* ParseAligns/ParseAligns.cpp (handleAlignmentPair): when writing the

paired alignment for alignments to the same contigs, write the alignment and swapped alignment. git-svn-id: https://svn.bcgsc.ca/svn/abyss/trunk@49766 ad02020f-2a26-4133-947e-1829317c1416
bcgsc · Mar 19, 2012 · 5d9cef2 · 5d9cef2
1 parent ac20cd7
commit 5d9cef2
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/ParseAligns/ParseAligns.cpp b/ParseAligns/ParseAligns.cpp
@@ -301,7 +301,9 @@ static void handleAlignmentPair(ReadAlignMap::const_iterator iter,
 						// Print the alignment
 						pairedAlignFile
 							<< currID << ' ' << a0 << ' '
-							<< pairID << ' ' << a1 << '\n';
+							<< pairID << ' ' << a1 << '\n'
+							<< pairID << ' ' << a1 << ' '
+							<< currID << ' ' << a0 << '\n';
 						assert(pairedAlignFile.good());
 					}
 				} else {