fix bugs on extracting median and counting profile size

Author: y3tseng

src/io.cpp

@@ -124,6 +124,8 @@ void msa::io::readSequences(std::string fileName, SequenceDB* database, Option*
         exit(1);
     }
 
+    std::sort(seqsLens.begin(), seqsLens.end());
+
     uint32_t avgLen = totalLen/(seqNum - seqNum_init);
     uint32_t medLen = seqsLens[(seqNum - seqNum_init)/2];
     int minLenTh = (option->lenDev > 0) ? static_cast<int>(medLen*(1-option->lenDev)) : option->minLen;

src/progressive.cpp

@@ -280,8 +280,8 @@ void msa::progressive::msaOnSubtree(Tree *T, SequenceDB *database, Option *optio
     alnPairsPerLevel.clear();
     for (auto bad: database->fallback_nodes) badSeqBefore += bad->seqsIncluded.size();
     std::sort(database->fallback_nodes.begin(), database->fallback_nodes.end(), [&](Node* &a, Node* &b) {
-        if (a->seqsIncluded.size() == b->seqsIncluded.size()) return a->getAlnLen(database->currentTask) > b->getAlnLen(database->currentTask);
-        return a->seqsIncluded.size() > b->seqsIncluded.size();  // descending
+        if (a->alnNum == b->alnNum) return a->getAlnLen(database->currentTask) > b->getAlnLen(database->currentTask);
+        return a->alnNum > b->alnNum;  // descending
     });
     for (auto bad: database->fallback_nodes) {
         alnPairsPerLevel.push_back(std::vector<NodePair>(1, {T->root, bad}));