added defaults

vgl-hub · Jul 4, 2024 · d0ec5da · d0ec5da
1 parent bac555e
commit d0ec5da
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/include/kreeq.h b/include/kreeq.h
@@ -167,6 +167,15 @@ class DBG : public Kmap<DBG, UserInputKreeq, uint64_t, DBGkmer, DBGkmer32> { //
 
     DBG(UserInputKreeq& userInput) : Kmap{userInput}, userInput(userInput) {
         DBextension = "kreeq";
+
+        if (userInput.kmerDepth == -1) {
+            if (userInput.travAlgorithm == "best-first") {
+                this->userInput.kmerDepth = userInput.kmerLen; // unidirectional search
+                this->userInput.maxSpan = userInput.kmerLen;
+            }
+            else if (userInput.travAlgorithm == "traversal")
+                this->userInput.kmerDepth = std::ceil((float)userInput.kmerLen/2); // kmer search is in both directions
+        }
     }
 
     ~DBG(){

diff --git a/src/subgraph.cpp b/src/subgraph.cpp
@@ -289,12 +289,8 @@ bool DBG::DBGsubgraphFromSegment(InSegment *inSegment, std::array<uint16_t, 2> m
 
 void DBG::searchGraph() {
     if (userInput.travAlgorithm == "best-first") {
-        if (this->userInput.kmerDepth == -1)
-            userInput.kmerDepth = userInput.kmerLen; // unidirectional search
         bestFirst();
     }else if (userInput.travAlgorithm == "traversal") {
-        if (userInput.kmerDepth == -1)
-            userInput.kmerDepth = std::ceil((float)userInput.kmerLen/2); // kmer search is in both directions
         traversal();
     }else{
         fprintf(stderr, "Cannot find input algorithm (%s). Terminating.\n", userInput.travAlgorithm.c_str());