From 1899493ea9e82a317e23f9fb170438f3bb9d7d7d Mon Sep 17 00:00:00 2001
From: tcarver <tjc@sanger.ac.uk>
Date: Thu, 7 Feb 2013 16:09:56 +0000
Subject: [PATCH] add bam clone options
---
docs/jvm_options.sgml | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/docs/jvm_options.sgml b/docs/jvm_options.sgml
index 1ec9b2842..18ba2035d 100644
--- a/docs/jvm_options.sgml
+++ b/docs/jvm_options.sgml
@@ -52,6 +52,29 @@ using these file types). This can take a path name to a file or an HTTP address.
</PARA>
</SECT2>
+ <SECT2 ID="JVM-NG2">
+ <TITLE><LITERAL>-Dbam1=pathToFile1 -Dbam2=pathToFile2</LITERAL></TITLE>
+ <PARA>
+The following will open BAM files in separate panels (using -Dbam[1,2,3...]):
+ </PARA>
+ <PARA>
+<COMMAND>art -Dbam1=fileA.bam -Dbam2=fileB.bam</COMMAND>
+ </PARA>
+ </SECT2>
+
+ <SECT2 ID="JVM-NG3">
+ <TITLE><LITERAL>-DbamClone=n</LITERAL></TITLE>
+ <PARA>
+Multiple BAM panels can be opened using the bamClone flag this is used with the -Dbam flag:
+ </PARA>
+ <PARA>
+<COMMAND>art -Dbam='/pathToFile/file1.bam,/pathToFile/file2.bam' -DbamClone=n</COMMAND>
+ </PARA>
+ <PARA>
+(where n is an integer greater than 1). All BAM files are then shown in each panel.
+ </PARA>
+ </SECT2>
+
<SECT2 ID="JVM-CHADO">
<TITLE><LITERAL>-Dchado="hostname:port/database?username"</LITERAL></TITLE>
<PARA>
--
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