remove unused block coordinate info

waveygang · Sep 15, 2024 · c7c171e · c7c171e
1 parent 90fe5b6
commit c7c171e
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Showing 3 changed files with 10 additions and 31 deletions.
diff --git a/src/map/include/base_types.hpp b/src/map/include/base_types.hpp
@@ -157,10 +157,6 @@ namespace skch
     seqno_t refSeqId;                                   //internal sequence id of the reference contig
     seqno_t querySeqId;                                 //internal sequence id of the query sequence
     offset_t blockLength;                                    //the block length of the mapping
-    offset_t blockRefStartPos;
-    offset_t blockRefEndPos;
-    offset_t blockQueryStartPos;
-    offset_t blockQueryEndPos;
     float blockNucIdentity;
 
     float nucIdentity;                                  //calculated identity

diff --git a/src/map/include/computeMap.hpp b/src/map/include/computeMap.hpp
@@ -462,17 +462,6 @@ namespace skch
               readMappings.end());
       }
 
-      void setBlockCoordsToMappingCoords(MappingResultsVector_t &readMappings) {
-          for (auto& m : readMappings) {
-              m.blockRefStartPos = m.refStartPos;
-              m.blockRefEndPos = m.refEndPos;
-              m.blockQueryStartPos = m.queryStartPos;
-              m.blockQueryEndPos = m.queryEndPos;
-              m.blockLength = std::max(m.blockRefEndPos - m.blockRefStartPos, m.blockQueryEndPos - m.blockQueryStartPos);
-              m.blockNucIdentity = m.nucIdentity;
-          }
-      }
-
       /**
        * @brief               helper to main mapping function
        * @details             filters mappings whose identity and query/ref length don't agree
@@ -485,8 +474,8 @@ namespace skch
               std::remove_if(readMappings.begin(),
                              readMappings.end(),
                              [&](MappingResult &e){
-                                 int64_t q_l = (int64_t)e.blockQueryEndPos - (int64_t)e.blockQueryStartPos;
-                                 int64_t r_l = (int64_t)e.blockRefEndPos - (int64_t)e.blockRefStartPos;
+                                 int64_t q_l = (int64_t)e.queryEndPos - (int64_t)e.queryStartPos;
+                                 int64_t r_l = (int64_t)e.refEndPos - (int64_t)e.refStartPos;
                                  uint64_t delta = std::abs(r_l - q_l);
                                  double len_id_bound = (1.0 - (double)delta/(((double)q_l+r_l)/2));
                                  return len_id_bound < std::min(0.7, std::pow(param.percentageIdentity,3));
@@ -770,8 +759,6 @@ namespace skch
        */
       void filterNonMergedMappings(MappingResultsVector_t &readMappings, const Parameters& param)
       {
-          setBlockCoordsToMappingCoords(readMappings);
-
           if (param.filterMode == filter::MAP || param.filterMode == filter::ONETOONE) {
               MappingResultsVector_t filteredMappings;
               filterByGroup(readMappings, filteredMappings, param.numMappingsForSegment - 1, false);
@@ -1800,10 +1787,6 @@ namespace skch
           for (auto it = begin; it != end; ++it) {
               it->n_merged = n_in_full_chain;
               it->blockLength = block_length;
-              it->blockQueryStartPos = chain_start_query;
-              it->blockQueryEndPos = chain_end_query;
-              it->blockRefStartPos = chain_start_ref;
-              it->blockRefEndPos = chain_end_ref;
               it->blockNucIdentity = chain_nuc_identity;
           }
       }

diff --git a/src/map/include/filter.hpp b/src/map/include/filter.hpp
@@ -70,11 +70,11 @@ namespace skch
 
         // compute the overlap of the two mappings
         double get_overlap(const int x, const int y) const {
-            offset_t overlap_start = std::max(vec[x].blockQueryStartPos, vec[y].blockQueryStartPos);
-            offset_t overlap_end = std::min(vec[x].blockQueryEndPos, vec[y].blockQueryEndPos);
+            offset_t overlap_start = std::max(vec[x].queryStartPos, vec[y].queryStartPos);
+            offset_t overlap_end = std::min(vec[x].queryEndPos, vec[y].queryEndPos);
             offset_t overlap_length = std::max(0, static_cast<int>(overlap_end - overlap_start));
-            offset_t x_length = vec[x].blockQueryEndPos - vec[x].blockQueryStartPos;
-            offset_t y_length = vec[y].blockQueryEndPos - vec[y].blockQueryStartPos;
+            offset_t x_length = vec[x].queryEndPos - vec[x].queryStartPos;
+            offset_t y_length = vec[y].queryEndPos - vec[y].queryStartPos;
             return static_cast<double>(overlap_length) / std::min(x_length, y_length);
         }
 
@@ -343,11 +343,11 @@ namespace skch
 
         // compute the overlap of the two mappings
         double get_overlap(const int x, const int y) const {
-            offset_t overlap_start = std::max(vec[x].blockRefStartPos, vec[y].blockRefStartPos);
-            offset_t overlap_end = std::min(vec[x].blockRefEndPos, vec[y].blockRefEndPos);
+            offset_t overlap_start = std::max(vec[x].refStartPos, vec[y].refStartPos);
+            offset_t overlap_end = std::min(vec[x].refEndPos, vec[y].refEndPos);
             offset_t overlap_length = std::max(0, static_cast<int>(overlap_end - overlap_start));
-            offset_t x_length = vec[x].blockRefEndPos - vec[x].blockRefStartPos;
-            offset_t y_length = vec[y].blockRefEndPos - vec[y].blockRefStartPos;
+            offset_t x_length = vec[x].refEndPos - vec[x].refStartPos;
+            offset_t y_length = vec[y].refEndPos - vec[y].refStartPos;
             return static_cast<double>(overlap_length) / std::min(x_length, y_length);
         }