# HG changeset patch
# User Chris Cannam
# Date 1416503865 0
# Node ID 5882462fa747c2b40a7ef6e16220760d54ed7e80
# Parent  d044682967ca24bf50275c5237163edb94887c85
Seems more logical for the external alignment program to emit reference,other rather than other,reference

diff -r d044682967ca -r 5882462fa747 framework/Align.cpp
--- a/framework/Align.cpp	Thu Nov 20 16:18:17 2014 +0000
+++ b/framework/Align.cpp	Thu Nov 20 17:17:45 2014 +0000
@@ -202,8 +202,14 @@
 	format.setTimingType(CSVFormat::ExplicitTiming);
 	format.setTimeUnits(CSVFormat::TimeSeconds);
 	format.setColumnCount(2);
-	format.setColumnPurpose(0, CSVFormat::ColumnStartTime);
-	format.setColumnPurpose(1, CSVFormat::ColumnValue);
+        // The output format has time in the reference file first, and
+        // time in the "other" file in the second column. This is a
+        // more natural approach for a command-line alignment tool,
+        // but it's the opposite of what we expect for native
+        // alignment paths, which map from "other" file to
+        // reference. These column purpose settings reflect that.
+	format.setColumnPurpose(1, CSVFormat::ColumnStartTime);
+	format.setColumnPurpose(0, CSVFormat::ColumnValue);
 	format.setAllowQuoting(false);
 	format.setSeparator(',');