reload high-copy kmers if tmp maps are used

vgl-hub · May 9, 2024 · 0ee2f65 · 0ee2f65
1 parent 91a3803
commit 0ee2f65
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Showing 2 changed files with 22 additions and 1 deletion.
diff --git a/include/kreeq.h b/include/kreeq.h
@@ -139,6 +139,8 @@ class DBG : public Kmap<UserInputKreeq, DBGkmer, uint8_t> {
 
     bool mergeTmpMaps(uint16_t m);
 
+    bool reloadMap32(uint16_t m);
+
     bool dumpMap(std::string prefix, uint16_t m);
 
     bool loadMap(std::string prefix, uint16_t m);

diff --git a/src/graph-builder.cpp b/src/graph-builder.cpp
@@ -396,8 +396,10 @@ bool DBG::processBuffers(uint16_t m) {
         delete buf;
         alloc += mapSize(*maps[m]) - map_size;
 
-        if (freeMemory || !bufFile || bufFile.peek() == EOF)
+        if (freeMemory || !bufFile || bufFile.peek() == EOF) {
             dumpTmpMap(userInput.prefix, m);
+            reloadMap32(m);
+        }
     }
 
     bufFile.close();
@@ -486,6 +488,23 @@ bool DBG::mergeTmpMaps(uint16_t m) { // a single job merging maps with the same
 
 }
 
+bool DBG::reloadMap32(uint16_t m) {
+
+    parallelMap& map = *maps[m]; // the map associated to this buffer
+    parallelMap32& map32 = *maps32[m];
+
+    for (auto pair : map32) {
+
+        DBGkmer dbgkmer;
+        dbgkmer.cov = 255;
+        auto newPair = std::make_pair(pair.first, dbgkmer);
+        map.insert(newPair);
+    }
+
+    return true;
+
+}
+
 bool DBG::dumpMap(std::string prefix, uint16_t m) {
 
     prefix.append("/.map." + std::to_string(m) + ".bin");