update

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15308 ee4ac58c-ac51-4696-9907-e4b3aa274f04

docs/jvm_options.sgml

@@ -44,6 +44,24 @@ using these file types).
       </PARA>
     </SECT2>
 
+    <SECT2 ID="JVM-CHADO">
+       <TITLE><LITERAL>-Dchado="hostname:port/database?username"</LITERAL></TITLE>
+      <PARA>
+This is used to get &prog; to look for the database. The address of the database
+(hostname, port and name) can be conveniently included
+(e.g. -Dchado="genedb-db.sanger.ac.uk:5432/snapshot?genedb_ro") and
+these details are then the default database address in the popup login window. 
+      </PARA>
+    </SECT2>
+
+    <SECT2 ID="JVM-CHADO-READONLY">
+       <TITLE><LITERAL>-Dread_only</LITERAL></TITLE>
+      <PARA>
+For a read only chado connection -Dread_only is specified on the command line
+(e.g. art -Dchado="genedb-db.sanger.ac.uk:5432/snapshot?genedb_ro" -Dread_only).
+      </PARA>
+    </SECT2>
+
     <SECT2 ID="JVM-FWD-LINES">
        <TITLE><LITERAL>-Dshow_forward_lines=false</LITERAL></TITLE>
       <PARA>

docs/next_gen.sgml

   <SECT2 ID="FILEMENU-READ-BAM">
     <TITLE>Read BAM / VCF ...</TITLE>
      <PARA>
-Read a BAM file that has been sorted and indexed using <ULINK
-URL="http://samtools.sourceforge.net/">samtools</ULINK>. This provides an integrated
-<ULINK URL="http://bamview.sourceforge.net/">BamView</ULINK> panel displaying
-sequence alignment mappings to a reference sequence. This require Artemis to
-be run with Java 1.6 as it makes use of <ULINK URL="http://picard.sourceforge.net/">
-picard</ULINK> to read from the BAM file.
+&prog; can read in and visualise BAM, VCF and BCF files. These files need
+to be indexed as described below. They require &prog; to be run with at least
+Java 1.6.
+     </PARA>
+     <PARA>
+BAM files need to be sorted and indexed using <ULINK
+URL="http://samtools.sourceforge.net/">samtools</ULINK>. The index file should be in
+the same directory as the BAM file. This provides an integrated
+<ULINK URL="http://bamview.sourceforge.net/">BamView</ULINK> panel in &prog;, displaying
+sequence alignment mappings to a reference sequence. Multiple BAM files can be loaded
+in from here either by selecting each file individually or by selecting a file of
+path names to the BAM files.
       </PARA>
       <PARA>
 Variant Call Format (<ULINK