Cleanup for -Werror build

soedinglab · Oct 30, 2023 · 932d32b · 932d32b
1 parent e26b9ad
commit 932d32b
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Showing 11 changed files with 19 additions and 28 deletions.
diff --git a/lib/alp/sls_pvalues.hpp b/lib/alp/sls_pvalues.hpp
@@ -258,7 +258,7 @@ namespace Sls {
 			return rand_C;	
 		};
 
-		static inline double standard_normal()//generates standard normal random value using the Box–Muller transform
+		static inline double standard_normal()//generates standard normal random value using the Box-Muller transform
 		{
 			double r1=0;
 			while(r1==0)

diff --git a/src/alignment/Matcher.cpp b/src/alignment/Matcher.cpp
@@ -282,7 +282,7 @@ size_t Matcher::resultToBuffer(char * buff1, const result_t &result, bool addBac
     *(tmpBuff-1) = '\t';
     tmpBuff = Util::fastSeqIdToBuffer(result.seqId, tmpBuff);
     *(tmpBuff-1) = '\t';
-    tmpBuff += sprintf(tmpBuff,"%.3E",result.eval);
+    tmpBuff += snprintf(tmpBuff, 32, "%.3E", result.eval);
     tmpBuff++;
     *(tmpBuff-1) = '\t';
     tmpBuff = Itoa::i32toa_sse2(result.qStartPos, tmpBuff);

diff --git a/src/alignment/MultipleAlignment.cpp b/src/alignment/MultipleAlignment.cpp
@@ -47,25 +47,23 @@ void MultipleAlignment::computeQueryGaps(unsigned int *queryGaps, Sequence *cent
     for(size_t i = 0; i < alignmentResults.size(); i++) {
         const Matcher::result_t& alignment = alignmentResults[i];
         const std::string& bt = alignment.backtrace;
-        size_t queryPos = 0;
-        size_t targetPos = 0;
         size_t currentQueryGapSize = 0;
-        queryPos = alignment.qStartPos;
-        targetPos = alignment.dbStartPos;
+        size_t queryPos = alignment.qStartPos;
+        // size_t targetPos = alignment.dbStartPos;
         // compute query gaps (deletions)
         for (size_t pos = 0; pos < bt.size(); ++pos) {
             char bt_letter = bt.at(pos);
             if (bt_letter == 'M') { // match state
                 ++queryPos;
-                ++targetPos;
+                // ++targetPos;
                 currentQueryGapSize = 0;
             } else {
                 if (bt_letter == 'I') { // insertion
                     ++queryPos;
                     currentQueryGapSize = 0;
                 }
                 else { // deletion
-                    ++targetPos;
+                    // ++targetPos;
                     currentQueryGapSize += 1;
                     size_t gapCount = queryGaps[queryPos];
                     queryGaps[queryPos] = std::max(gapCount, currentQueryGapSize);

diff --git a/src/commons/CSProfile.cpp b/src/commons/CSProfile.cpp
@@ -135,12 +135,12 @@ void ContextLibrary::readContextProfile(std::stringstream &in, LibraryReader &re
     }
     // Calculate maximum of pseudocount weights
     double max = -DBL_MAX;
-    double mean = 0.0;
+    // double mean = 0.0;
     for (size_t a = 0; a < 20; ++a) {
-        mean += pc_weight[a];
+        // mean += pc_weight[a];
         if (pc_weight[a] > max) max = pc_weight[a];
     }
-    mean /= 20.0;
+    // mean /= 20.0;
 
     // Rescale pseudocount weights and calculate their sum in lin-space
     long double sum = 0.0;

diff --git a/src/commons/Parameters.cpp b/src/commons/Parameters.cpp
@@ -1631,7 +1631,6 @@ void Parameters::parseParameters(int argc, const char *pargv[], const Command &c
         }
     }
 
-    size_t parametersFound = 0;
     for (int argIdx = 0; argIdx < argc; argIdx++) {
         // it is a parameter if it starts with - or --
         const bool longParameter = (pargv[argIdx][0] == '-' && pargv[argIdx][1] == '-');
@@ -1848,8 +1847,6 @@ void Parameters::parseParameters(int argc, const char *pargv[], const Command &c
 
                 EXIT(EXIT_FAILURE);
             }
-
-            parametersFound++;
         } else {
             // parameter is actually a filename
 #ifdef __CYGWIN__

diff --git a/src/commons/ProfileStates.cpp b/src/commons/ProfileStates.cpp
@@ -135,15 +135,15 @@ int ProfileStates::readProfile(std::stringstream &in, float * profile,  float *
         pos += Util::skipWhitespace(pos);
         pos += Util::skipNoneWhitespace(pos);
         pos += Util::skipWhitespace(pos);
-        float s = 0.0;
+        // float s = 0.0;
 
         // Store the probabilities
         for (int k = 0 ; k < nalph ; k++)
         {
             float score = std::strtod(pos, NULL);
             float prob = MathUtil::fpow2(-score/kScale);
             profile[ProfileStates::hh2mmseqsAAorder(k)] = prob;// /background[k];
-            s+=prob;
+            // s+=prob;
             char* oldPos = pos;
             pos += Util::skipNoneWhitespace(pos);
             pos += Util::skipWhitespace(pos);

diff --git a/src/linclust/LinsearchIndexReader.cpp b/src/linclust/LinsearchIndexReader.cpp
@@ -25,7 +25,6 @@ size_t LinsearchIndexReader::pickCenterKmer(KmerPosition<short> *hashSeqPair, si
         prevHash = BIT_SET(prevHash, 63);
     }
     size_t prevHashStart = 0;
-    size_t prevSetSize = 0;
     for (size_t elementIdx = 0; elementIdx < splitKmerCount + 1; elementIdx++) {
         size_t currKmer = hashSeqPair[elementIdx].kmer;
         if (TYPE == Parameters::DBTYPE_NUCLEOTIDES) {
@@ -52,7 +51,6 @@ size_t LinsearchIndexReader::pickCenterKmer(KmerPosition<short> *hashSeqPair, si
         if (hashSeqPair[elementIdx].kmer == SIZE_T_MAX) {
             break;
         }
-        prevSetSize++;
         prevHash = hashSeqPair[elementIdx].kmer;
         if (TYPE == Parameters::DBTYPE_NUCLEOTIDES) {
             prevHash = BIT_SET(prevHash, 63);

diff --git a/src/multihit/combinepvalperset.cpp b/src/multihit/combinepvalperset.cpp
@@ -105,13 +105,13 @@ class PvalueAggregator : public Aggregation {
                 return buffer;
             }
 
-            size_t k = 0;
+            // size_t k = 0;
             double r = 0;
             const double logPvalThr = log(pvalThreshold);
             for (size_t i = 0; i < dataToAggregate.size(); ++i) {
                 double logPvalue = std::strtod(dataToAggregate[i][1].c_str(), NULL);
                 if (logPvalue < logPvalThr) {
-                    k++;
+                    // k++;
                     r -= logPvalue - logPvalThr;
                 }
             }

diff --git a/src/prefiltering/IndexTable.h b/src/prefiltering/IndexTable.h
@@ -264,14 +264,14 @@ class IndexTable {
 
         size_t entrySize = 0;
         size_t minKmer = 0;
-        size_t emptyKmer = 0;
+        // size_t emptyKmer = 0;
         for (size_t i = 0; i < tableSize; i++) {
             const ptrdiff_t size = offsets[i + 1] - offsets[i];
             minKmer = std::min(minKmer, (size_t) size);
             entrySize += size;
-            if (size == 0) {
-                emptyKmer++;
-            }
+            // if (size == 0) {
+            //     emptyKmer++;
+            // }
             if (((size_t) size) < topElements[top_N - 1].first)
                 continue;
             for (size_t j = 0; j < top_N; j++) {

diff --git a/src/util/extractframes.cpp b/src/util/extractframes.cpp
@@ -78,12 +78,12 @@ int extractframes(int argc, const char **argv, const Command& command) {
 
             if(reverseFrames != 0){
                 size_t sequenceLength =  dataLength -2;
-                bool hasWrongChar = false;
+                // bool hasWrongChar = false;
                 for(size_t pos = 0; pos < sequenceLength; ++pos) {
                     char reverseComplement = Orf::complement(data[sequenceLength - pos - 1]);
                     reverseComplement = (reverseComplement == '.') ? 'N' : reverseComplement;
                     reverseComplementStr.push_back(reverseComplement);
-                    hasWrongChar |= (reverseComplement == '.');
+                    // hasWrongChar |= (reverseComplement == '.');
                 }
 //                if(hasWrongChar == true){
 //                    continue;

diff --git a/src/util/result2stats.cpp b/src/util/result2stats.cpp
@@ -383,7 +383,6 @@ int StatsComputer::sequenceWise(typename PerSequence<T>::type call, bool onlyRes
                 buffer.append("\n");
             } else {
                 // for every hit
-                int cnt = 0;
                 while (*results != '\0') {
                     Util::parseKey(results, dbKey);
                     char *rest;
@@ -402,7 +401,6 @@ int StatsComputer::sequenceWise(typename PerSequence<T>::type call, bool onlyRes
                     buffer.append("\n");
 
                     results = Util::skipLine(results);
-                    cnt++;
                 }
             }
             statWriter->writeData(buffer.c_str(), buffer.length(), resultReader->getDbKey(id), thread_idx);