X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.cpp;h=eb00b59a324e5ef93850fa2a0aa16e1a0216a9dc;hb=41f3f520282eb972d450ac6d23a0e80c546aa76e;hp=eae6acf4e20b717d5327722ec22085fa96ecc0af;hpb=002421a439168e2610a2b62f1318f21c7202fe6d;p=mothur.git

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index eae6acf..eb00b59 100644
--- 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; }