add bam clone options

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>