fixing anchor coordinates for clasp in fine search mode

vpc-ccg · Dec 18, 2017 · af1f537 · af1f537
1 parent 90db963
commit af1f537
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Showing 2 changed files with 17 additions and 1 deletion.
diff --git a/src/Clasp.cpp b/src/Clasp.cpp
@@ -41,7 +41,7 @@ int clasp_chain_seed_best(Seed_t *fragment_list, uint32_t nFragment, Chain_t &be
 	char chainmode = SOP;
 	// char chainmode = LIN;
 	// double lambda = 0.5;
-	double lambda = 0.2;
+	double lambda = 0.15;
 	double epsilon = 0;
 	double minscore = 0;
 	int maxgap = -1;

diff --git a/src/LordFAST.cpp b/src/LordFAST.cpp
@@ -480,8 +480,16 @@ float calcChainScore(uint32_t rLen, uint32_t tStart, uint32_t tEnd, int isRevers
 			}
 		}
 
+        if(seedPos_Low > 2000000000)
+            for(i = 0; i < _pf_seedsSelected[id].num; i++)
+                _pf_seedsSelected[id].list[i].tPos -= 2000000000;
+
 		clasp_chain_seed_best(_pf_seedsSelected[id].list, _pf_seedsSelected[id].num, _pf_topChains[id].list[0]);
 		retScore = _pf_topChains[id].list[0].score;
+
+		if(seedPos_Low > 2000000000)
+			for(i = 0; i < _pf_topChains[id].list[0].chainLen; i++)
+				_pf_topChains[id].list[0].seeds[i].tPos += 2000000000;
 	}
 	else
 	{
@@ -494,8 +502,16 @@ float calcChainScore(uint32_t rLen, uint32_t tStart, uint32_t tEnd, int isRevers
 			}
 		}
 
+        if(seedPos_Low > 2000000000)
+            for(i = 0; i < _pf_seedsSelected[id].num; i++)
+                _pf_seedsSelected[id].list[i].tPos -= 2000000000;
+
 		clasp_chain_seed_best(_pf_seedsSelected[id].list, _pf_seedsSelected[id].num, _pf_topChains[id].list[0]);
 		retScore = _pf_topChains[id].list[0].score;
+
+		if(seedPos_Low > 2000000000)
+			for(i = 0; i < _pf_topChains[id].list[0].chainLen; i++)
+				_pf_topChains[id].list[0].seeds[i].tPos += 2000000000;
 	}
 	return retScore;
 }