added chimera.uchime

[mothur.git] / maligner.h

diff --git a/maligner.h b/maligner.h
index 3deacfe875eb6ed266dca8514109ea515f035fc9..4f5c949a45112ebed570f4f6df46cd60f1aeb23e 100644 (file)
--- a/maligner.h
+++ b/maligner.h
@@ -36,14 +36,14 @@ class Maligner {
                float minDivR, percentIdenticalQueryChimera;
                vector<results> outputResults;
                map<int, int> spotMap;
-               
+               vector<int> unalignedMap;
                vector<Sequence*> minCoverageFilter(vector<Sequence*>);  //removes top matches that do not have minimum coverage with query.
                int computeChimeraPenalty();
                void verticalFilter(vector<Sequence*>);
                
                vector< vector<score_struct> > buildScoreMatrix(int, int);
                void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence*>, int);
-               vector<trace_struct> extractHighestPath(vector<vector<score_struct> >);
+               vector<score_struct> extractHighestPath(vector<vector<score_struct> >);
                vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>, vector<Sequence*>);
                string constructChimericSeq(vector<trace_struct>, vector<Sequence*>);
                string constructAntiChimericSeq(vector<trace_struct>, vector<Sequence*>);