From 85df2b4a4e564cc77dc11ffce27d76d55db92694 Mon Sep 17 00:00:00 2001
From: nkindlon <nek3d@virginia.edu>
Date: Thu, 6 Feb 2014 11:20:22 -0500
Subject: [PATCH] Added -split option to map help.
---
src/mapFile/mapMain.cpp | 2 ++
1 file changed, 2 insertions(+)
diff --git a/src/mapFile/mapMain.cpp b/src/mapFile/mapMain.cpp
index fe87c9f3..a9eeb369 100644
--- a/src/mapFile/mapMain.cpp
+++ b/src/mapFile/mapMain.cpp
@@ -215,6 +215,8 @@ void map_help(void) {
cerr << "\t\tthat overlap A on the _opposite_ strand." << endl;
cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+ cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
+
cerr << "\t-g\t" << "Provide a genome file to enforce consistent chromosome sort order" << endl;
cerr <<"\t\tacross input files." << endl << endl;
--
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