Cleanup merge issues

.gitignore

@@ -40,5 +40,5 @@ BacteriaBench/
 EliTestFiles/
 NCBI_Bacteria_Orfs/
 build.old/
-.vscode/c_cpp_properties.json
+.vscode/
 vsc.code-workspace

README.md

@@ -143,8 +143,3 @@ To search with multiple servers, call the `search` or `cluster` workflow with th
 
         RUNNER="mpirun -pernode -np 42" mmseqs search queryDB targetDB resultDB tmp
 
-
-<<<<<<< HEAD
-        RUNNER="mpirun -pernode -np 42" mmseqs search queryDB targetDB resultDB tmp
-=======
->>>>>>> e601ea0c213fb12391b70751220e361c96eb98ea

src/commons/Parameters.cpp

@@ -206,7 +206,7 @@ Parameters::Parameters():
         PARAM_SIMPLE_BEST_HIT(PARAM_SIMPLE_BEST_HIT_ID, "--simple-best-hit", "Use simple best hit", "Update the p-value by a single best hit, or by best and second best hits", typeid(bool), (void*) &simpleBestHit, ""),
         PARAM_ALPHA(PARAM_ALPHA_ID, "--alpha", "Alpha", "Set alpha for combining p-values during aggregation", typeid(float), (void*) &alpha, ""),
         PARAM_SHORT_OUTPUT(PARAM_SHORT_OUTPUT_ID, "--short-output", "Short output", "The output database will contain only the spread p-value", typeid(bool), (void*) &shortOutput, ""),
-        PARAM_AGGREGATION_MODE(PARAM_AGGREGATION_MODE_ID, "--aggregation-mode", "Aggregation mode", "Combined P-values computed from 0: multi-hit, 1:minimum of all P-values, 2: product-of-P-values, 3: truncated product", typeid(int), (void*) &aggregationMode, "^[0-4]{1}$"),
+        PARAM_AGGREGATION_MODE(PARAM_AGGREGATION_MODE_ID, "--aggregation-mode", "Aggregation mode", "Combined P-values computed from 0: multi-hit, 1: minimum of all P-values, 2: product-of-P-values, 3: truncated product", typeid(int), (void*) &aggregationMode, "^[0-4]{1}$"),
         // concatdb
         PARAM_PRESERVEKEYS(PARAM_PRESERVEKEYS_ID,"--preserve-keys", "Preserve the keys", "the keys of the two DB should be distinct, and they will be preserved in the concatenation.",typeid(bool), (void *) &preserveKeysB, ""),
         PARAM_TAKE_LARGER_ENTRY(PARAM_TAKE_LARGER_ENTRY_ID,"--take-larger-entry", "Take the larger entry", "only keeps the larger entry (dataSize >) in the concatenation, both databases need the same keys in the index",typeid(bool), (void *) &takeLargerEntry, ""),

src/commons/Parameters.h

@@ -229,7 +229,6 @@ class Parameters {
     static const int AGGREGATION_MODE_MIN_PVAL = 1;
     static const int AGGREGATION_MODE_PRODUCT = 2;
     static const int AGGREGATION_MODE_TRUNCATED_PRODUCT = 3;
-    static const int AGGREGATION_MODE_RANK_TRUNCATED_PRODUCT = 4;
 
     // header type
     static const int HEADER_TYPE_UNICLUST = 1;

src/multihit/Aggregation.cpp

@@ -84,8 +84,7 @@ int Aggregation::run() {
             buffer.clear();
         }
     };
-    //TODO what dbtype?
-    writer.close(true);
+    writer.close();
     reader.close();
 
     return EXIT_SUCCESS;

src/multihit/besthitperset.cpp

@@ -29,7 +29,7 @@ public :
     std::string aggregateEntry(std::vector<std::vector<std::string>> &dataToAggregate, unsigned int, unsigned int targetSetKey, unsigned int thread_idx)  {
         std::string buffer;
         buffer.reserve(1024);
-        
+
         double bestScore = -DBL_MAX;
         double secondBestScore = -DBL_MAX;
         double bestEval = DBL_MAX;
@@ -48,15 +48,15 @@ public :
         unsigned int nbrGenes = Util::fast_atoi<unsigned int>(data);
 
         std::vector<std::string> *bestEntry = NULL;
-        for (size_t i = 0; i < dataToAggregate.size(); i++) {       
+        for (size_t i = 0; i < dataToAggregate.size(); i++) {
             double eval = strtod(dataToAggregate[i][3].c_str(), NULL);
             double pval = eval/nbrGenes;
             //prevent log(0)
             if (pval == 0) {
                 pval = DBL_MIN;
             }
             double score = -log(pval);
-                
+
             //if only one hit use simple best hit
             if(simpleBestHitMode ||dataToAggregate.size() < 2) {
                 if(bestEval > eval){

src/util/mergeresultsbyset.cpp

@@ -47,7 +47,7 @@ int mergeresultsbyset(int argc, const char **argv, const Command &command) {
             buffer.clear();
         }
     }
-    dbw.close(true);
+    dbw.close();
     resultReader.close();
     setReader.close();