From e78f34fb4959f74eca2827a22ecec124eb25f283 Mon Sep 17 00:00:00 2001
From: Guruprasad Anada <gua110@bx.psu.edu>
Date: Mon, 6 Oct 2008 09:33:52 -0400
Subject: [PATCH] Modified help message for indel rate tool.

---
 tools/regVariation/getIndelRates_3way.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/regVariation/getIndelRates_3way.xml b/tools/regVariation/getIndelRates_3way.xml
index 956d3e87686..8f4fe3126ec 100644
--- a/tools/regVariation/getIndelRates_3way.xml
+++ b/tools/regVariation/getIndelRates_3way.xml
@@ -14,8 +14,8 @@
         
         <conditional name="region">
           <param name="type" type="select" label="Estimate rates corresponding to" multiple="false">
-            <option value="align" selected="True">Alignment block</option>
-            <option value="win">Intervals in your history</option>
+            <option value="win" selected="True">Intervals in your history</option>
+            <option value="align">Alignment block</option>
          </param>
          <when value="win">
             <param format="interval" name="input2" type="data" label="Choose intervals">
@@ -45,8 +45,8 @@
 
 **What it does**
 
-This tool estimates the insertion and deletion rates for alignments in a window of specified size. 
-
+This tool estimates the insertion and deletion rates for alignments in a window of specified size. Rates are computed over the total adjusted lengths (adjusted by disregarding masked bases) of all the alignments blocks from the indel file that fall within that window.
+  
 -----
 
 .. class:: warningmark