fix bug

Author: y3tseng

src/alignment-cpu.cpp

@@ -88,9 +88,9 @@ void msa::progressive::cpu::parallelAlignmentCPU(Tree *tree, NodePairVec &nodes,
         if (database->currentTask == 1 || database->currentTask == 2 || refNum > 10000 || qryNum > 10000) talco_params->gapCharScore = 0;
         if (refLen == 0) for (int j = 0; j < qryLen; ++j) aln_wo_gc.push_back(1);
         if (qryLen == 0) for (int j = 0; j < refLen; ++j) aln_wo_gc.push_back(2);
-        bool lowQ_r = (option->alnMode == MERGE_MSA) ? false : ((refNum == 1) && database->sequences[nodes[nIdx].first->seqsIncluded[0]]->lowQuality);
-        bool lowQ_q = (option->alnMode == MERGE_MSA) ? false : ((qryNum == 1) && database->sequences[nodes[nIdx].second->seqsIncluded[0]]->lowQuality);
-        if (option->noFilter || (!lowQ_r && !lowQ_q)) {
+        bool lowQ_r = (option->alnMode == MERGE_MSA) ? false : ((refNum > 1) ? false : database->sequences[nodes[nIdx].first->seqsIncluded[0]]->lowQuality);
+        bool lowQ_q = (option->alnMode == MERGE_MSA) ? false : ((qryNum > 1) ? false : database->sequences[nodes[nIdx].second->seqsIncluded[0]]->lowQuality);
+       if (!lowQ_r && !lowQ_q) {
             auto talcoStart = std::chrono::high_resolution_clock::now();
             while (aln_wo_gc.empty()) {
                 int16_t errorType = 0;

src/alignment-helper.cpp

@@ -523,10 +523,10 @@ void msa::alignment_helper::fallback2cpu(std::vector<int>& fallbackPairs,  NodeP
     std::sort(fallbackPairs.begin(), fallbackPairs.end());
     for (int i = 0; i < fallbackPairs.size(); ++i) {
         int nIdx = fallbackPairs[i];
-        int32_t refNum = nodes[nIdx].first->seqsIncluded.size();
-        int32_t qryNum = nodes[nIdx].second->seqsIncluded.size();
-        bool lowQ_r = (refNum == 1 && database->sequences[nodes[nIdx].first->seqsIncluded[0]]->lowQuality);
-        bool lowQ_q = (qryNum == 1 && database->sequences[nodes[nIdx].second->seqsIncluded[0]]->lowQuality);
+        int32_t refNum = nodes[nIdx].first->alnNum;
+        int32_t qryNum = nodes[nIdx].second->alnNum;
+        bool lowQ_r = (refNum > 1) ? false : (database->sequences[nodes[nIdx].first->seqsIncluded[0]]->lowQuality);
+        bool lowQ_q = (qryNum > 1) ? false : (database->sequences[nodes[nIdx].second->seqsIncluded[0]]->lowQuality);
         if ((refNum < qryNum) || lowQ_r) {
             bool fallback = (!filtering) || (!lowQ_r);
             if (fallback) {
@@ -536,8 +536,14 @@ void msa::alignment_helper::fallback2cpu(std::vector<int>& fallbackPairs,  NodeP
             // swap reference and query
             int32_t refLen = nodes[nIdx].first->alnLen;
             int32_t qryLen = nodes[nIdx].second->alnLen;
+            float refWeight = nodes[nIdx].first->alnWeight;
+            float qryWeight = nodes[nIdx].second->alnWeight;
             nodes[nIdx].second->alnLen = refLen;
             nodes[nIdx].first->alnLen = qryLen;
+            nodes[nIdx].second->alnNum = refNum;
+            nodes[nIdx].first->alnNum = qryNum;
+            nodes[nIdx].second->alnWeight = refWeight;
+            nodes[nIdx].first->alnWeight = qryWeight;
             auto temp = nodes[nIdx].second->seqsIncluded;
             nodes[nIdx].second->seqsIncluded = nodes[nIdx].first->seqsIncluded;
             nodes[nIdx].first->seqsIncluded = temp;

src/tree.cpp

@@ -347,7 +347,7 @@ void phylogeny::Tree::showTree() {
                   << std::setw(10) << (node->parent ? node->parent->identifier : "ROOT")  // Parent or ROOT
                   << std::setw(8)  << node->level
                   << std::setw(8)  << node->grpID
-                  << std::setw(10) << std::fixed << std::setprecision(3) << node->children.size()
+                  << std::setw(10) << std::fixed << std::setprecision(3) << node->weight
                   << '\n';
         for (auto& c : node->children) {
             showTreeImpl(c);