Merge pull request #1027 from sooyoung-cha/mmseqsSET2

lookup order doesn't matter in clust

Author: sooyoung-cha

src/clustering/Clustering.cpp

@@ -51,58 +51,56 @@ Clustering::Clustering(const std::string &seqDB, const std::string &seqDBIndex,
             std::ifstream mappingStream(seqDB + ".lookup");
             std::string line;
             unsigned int setkey = 0;
+            unsigned int maxsetkey = 0;
             while (std::getline(mappingStream, line)) {
                 std::vector<std::string> split = Util::split(line, "\t");
                 unsigned int key = strtoul(split[0].c_str(), NULL, 10);
                 setkey = strtoul(split[2].c_str(), NULL, 10);
                 keyToSet[key] = setkey;
+                if (maxsetkey < setkey) {
+                    maxsetkey = setkey;
+                }
             }
             for (size_t id = 0; id < originalseqDbr->getSize(); id++) {
                 setToLength[keyToSet[seqIndex[id].id]] += seqIndex[id].length;
                 keysInSeq[seqIndex[id].id] = 1;
             }
-            unsigned int sourceLen = setkey + 1;
+            unsigned int sourceLen = maxsetkey + 1;
             seqnum = setToLength.size();
             sourceList = new(std::nothrow) unsigned int[lastKey];
-            sourceOffsets = new(std::nothrow) size_t[sourceLen + 1];
+            sourceOffsets = new(std::nothrow) size_t[sourceLen + 1]();
             sourceLookupTable = new(std::nothrow) unsigned int *[sourceLen];
+            size_t * sourceOffsetsDecrease = new(std::nothrow) size_t[sourceLen + 1]();
 
             mappingStream.close();
             mappingStream.open(seqDB + ".lookup");
+
+            line = "";
+            while (std::getline(mappingStream, line)) {
+                std::vector<std::string> split = Util::split(line, "\t");
+                setkey = strtoul(split[2].c_str(), NULL, 10);
+                sourceOffsets[setkey]++;
+                sourceOffsetsDecrease[setkey]++;
+            }
+            AlignmentSymmetry::computeOffsetFromCounts(sourceOffsets, sourceLen);
+            AlignmentSymmetry::setupPointers<unsigned int>(sourceList, sourceLookupTable, sourceOffsets, sourceLen, lastKey);
+            
+            mappingStream.close();
+            mappingStream.open(seqDB + ".lookup");
+
             line = "";
-            unsigned int prevsetkey = UINT_MAX;
-            size_t n = 0;
-            size_t lookupOrder = 0;
-            setkey = UINT_MAX;
             while (std::getline(mappingStream, line)) {
                 std::vector<std::string> split = Util::split(line, "\t");
                 unsigned int key = strtoul(split[0].c_str(), NULL, 10);
                 setkey = strtoul(split[2].c_str(), NULL, 10);
-                if(setkey != prevsetkey) {
-                    if (prevsetkey != UINT_MAX){
-                        sourceOffsets[prevsetkey] = n;
-                        for (size_t k = prevsetkey+1; k<setkey; k++) {
-                            sourceOffsets[k] = 0;
-                        }
-                    }
-                    prevsetkey = setkey;
-                    if(keysInSeq[key] == 1) {
-                        sourceKeyVec.emplace_back(setkey);
-                    }
-                    n = 0;
-                }
+                size_t order = sourceOffsets[setkey + 1] - sourceOffsetsDecrease[setkey];
                 if(keysInSeq[key] == 1) {
-                    sourceList[lookupOrder] = key;
+                    sourceList[order] = key;
                 } else {
-                    sourceList[lookupOrder] = UINT_MAX;
+                    sourceList[order] = UINT_MAX;
                 }
-                n++;
-                lookupOrder++;
+                sourceOffsetsDecrease[setkey]--;
             }
-            sourceOffsets[prevsetkey] = n;
-            AlignmentSymmetry::computeOffsetFromCounts(sourceOffsets, sourceLen);
-            AlignmentSymmetry::setupPointers<unsigned int>(sourceList, sourceLookupTable, sourceOffsets, sourceLen, lastKey);
-            
             char* data = (char*)malloc(
                 sizeof(size_t) +
                 sizeof(size_t) +
@@ -114,7 +112,7 @@ Clustering::Clustering(const std::string &seqDB, const std::string &seqDBIndex,
 
             std::vector<DBReader<unsigned int>::Index*> indexStorage(seqnum);
 
-            n = 0;
+            size_t n = 0;
             for (const auto& pairs : setToLength) {
                 indexStorage[n] = new DBReader<unsigned int>::Index;
                 indexStorage[n]->id = pairs.first;

src/clustering/Clustering.h

@@ -41,7 +41,6 @@ class Clustering {
     int compressed;
     std::string outDB;
     std::string outDBIndex;
-    std::vector<unsigned int> sourceKeyVec;
 };
 
 #endif