Replace stl map/set with robinhood map/set (and 'auto' some iterators).

Author: brianwalenz

LICENSE.txt

@@ -17,6 +17,10 @@ Open Bloom Filter
   https://code.google.com/p/bloom/source/browse/trunk/bloom_filter.hpp
   Common Public License
 
+Robin_Hood Unordered Map and Set
+  https://github.com/martinus/robin-hood-hashing
+  MIT License
+
 COPYRIGHT LICENSE
 
 Copyright © 2015, Battelle National Biodefense Institute (BNBI);

src/mash/CommandFind.cpp

@@ -10,7 +10,7 @@
 #include "kseq.h"
 #include <iostream>
 #include <set>
-#include <unordered_set>
+#include "robin_hood.h"
 #include "ThreadPool.h"
 #include "sketchParameterSetup.h"
 
@@ -229,11 +229,9 @@ CommandFind::FindOutput * find(CommandFind::FindInput * data)
 
 void findPerStrand(const CommandFind::FindInput * input, CommandFind::FindOutput * output, bool minusStrand)
 {
-    typedef std::unordered_map < uint32_t, std::set<uint32_t> > PositionsBySequence_umap;
-    
     bool verbose = false;
 
-    Sketch::Hash_set minHashes;
+    robin_hood::unordered_set<Sketch::hash_t> minHashes;
 
     const Sketch & sketch = input->sketch;
     int kmerSize = sketch.getKmerSize();
@@ -302,9 +300,9 @@ void findPerStrand(const CommandFind::FindInput * input, CommandFind::FindOutput
     // get sorted lists of positions, per reference sequence, that have
     // mutual min-hashes with the query
     //
-    PositionsBySequence_umap hits;
-    //
-    for ( Sketch::Hash_set::const_iterator i = minHashes.begin(); i != minHashes.end(); i++ )
+    robin_hood::unordered_map < uint32_t, std::set<uint32_t> >   hits;
+
+    for ( auto i = minHashes.begin(); i != minHashes.end(); i++ )
     {
         Sketch::hash_t hash = *i;
 
@@ -326,7 +324,7 @@ void findPerStrand(const CommandFind::FindInput * input, CommandFind::FindOutput
         }
     }
 
-    for ( PositionsBySequence_umap::iterator i = hits.begin(); i != hits.end(); i++ )
+    for ( auto i = hits.begin(); i != hits.end(); i++ )
     {
     	using std::set;
 

src/mash/CommandScreen.cpp

@@ -12,7 +12,7 @@
 #include <zlib.h>
 #include "ThreadPool.h"
 #include <math.h>
-#include <set>
+#include "robin_hood.h"
 
 #ifdef USE_BOOST
 	#include <boost/math/distributions/binomial.hpp>
@@ -29,8 +29,6 @@ using std::cout;
 using std::endl;
 using std::list;
 using std::string;
-using std::unordered_map;
-using std::unordered_set;
 using std::vector;
 
 namespace mash {
@@ -93,8 +91,8 @@ int CommandScreen::run() const
 	parameters.minHashesPerWindow = sketch.getMinHashesPerWindow();
 
 	HashTable hashTable;
-	unordered_map<uint64_t, std::atomic<uint32_t>> hashCounts;
-	unordered_map<uint64_t, list<uint32_t> > saturationByIndex;
+	robin_hood::unordered_map<uint64_t, std::atomic<uint32_t>> hashCounts;
+	robin_hood::unordered_map<uint64_t, list<uint32_t> > saturationByIndex;
 
 	cerr << "Loading " << arguments[0] << "..." << endl;
 
@@ -117,7 +115,7 @@ int CommandScreen::run() const
 
 	cerr << "   " << hashTable.size() << " distinct hashes." << endl;
 
-	unordered_set<MinHashHeap *> minHashHeaps;
+	robin_hood::unordered_set<MinHashHeap *> minHashHeaps;
 
 	bool trans = (alphabet == alphabetProtein);
 
@@ -289,7 +287,7 @@ int CommandScreen::run() const
 
 	MinHashHeap minHashHeap(sketch.getUse64(), sketch.getMinHashesPerWindow());
 
-	for ( unordered_set<MinHashHeap *>::const_iterator i = minHashHeaps.begin(); i != minHashHeaps.end(); i++ )
+	for ( auto i = minHashHeaps.begin(); i != minHashHeaps.end(); i++ )
 	{
 		HashList hashList(parameters.use64);
 
@@ -337,13 +335,13 @@ int CommandScreen::run() const
 
 	memset(shared, 0, sizeof(uint64_t) * sketch.getReferenceCount());
 
-	for ( unordered_map<uint64_t, std::atomic<uint32_t> >::const_iterator i = hashCounts.begin(); i != hashCounts.end(); i++ )
+	for ( auto i = hashCounts.begin(); i != hashCounts.end(); i++ )
 	{
 		if ( i->second >= minCov )
 		{
-			const unordered_set<uint64_t> & indeces = hashTable.at(i->first);
+			const auto & indeces = hashTable.at(i->first);
 
-			for ( unordered_set<uint64_t>::const_iterator k = indeces.begin(); k != indeces.end(); k++ )
+			for ( auto k = indeces.begin(); k != indeces.end(); k++ )
 			{
 				shared[*k]++;
 				depths[*k].push_back(i->second);
@@ -381,12 +379,12 @@ int CommandScreen::run() const
 				continue;
 			}
 
-			const unordered_set<uint64_t> & indeces = i->second;
+			const auto & indeces = i->second;
 			double maxScore = 0;
 			uint64_t maxLength = 0;
 			uint64_t maxIndex;
 
-			for ( unordered_set<uint64_t>::const_iterator k = indeces.begin(); k != indeces.end(); k++ )
+			for ( auto k = indeces.begin(); k != indeces.end(); k++ )
 			{
 				if ( scores[*k] > maxScore )
 				{
@@ -456,6 +454,7 @@ int CommandScreen::run() const
 		}
 	}
 
+	delete [] depths;
 	delete [] shared;
 
 	return 0;
@@ -809,7 +808,7 @@ char aaFromCodon(const char * codon)
 	return aa;//(aa == '*') ? 0 : aa;
 }
 
-void useThreadOutput(CommandScreen::HashOutput * output, unordered_set<MinHashHeap *> & minHashHeaps)
+void useThreadOutput(CommandScreen::HashOutput * output, robin_hood::unordered_set<MinHashHeap *> & minHashHeaps)
 {
 	minHashHeaps.emplace(output->minHashHeap);
 	delete output;

src/mash/CommandScreen.h

@@ -13,8 +13,7 @@
 #include <string>
 #include <vector>
 #include <atomic>
-#include <unordered_set>
-#include <unordered_map>
+#include "robin_hood.h"
 #include "MinHashHeap.h"
 
 namespace mash {
@@ -24,13 +23,13 @@ struct HashTableEntry
 	HashTableEntry() : count(0) {}
 
 	uint32_t count;
-	std::unordered_set<uint64_t> indices;
+	robin_hood::unordered_set<uint64_t> indices;
 };
 
-//typedef std::unordered_map< uint64_t, HashTableEntry > HashTable;
-typedef std::unordered_map< uint64_t, std::unordered_set<uint64_t> > HashTable;
+//typedef robin_hood::unordered_map< uint64_t, HashTableEntry > HashTable;
+typedef robin_hood::unordered_map< uint64_t, robin_hood::unordered_set<uint64_t> > HashTable;
 
-static const std::unordered_map< std::string, char > codons =
+static const robin_hood::unordered_map< std::string, char > codons =
 {
 	{"AAA",	'K'},
 	{"AAC",	'N'},
@@ -104,7 +103,7 @@ class CommandScreen : public Command
 
     struct HashInput
     {
-    	HashInput(std::unordered_map<uint64_t, std::atomic<uint32_t> > & hashCountsNew, MinHashHeap * minHashHeapNew, char * seqNew, uint64_t lengthNew, const Sketch::Parameters & parametersNew, bool transNew)
+    	HashInput(robin_hood::unordered_map<uint64_t, std::atomic<uint32_t> > & hashCountsNew, MinHashHeap * minHashHeapNew, char * seqNew, uint64_t lengthNew, const Sketch::Parameters & parametersNew, bool transNew)
     	:
     	hashCounts(hashCountsNew),
     	minHashHeap(minHashHeapNew),
@@ -129,7 +128,7 @@ class CommandScreen : public Command
     	bool trans;
 
     	Sketch::Parameters parameters;
-		std::unordered_map<uint64_t, std::atomic<uint32_t> > & hashCounts;
+		robin_hood::unordered_map<uint64_t, std::atomic<uint32_t> > & hashCounts;
 		MinHashHeap * minHashHeap;
     };
 
@@ -165,7 +164,7 @@ double estimateIdentity(uint64_t common, uint64_t denom, int kmerSize, double km
 CommandScreen::HashOutput * hashSequence(CommandScreen::HashInput * input);
 double pValueWithin(uint64_t x, uint64_t setSize, double kmerSpace, uint64_t sketchSize);
 void translate(const char * src, char * dst, uint64_t len);
-void useThreadOutput(CommandScreen::HashOutput * output, std::unordered_set<MinHashHeap *> & minHashHeaps);
+void useThreadOutput(CommandScreen::HashOutput * output, robin_hood::unordered_set<MinHashHeap *> & minHashHeaps);
 
 } // namespace mash
 

src/mash/HashSet.cpp

@@ -78,14 +78,14 @@ void HashSet::toCounts(std::vector<uint32_t> & counts) const
 {
     if ( use64 )
     {
-        for ( std::unordered_map<hash64_t, uint32_t>::const_iterator i = hashes64.begin(); i != hashes64.end(); i++ )
+        for ( auto i = hashes64.begin(); i != hashes64.end(); i++ )
         {
             counts.push_back(i->second);
         }
     }
     else
     {
-        for ( std::unordered_map<hash32_t, uint32_t>::const_iterator i = hashes32.begin(); i != hashes32.end(); i++ )
+        for ( auto i = hashes32.begin(); i != hashes32.end(); i++ )
         {
             counts.push_back(i->second);
         }
@@ -96,14 +96,14 @@ void HashSet::toHashList(HashList & hashList) const
 {
     if ( use64 )
     {
-        for ( std::unordered_map<hash64_t, uint32_t>::const_iterator i = hashes64.begin(); i != hashes64.end(); i++ )
+        for ( auto i = hashes64.begin(); i != hashes64.end(); i++ )
         {
             hashList.push_back64(i->first);
         }
     }
     else
     {
-        for ( std::unordered_map<hash32_t, uint32_t>::const_iterator i = hashes32.begin(); i != hashes32.end(); i++ )
+        for ( auto i = hashes32.begin(); i != hashes32.end(); i++ )
         {
             hashList.push_back32(i->first);
         }

src/mash/HashSet.h

@@ -8,7 +8,7 @@
 #define HashSet_h
 
 #include "HashList.h"
-#include <unordered_map>
+#include "robin_hood.h"
 #include <vector>
 
 class HashSet
@@ -28,8 +28,8 @@ class HashSet
 private:
 
     bool use64;
-    std::unordered_map<hash32_t, uint32_t> hashes32;
-    std::unordered_map<hash64_t, uint32_t> hashes64;
+    robin_hood::unordered_map<hash32_t, uint32_t> hashes32;
+    robin_hood::unordered_map<hash64_t, uint32_t> hashes64;
 };
 
 #endif

src/mash/Sketch.h

@@ -8,8 +8,7 @@
 #define Sketch_h
 
 #include "mash/capnp/MinHash.capnp.h"
-#include <unordered_map>
-#include <unordered_set>
+#include "robin_hood.h"
 #include <map>
 #include <vector>
 #include <string>
@@ -126,8 +125,6 @@ class Sketch
         uint32_t position;
     };
 
-    typedef std::unordered_set<hash_t> Hash_set;
-    
     struct Reference
     {
         // no sequence for now
@@ -215,9 +212,9 @@ class Sketch
     void createIndex();
 
     std::vector<Reference> references;
-    std::unordered_map<std::string, int> referenceIndecesById;
+    robin_hood::unordered_map<std::string, int> referenceIndecesById;
     std::vector<std::vector<PositionHash>> positionHashesByReference;
-    std::unordered_map<hash_t, std::vector<Locus>> lociByHash;
+    robin_hood::unordered_map<hash_t, std::vector<Locus>> lociByHash;
 
     Parameters parameters;
     double kmerSpace;

src/mash/robin_hood.h

@@ -0,0 +1 @@
+/work/mash-profile/robin-hood-hashing/src/include/robin_hood.h