fixed memory leaks and renamed weightThr parameter

Author: AnnSeidel

src/clustering/Clustering.cpp

@@ -31,6 +31,7 @@ Clustering::Clustering(const std::string &seqDB, const std::string &seqDBIndex,
         }
         seqDbr->sortIndex(localid2weight);
         delete[] localid2weight;
+        delete sequenceWeights;
 
     } else
         seqDbr->open(DBReader<unsigned int>::SORT_BY_LENGTH);

src/commons/Parameters.cpp

@@ -152,7 +152,7 @@ Parameters::Parameters():
         PARAM_ADJUST_KMER_LEN(PARAM_ADJUST_KMER_LEN_ID, "--adjust-kmer-len", "Adjust k-mer length", "Adjust k-mer length based on specificity (only for nucleotides)", typeid(bool), (void *) &adjustKmerLength, "", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
         PARAM_RESULT_DIRECTION(PARAM_RESULT_DIRECTION_ID, "--result-direction", "Result direction", "result is 0: query, 1: target centric", typeid(int), (void *) &resultDirection, "^[0-1]{1}$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
         PARAM_WEIGHT_FILE(PARAM_WEIGHT_FILE_ID, "--weights", "Weight file name", "Weights used for cluster priorization", typeid(std::string), (void*) &weightFile, "", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT ),
-        PARAM_WEIGHT_THR(PARAM_WEIGHT_THR_ID, "--weightThr", "Weight threshold", "Weight threshold used for cluster priorization", typeid(float), (void*) &weightThr, "^[0-9]*(\\.[0-9]+)?$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT ),
+        PARAM_WEIGHT_THR(PARAM_WEIGHT_THR_ID, "--cluster-weight-threshold", "Cluster Weight threshold", "Weight threshold used for cluster priorization", typeid(float), (void*) &weightThr, "^[0-9]*(\\.[0-9]+)?$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT ),
         // workflow
         PARAM_RUNNER(PARAM_RUNNER_ID, "--mpi-runner", "MPI runner", "Use MPI on compute cluster with this MPI command (e.g. \"mpirun -np 42\")", typeid(std::string), (void *) &runner, "", MMseqsParameter::COMMAND_COMMON | MMseqsParameter::COMMAND_EXPERT),
         PARAM_REUSELATEST(PARAM_REUSELATEST_ID, "--force-reuse", "Force restart with latest tmp", "Reuse tmp filse in tmp/latest folder ignoring parameters and version changes", typeid(bool), (void *) &reuseLatest, "", MMseqsParameter::COMMAND_COMMON | MMseqsParameter::COMMAND_EXPERT),

src/commons/SequenceWeights.cpp

@@ -53,3 +53,7 @@ float SequenceWeights::getWeightById(unsigned int id) {
     return (pos < indexSize && weightIndex[pos].id == id ) ? weightIndex[pos].weight : std::numeric_limits<float>::min();
 }
 
+SequenceWeights::~SequenceWeights() {
+    delete[] weightIndex;
+}
+

src/linclust/kmermatcher.cpp

@@ -488,6 +488,8 @@ KmerPosition<T> * doComputation(size_t totalKmers, size_t hashStartRange, size_t
         writePos = assignGroup<Parameters::DBTYPE_AMINO_ACIDS, T>(hashSeqPair, totalKmers, par.includeOnlyExtendable, par.covMode, par.covThr, sequenceWeights, par.weightThr);
     }
 
+    delete sequenceWeights;
+
     // sort by rep. sequence (stored in kmer) and sequence id
     Debug(Debug::INFO) << "Sort by rep. sequence ";
     timer.reset();