From 511948890a4b72f7a9a6c33579f2c66555c46ae6 Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Thu, 26 Sep 2013 14:50:32 -0400
Subject: [PATCH] Modify gatkdoc template to handle downsampling info better

---
 settings/helpTemplates/generic.template.html | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/settings/helpTemplates/generic.template.html b/settings/helpTemplates/generic.template.html
index 098d294cb..b78bba48c 100644
--- a/settings/helpTemplates/generic.template.html
+++ b/settings/helpTemplates/generic.template.html
@@ -174,11 +174,16 @@
 		</#if>
 		<#if downsampling?size != 0>
 			<h3>Downsampling settings</h3>
-			<p>This tool overrides the engine's default downsampling settings.</p>
-			<ul>
-				<li>Mode: <b>${downsampling.by}</b></li>
-				<li>To coverage: <b>${downsampling.to_cov}</b></li>
-			</ul>
+			<#if downsampling.by == "NONE">
+				<p>This tool does not apply any downsampling by default.</p>
+			</#if>
+			<#if downsampling.by != "NONE">
+				<p>This tool applies the following downsampling settings by default.</p>
+				<ul>
+					<li>Mode: <b>${downsampling.by}</b></li>
+					<li>To coverage: <b>${downsampling.to_cov}</b></li>
+				</ul>
+			</#if>
 		</#if>
 		<#if refwindow?size != 0>
 			<h3>Window size</h3>