Fix off by one in kmermatcher #274 (comment)

soedinglab · Feb 26, 2020 · aa175d6 · aa175d6
1 parent d1607bc
commit aa175d6
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/src/linclust/kmerindexdb.cpp b/src/linclust/kmerindexdb.cpp
@@ -87,7 +87,7 @@ int kmerindexdb(int argc, const char **argv, const Command &command) {
     // compute splits
     size_t splits = static_cast<size_t>(std::ceil(static_cast<float>(totalSizeNeeded) / memoryLimit));
     size_t totalKmersPerSplit = std::max(static_cast<size_t>(1024+1),
-                                         static_cast<size_t>(std::min(totalSizeNeeded, memoryLimit)/sizeof(KmerPosition<short>)));
+                                         static_cast<size_t>(std::min(totalSizeNeeded, memoryLimit)/sizeof(KmerPosition<short>))+1);
     std::vector<std::pair<size_t, size_t>> hashRanges = setupKmerSplits<short>(par, subMat, seqDbr, totalKmersPerSplit, splits);
 
     Debug(Debug::INFO) << "Process file into " << hashRanges.size() << " parts\n";

diff --git a/src/linclust/kmermatcher.cpp b/src/linclust/kmermatcher.cpp
@@ -600,7 +600,7 @@ int kmermatcherInner(Parameters& par, DBReader<unsigned int>& seqDbr) {
     // compute splits
     size_t splits = static_cast<size_t>(std::ceil(static_cast<float>(totalSizeNeeded) / memoryLimit));
     size_t totalKmersPerSplit = std::max(static_cast<size_t>(1024+1),
-                                         static_cast<size_t>(std::min(totalSizeNeeded, memoryLimit)/sizeof(KmerPosition<T>)));
+                                         static_cast<size_t>(std::min(totalSizeNeeded, memoryLimit)/sizeof(KmerPosition<T>))+1);
 
     std::vector<std::pair<size_t, size_t>> hashRanges = setupKmerSplits<T>(par, subMat, seqDbr, totalKmersPerSplit, splits);
     if(splits > 1){

diff --git a/src/linclust/kmersearch.cpp b/src/linclust/kmersearch.cpp
@@ -218,7 +218,7 @@ int kmersearch(int argc, const char **argv, const Command &command) {
     // compute splits
     size_t splits = static_cast<size_t>(std::ceil(static_cast<float>(totalSizeNeeded) / memoryLimit));
     size_t totalKmersPerSplit = std::max(static_cast<size_t>(1024+1),
-                                         static_cast<size_t>(std::min(totalSizeNeeded, memoryLimit)/sizeof(KmerPosition<short>)));
+                                         static_cast<size_t>(std::min(totalSizeNeeded, memoryLimit)/sizeof(KmerPosition<short>))+1);
 
     std::vector<std::pair<size_t, size_t>> hashRanges = setupKmerSplits<short>(par, subMat, queryDbr, totalKmersPerSplit, splits);