Merge pull request #164 from jaebeom-kim/master

Author: jaebeom-kim

lib/fastq_utils/hash.cpp

@@ -185,7 +185,7 @@ int insere(hashtable table,ulong key,__ptr_t obj)
 
 void free_hashtable(hashtable table)
 {
-   register ulong i;
+   ulong i;
    hashnode *n,*tmp;
    //fprintf(stderr,"free_hashtable\n");fflush(stderr);
    if (table==NULL) return;
@@ -203,7 +203,7 @@ void free_hashtable(hashtable table)
 }
 void reset_hashtable(hashtable table)
 {
-   register ulong i;
+   ulong i;
    hashnode *n,*tmp;
    //fprintf(stderr,"free_hashtable\n");fflush(stderr);
    if (table==NULL) return;

src/commons/IndexCreator.h

@@ -358,7 +358,7 @@ void IndexCreator::mergeTargetFiles() {
     std::vector<std::atomic<bool>> completedSplits(splitNum);
     int remainingSplits = splitNum;
     vector<pair<size_t, size_t>> uniqKmerIdxRanges;
-    size_t lastKmer = 0;
+    uint64_t lastKmer = 0;
     auto * uniqKmerIdx = new size_t[kmerBuffer.bufferSize];
     vector<size_t> splitToProcess;
     while (remainingSplits > 0) {
@@ -378,7 +378,7 @@ void IndexCreator::mergeTargetFiles() {
                 }
                 splitToProcess.push_back(i);
             }
-#pragma omp parallel for default(none), shared(cout, kmerBuffer, deltaIdxReaders, splitToProcess, completedSplits, posToWrite, max, splitNum, valueBufferSize, taxId2speciesId, mask, remainingSplits)
+            #pragma omp parallel for default(none), shared(cout, kmerBuffer, deltaIdxReaders, splitToProcess, completedSplits, posToWrite, max, splitNum, valueBufferSize, taxId2speciesId, mask, remainingSplits)
             for (size_t i = 0; i < splitToProcess.size(); i ++) {
                 size_t split = splitToProcess[i];
                 size_t offset = posToWrite + i * valueBufferSize;

src/commons/KmerExtractor.cpp

@@ -744,7 +744,7 @@ bool KmerExtractor::extractQueryKmers_aa2aa(
             while (moreData && bufferNotFull) {
                 auto & seqChunk = readsPerThread[producerBufferIndex];
                 // auto & nameChunk = seqNamesPerThread[producerBufferIndex];
-                size_t seqCnt = 0;
+                uint32_t seqCnt = 0;
                 size_t kmerCnt = 0;
                 while (queryIdx + chunkSize - 1 >= queryList.size()) {
                     queryList.resize(queryList.size() * 2);