Error messages

Author: alexandrutomescu

src/Aligner.cpp

@@ -630,9 +630,9 @@ void runComponentMappings(const AlignmentGraph& alignmentGraph, moodycamel::Conc
 			bool necessary = true;
 			AlignmentResult long_alignments;
 			size_t long_edit_distance;
-			cerroutput << "Trying to align long read" << fastq->seq_id << BufferedWriter::Flush;
+			cerroutput << "Trying to align long read" << fastq->seq_id;
 			long_alignments = align_fn(fastq->seq_id, fastq->sequence, false);
-			cerroutput << "Aligned long read" << fastq->seq_id << BufferedWriter::Flush;
+			cerroutput << " Aligned long read" << fastq->seq_id;
 
 			// Getting the best alignment of GA
 			AlignmentSelection::SelectionOptions gaSelectionOptions = selectionOptions;
@@ -650,7 +650,7 @@ void runComponentMappings(const AlignmentGraph& alignmentGraph, moodycamel::Conc
 					long_edit_distance = result.editDistance;
 				}
 				edlibFreeAlignResult(result);
-				cerroutput << " with long_edit_distance" << long_edit_distance << BufferedWriter::Flush;
+				cerroutput << " Aligned long read" << fastq->seq_id << " with long_edit_distance" << long_edit_distance << BufferedWriter::Flush;
 			}
 
 			if (necessary) {
@@ -674,7 +674,7 @@ void runComponentMappings(const AlignmentGraph& alignmentGraph, moodycamel::Conc
 						sr++;
 					while (sl < sr && seeds[sl].seqPos < l)
 						sl++;
-					cerroutput << short_id << " : " << l << " / " << fastq->sequence.length() << " " << sl << " " << sr << BufferedWriter::Flush;
+					// cerroutput << short_id << " : " << l << " / " << fastq->sequence.length() << " " << sl << " " << sr << BufferedWriter::Flush;
 					if (sl >= sr)
 						continue;
 					std::string seq = fastq->sequence.substr(l, len);
@@ -730,7 +730,7 @@ void runComponentMappings(const AlignmentGraph& alignmentGraph, moodycamel::Conc
 				}
 				auto anchorsEnd = std::chrono::system_clock::now();
 				auto anchorsms = std::chrono::duration_cast<std::chrono::milliseconds>(anchorsEnd - anchorsStart).count();
-				cerroutput << short_id << " : chaining " << A.size() << " anchors" << BufferedWriter::Flush;
+				// cerroutput << short_id << " : chaining " << A.size() << " anchors" << BufferedWriter::Flush;
 				auto clcStart = std::chrono::system_clock::now();
 				std::vector<size_t> ids = alignmentGraph.colinearChaining(A, params.colinearGap);
 				auto clcEnd = std::chrono::system_clock::now();
@@ -743,7 +743,7 @@ void runComponentMappings(const AlignmentGraph& alignmentGraph, moodycamel::Conc
 				size_t firstNodeOffset, lastNodeOffset;
 				auto connectStart = std::chrono::system_clock::now();
 				int ai_idx = 0;
-				cerroutput << short_id << " : chaining " << ids.size() << " / " << A.size() << " anchors" << BufferedWriter::Flush;
+				// cerroutput << short_id << " : chaining " << ids.size() << " / " << A.size() << " anchors" << BufferedWriter::Flush;
 				int one_node_overlaps_tmp = 0, one_node_overlaps_now = 0, one_node_overlaps_all = 0;
 				for (size_t ai : ids) {
 					for (size_t j =0 ; j<Apos[ai].size();j++) {
@@ -825,7 +825,7 @@ void runComponentMappings(const AlignmentGraph& alignmentGraph, moodycamel::Conc
 				std::string pathseq = "";
 				// not convert back to original node ids, to call alignmentGraph.NodeSequences()
 				for (AlignmentGraph::MatrixPosition &p : longest) {
-				cerroutput << p.node << " : " << p.nodeOffset << " bps " << alignmentGraph.NodeLength(p.node) << BufferedWriter::Flush;
+				// cerroutput << p.node << " : " << p.nodeOffset << " bps " << alignmentGraph.NodeLength(p.node) << BufferedWriter::Flush;
 
 					pathseq.push_back(alignmentGraph.NodeSequences(p.node, p.nodeOffset));
 				}
@@ -871,7 +871,7 @@ void runComponentMappings(const AlignmentGraph& alignmentGraph, moodycamel::Conc
 							pos_i = std::min(pos_i, longest.size() - 1);
 
 						}
-						cerroutput << "eds " << trace.size() << " " << longest.size() << " : " << pos_i << " / " << seq_i << BufferedWriter::Flush;;
+						// cerroutput << "eds " << trace.size() << " " << longest.size() << " : " << pos_i << " / " << seq_i << BufferedWriter::Flush;;
 						longest.swap(trace);
 					}
 					edlibFreeAlignResult(result);
@@ -920,7 +920,11 @@ void runComponentMappings(const AlignmentGraph& alignmentGraph, moodycamel::Conc
 		stats.allAlignmentsCount += alignments.alignments.size();
 
 		coutoutput << "Read " << fastq->seq_id << " alignment took " << alntimems << "ms" << BufferedWriter::Flush;
-		//if (alignments.alignments.size() > 0) alignments.alignments = AlignmentSelection::SelectAlignments(alignments.alignments, selectionOptions);
+		if (!params.colinearChaining)
+		{
+			if (alignments.alignments.size() > 0) alignments.alignments = AlignmentSelection::SelectAlignments(alignments.alignments, selectionOptions);
+		}
+		
 
 		// for (size_t i = 0; i < alignments.alignments.size(); i++) {
 		// 	// c++ helloWorld.cpp edlib/src/edlib.cpp -o helloWorld -I edlib/include.