter < suffix.length() -1 && tree_reducted_pos < sib->next_length - 1 && isequal && sib->next_pos+tree_reducted_pos <  this->indexer->seq_length - 1 ) {
-
+		// LOG(ERROR) << "loop in reduction";
 		counter++;
 		suffix_char = suffix[counter];
 		tree_reducted_pos++;
@@ -233,9 +232,8 @@ bool CassieSearch::searchAtreduction(const string suffix, const tree<TreeNode>::
 		}
 
 		tree_char = this->indexer->getCharAtSuffix(sib->next_pos+tree_reducted_pos);
-		//LOG(INFO) << "match " << suffix_char << " with " << tree_char << " at " << tree_reducted_pos << ", max=" << sib->next_length;
-
-		bool isequal = this->isequal(tree_char,suffix_char);
+		// LOG(ERROR) << "match " << suffix_char << " with " << tree_char << " at " << tree_reducted_pos << ", max=" << sib->next_length;
+		isequal = this->isequal(tree_char,suffix_char);
 		if(!isequal) {
 			// If DNA/RNA and tree matches a N, check on max consecutive N allowed
 			if(this->mode!=2 && tree_char == 'n') {
@@ -248,20 +246,29 @@ bool CassieSearch::searchAtreduction(const string suffix, const tree<TreeNode>::
 				nbN = 0;
 			}
 		}
-
-		if(!isequal && this->max_subst>0 && nbSubst < this->max_subst) {
+		// LOG(ERROR) << "not equal, can substitute? " << isequal << ", " << nbSubst << ", " << this->max_subst;
+		if(!isequal) {
+			if(this->max_subst>0 && nbSubst < this->max_subst) {
 				// Check for substitutions
 				isequal = true;
 				nbSubst++;
 			}
+			else {
+				// LOG(ERROR) << "now break equal=" << isequal;
+				break;
+			}
+		}
+
 	}
+
 	if(isequal) {
+		// LOG(ERROR) << "IS EQUAL? " << isequal;
 		if(counter == suffix.length() -1) {
 		this->getMatchesFromNode(sib, nbSubst, nbIn, nbDel);
 		return true;
 		}
 		else {
-			//LOG(INFO) << "full match but not complete, search childs";
+			//LOG(ERROR) << "full match but not complete, search childs";
 			// complete match but suffix not over, should look at childs now
 			this->searchAtNode(suffix, counter+1, sib, NULL, nbSubst, nbIn, nbDel, nbN);
 		}
@@ -319,9 +326,8 @@ void CassieSearch::searchAtNode(string suffix, const long suffix_pos, const tree
 	char tree_char = sib->c;
 	char suffix_char = suffix[counter];
 
-	while(sib != last_sibling && sib.node!=0) {
-
-
+	//while(sib != last_sibling && sib.node!=0) {
+	while(sib.node!=0) {
 			if(this->max_indel > 0 && nbIn+nbDel < this->max_indel) {
 				//LOG(INFO) << "Check for indel, cur= " << sib->c;
 				// Move on suffix, keep same base node
@@ -351,6 +357,7 @@ void CassieSearch::searchAtNode(string suffix, const long suffix_pos, const tree
 			bool isequal = this->isequal(tree_char,suffix_char);
 
 			tree<TreeNode>::iterator next_sibling = sib;
+
 			while(this->mode!=2) {
 				next_sibling = tr->next_sibling(next_sibling);
 
@@ -399,31 +406,40 @@ void CassieSearch::searchAtNode(string suffix, const long suffix_pos, const tree
 					// Exact match, no more char to parse
 					// Search leafs
 					this->getMatchesFromNode(sib, nbSubst, nbIn, nbDel);
-
 					if(this->max_subst>0 && nbSubst < this->max_subst) {
 						// If one last substitution is allowed, also check with remaining siblings
 						sib = tr->next_sibling(sib);
 						while(sib.node!=0) {
 							this->getMatchesFromNode(sib, nbSubst+1, nbIn, nbDel);
 							sib = tr->next_sibling(sib);
+
 						}
 
 					}
 					break;
-
-
 				}
 				else if(sib->next_pos>=0){
+					//LOG(ERROR) << "-- " << sib->next_pos << ", " << sib->next_length;
 					//LOG(INFO) << "next " << sib->next_pos << ", " << sib->next_length;
 					long tree_reducted_pos = -1;
 					// Fix O.Sallou 08/04/16 search error with reduction
-					counter++;
+					// Fix O.Sallou 26/10/17 search error with reduction
+					//counter++;
 					bool matched =  this->searchAtreduction(suffix, sib, counter, tree_reducted_pos, nbSubst, nbIn, nbDel, nbN);
 					break;
 
 
 				}
 				else if(nb_childs > 0) {
+					this->searchAtNode(suffix, counter+1, sib, nbSubst, nbIn, nbDel, nbN);
+					sib = tr->next_sibling(sib);
+					if(sib.node != 0) {
+						tree_char = sib->c;
+					}
+					else {
+						tree_char = '\0';
+					}
+					/*
 					last_sibling = tr->end(sib);
 					parentnode = sib;
 					sib = tr->begin(sib);
@@ -431,6 +447,8 @@ void CassieSearch::searchAtNode(string suffix, const long suffix_pos, const tree
 					tree_char = sib->c;
 					counter++;
 					suffix_char = suffix[counter];
+					*/
+
 				}
 				else {
 					break;
@@ -451,7 +469,6 @@ void CassieSearch::searchAtNode(string suffix, const long suffix_pos, const tree
 				// anyway, test siblings
 
 				sib = tr->next_sibling(sib);
-
 				if(sib.node != 0) {
 					tree_char = sib->c;
 				}
@@ -515,7 +532,7 @@ char* CassieIndexer::loadSuffix(long pos)  {
 
 	assert(pos < this->seq_length);
 
-	long suffix_len = min(this->MAX_SUFFIX,this->seq_length - pos - 1);
+	long suffix_len = min(this->MAX_SUFFIX,this->seq_length - pos);
 
 	//char* suffix = new char[suffix_len+1]();
 	delete[] this->suffix;
@@ -621,7 +638,7 @@ void CassieIndexer::index() {
 	DLOG(INFO) << "Indexing " << this->filename ;
 
 
-	for (long i=0; i<this->seq_length-1; i++) {
+	for (long i=0; i<this->seq_length; i++) {
 		this->filltree(i);
 	}
 
@@ -733,7 +750,7 @@ void CassieIndexer::fillTreeWithSuffix(long suffix_pos, long pos) {
 	char node_char = this->getCharAtSuffix(pos+suffix_pos);
 	//long suffix_len = this->seq_length - (pos+suffix_pos) -1;
     // OSALLOU
-    long suffix_len = min(this->max_index_depth, this->seq_length - (pos+suffix_pos) -1);
+    long suffix_len = min(this->max_index_depth, this->seq_length - (pos+suffix_pos));
 
 	TreeNode* node = new TreeNode(node_char);
 
@@ -766,7 +783,7 @@ void CassieIndexer::fillTreeWithSuffix(long suffix_pos, long pos) {
 void CassieIndexer::fillTreeWithSuffix(tree<TreeNode>::iterator sib, long suffix_pos, long pos) {
 	//long suffix_len = this->seq_length - pos -1 ;
     //OSALLOU
-    long suffix_len = min(this->max_index_depth, this->seq_length - pos -1);
+    long suffix_len = min(this->max_index_depth, this->seq_length - pos);
 
 	for(long i=suffix_pos;i<suffix_len;i++) {
 		//char node_char = suffix[i];
@@ -815,7 +832,7 @@ void CassieIndexer::filltree(long pos) {
 
 	//long suffix_len = this->seq_length - pos - 1;
     // OSALLOU
-    long suffix_len = min(this->max_index_depth, this->seq_length - pos - 1);
+    long suffix_len = min(this->max_index_depth, this->seq_length - pos);
 
 
 	//LOG(INFO) << "new suffix " << pos << " l= " << suffix_len;