From 5fe4dd5af1afc25c3143d5432b4f3ea01c2d7384 Mon Sep 17 00:00:00 2001
From: tcarver <tjc@sanger.ac.uk>
Date: Wed, 29 Jan 2014 15:59:15 +0000
Subject: [PATCH] add options
---
docs/jvm_options.sgml | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/docs/jvm_options.sgml b/docs/jvm_options.sgml
index 242ae1fa2..65dde4285 100644
--- a/docs/jvm_options.sgml
+++ b/docs/jvm_options.sgml
@@ -99,6 +99,29 @@ first (top) sequence in ACT:
</SECT2>
]]>
+ <SECT2 ID="JVM-SHOW-SNPS">
+ <TITLE><LITERAL>-Dshow_snps</LITERAL></TITLE>
+ <PARA>
+Show SNP marks in BAM panels.
+</PARA>
+ </SECT2>
+
+ <SECT2 ID="JVM-SHOW-SNPS-PLOT">
+ <TITLE><LITERAL>-Dshow_snp_plot</LITERAL></TITLE>
+ <PARA>
+Automatically open SNP plots for BAM files that are opened.
+</PARA>
+ </SECT2>
+
+
+ <SECT2 ID="JVM-SHOW-COV-PLOT">
+ <TITLE><LITERAL>-Dshow_cov_plot</LITERAL></TITLE>
+ <PARA>
+Automatically open coverage plots for BAM files that are opened.
+</PARA>
+ </SECT2>
+
+
<SECT2 ID="JVM-CHADO">
<TITLE><LITERAL>-Dchado="hostname:port/database?username"</LITERAL></TITLE>
<PARA>
--
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