Simplify

ablab · Dec 4, 2024 · 67748a3 · 67748a3
1 parent 5e9367a
commit 67748a3
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Showing 2 changed files with 19 additions and 33 deletions.
diff --git a/src/common/alignment/kmer_map.hpp b/src/common/alignment/kmer_map.hpp
@@ -69,14 +69,15 @@ class KMerMap {
     KMerMap(unsigned k)
             : k_(k) {
         rawcnt_ = (unsigned)Seq::GetDataSize(k_);
+        key_size_ = rawcnt_ * sizeof(RawSeqData);
     }
 
     ~KMerMap() {
         clear();
     }
 
     void erase(const Kmer &key) {
-        auto res = mapping_.find_ks((const char*)key.data(), rawcnt_ * sizeof(RawSeqData));
+        auto res = mapping_.find_ks((const char*)key.data(), key_size_);
         if (res == mapping_.end())
             return;
 
@@ -86,30 +87,30 @@ class KMerMap {
 
     void set(const Kmer &key, const Seq &value) {
         RawSeqData *rawvalue = nullptr;
-        auto res = mapping_.find_ks((const char*)key.data(), rawcnt_ * sizeof(RawSeqData));
+        auto res = mapping_.find_ks((const char*)key.data(), key_size_);
         if (res == mapping_.end()) {
             rawvalue = new RawSeqData[rawcnt_];
-            mapping_.insert_ks((const char*)key.data(), rawcnt_ * sizeof(RawSeqData), rawvalue);
+            mapping_.insert_ks((const char*)key.data(), key_size_, rawvalue);
         } else {
             rawvalue = res.value();
         }
-        memcpy(rawvalue, value.data(), rawcnt_ * sizeof(RawSeqData));
+        memcpy(rawvalue, value.data(), key_size_);
     }
 
     bool count(const Kmer &key) const {
-        return mapping_.count_ks((const char*)key.data(), rawcnt_ * sizeof(RawSeqData));
+        return mapping_.count_ks((const char*)key.data(), key_size_);
     }
 
     const RawSeqData *find(const Kmer &key) const {
-        auto res = mapping_.find_ks((const char*)key.data(), rawcnt_ * sizeof(RawSeqData));
+        auto res = mapping_.find_ks((const char*)key.data(), key_size_);
         if (res == mapping_.end())
             return nullptr;
 
         return res.value();
     }
 
     const RawSeqData *find(const RawSeqData *key) const {
-        auto res = mapping_.find_ks((const char*)key, rawcnt_ * sizeof(RawSeqData));
+        auto res = mapping_.find_ks((const char*)key, key_size_);
         if (res == mapping_.end())
             return nullptr;
 
@@ -143,6 +144,7 @@ class KMerMap {
   private:
     unsigned k_;
     unsigned rawcnt_;
+    unsigned key_size_;
     HTMap mapping_;
 };
 

diff --git a/src/common/alignment/kmer_mapper.hpp b/src/common/alignment/kmer_mapper.hpp
@@ -31,19 +31,17 @@ class KmerMapper : public omnigraph::GraphActionHandler<Graph> {
     KMerMap mapping_;
     bool normalized_;
 
-    bool CheckAllDifferent(const Sequence &old_s, const Sequence &new_s) const {
-        std::set<Kmer> kmers;
-        Kmer kmer = old_s.start<Kmer>(k_) >> 0;
-        for (size_t i = k_ - 1; i < old_s.size(); ++i) {
-            kmer <<= old_s[i];
-            kmers.insert(kmer);
-        }
-        kmer = new_s.start<Kmer>(k_) >> 0;
-        for (size_t i = k_ - 1; i < new_s.size(); ++i) {
-            kmer <<= new_s[i];
-            kmers.insert(kmer);
+    const RawSeqData* GetRoot(const Kmer &kmer) const {
+        const RawSeqData *answer = nullptr;
+        const RawSeqData *rawval = mapping_.find(kmer);
+
+        while (rawval != nullptr) {
+            Seq val(k_, rawval);
+
+            answer = rawval;
+            rawval = mapping_.find(val);
         }
-        return kmers.size() == old_s.size() - k_ + 1 + new_s.size() - k_ + 1;
+        return answer;
     }
 
 public:
@@ -150,20 +148,6 @@ class KmerMapper : public omnigraph::GraphActionHandler<Graph> {
         RemapKmers(this->g().EdgeNucls(edge1), this->g().EdgeNucls(edge2));
     }
 
-    const RawSeqData* GetRoot(const Kmer &kmer) const {
-        const RawSeqData *answer = nullptr;
-        const RawSeqData *rawval = mapping_.find(kmer);
-
-        while (rawval != nullptr) {
-            Seq val(k_, rawval);
-
-            answer = rawval;
-            rawval = mapping_.find(val);
-        }
-        return answer;
-    }
-
-
     Kmer Substitute(const Kmer &kmer) const {
         VERIFY(this->IsAttached());
         const auto *rawval = mapping_.find(kmer);