finished the chimera.slayer split function

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index eae6acf4e20b717d5327722ec22085fa96ecc0af..eb00b59a324e5ef93850fa2a0aa16e1a0216a9dc 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -510,15 +510,15 @@ Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc, data_results leftP
                                                        for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
                                                }else { //both sides are chimeric, keep longest piece
                                                        
-                                                       int lengthLeftLeft = leftPiece.spotMap[leftPiece.results[0].winLStart] - leftPiece.spotMap[leftPiece.results[0].winLEnd];
-                                                       int lengthLeftRight = leftPiece.spotMap[leftPiece.results[0].winRStart] - leftPiece.spotMap[leftPiece.results[0].winREnd];
+                                                       int lengthLeftLeft = leftPiece.spotMap[leftPiece.results[0].winLEnd] - leftPiece.spotMap[leftPiece.results[0].winLStart];
+                                                       int lengthLeftRight = leftPiece.spotMap[leftPiece.results[0].winREnd] - leftPiece.spotMap[leftPiece.results[0].winRStart];
                                                        
                                                        int longest = 1; // leftleft = 1, leftright = 2, rightleft = 3 rightright = 4
                                                        int length = lengthLeftLeft;
                                                        if (lengthLeftLeft < lengthLeftRight) { longest = 2;  length = lengthLeftRight; }
                                                        
-                                                       int lengthRightLeft = rightPiece.spotMap[rightPiece.results[0].winLStart] - rightPiece.spotMap[rightPiece.results[0].winLEnd];
-                                                       int lengthRightRight = rightPiece.spotMap[rightPiece.results[0].winRStart] - rightPiece.spotMap[rightPiece.results[0].winREnd];
+                                                       int lengthRightLeft = rightPiece.spotMap[rightPiece.results[0].winLEnd] - rightPiece.spotMap[rightPiece.results[0].winLStart];
+                                                       int lengthRightRight = rightPiece.spotMap[rightPiece.results[0].winREnd] - rightPiece.spotMap[rightPiece.results[0].winRStart];
                                                        
                                                        if (lengthRightLeft > length) { longest = 3; length = lengthRightLeft;  }
                                                        if (lengthRightRight > length) { longest = 4; }
@@ -626,15 +626,15 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results lef
                                                        for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
                                                }else { //both sides are chimeric, keep longest piece
                                                        
-                                                       int lengthLeftLeft = leftPiece.spotMap[leftPiece.results[0].winLStart] - leftPiece.spotMap[leftPiece.results[0].winLEnd];
-                                                       int lengthLeftRight = leftPiece.spotMap[leftPiece.results[0].winRStart] - leftPiece.spotMap[leftPiece.results[0].winREnd];
+                                                       int lengthLeftLeft = leftPiece.spotMap[leftPiece.results[0].winLEnd] - leftPiece.spotMap[leftPiece.results[0].winLStart];
+                                                       int lengthLeftRight = leftPiece.spotMap[leftPiece.results[0].winREnd] - leftPiece.spotMap[leftPiece.results[0].winRStart];
                                                        
                                                        int longest = 1; // leftleft = 1, leftright = 2, rightleft = 3 rightright = 4
                                                        int length = lengthLeftLeft;
                                                        if (lengthLeftLeft < lengthLeftRight) { longest = 2;  length = lengthLeftRight; }
                                                        
-                                                       int lengthRightLeft = rightPiece.spotMap[rightPiece.results[0].winLStart] - rightPiece.spotMap[rightPiece.results[0].winLEnd];
-                                                       int lengthRightRight = rightPiece.spotMap[rightPiece.results[0].winRStart] - rightPiece.spotMap[rightPiece.results[0].winREnd];
+                                                       int lengthRightLeft = rightPiece.spotMap[rightPiece.results[0].winLEnd] - rightPiece.spotMap[rightPiece.results[0].winLStart];
+                                                       int lengthRightRight = rightPiece.spotMap[rightPiece.results[0].winREnd] - rightPiece.spotMap[rightPiece.results[0].winRStart];
                                                        
                                                        if (lengthRightLeft > length) { longest = 3; length = lengthRightLeft;  }
                                                        if (lengthRightRight > length) { longest = 4; }