Commit 2d903137 authored by Olivier Sallou's avatar Olivier Sallou
Browse files

New upstream version 1.0.8

parent 79a47eef

Changelog

+6 −0
Original line number Diff line number Diff line 
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

src/cassiopee.cxx

+42 −25
Original line number Diff line number Diff line
@@ -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;

src/CassiopeeConfig.h.in

+1 −1

File changed.

Contains only whitespace changes.