update

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15307 ee4ac58c-ac51-4696-9907-e4b3aa274f04

docs/jvm_options.sgml

+    <SECT2 ID="JVMOPTS-MEM">
+      <TITLE><LITERAL>-Xmsn -Xmxn</LITERAL></TITLE>
+      <PARA>
+Use <LITERAL>-Xmsn</LITERAL> to specify the initial size, in bytes, of the
+memory allocation pool. This value must be a multiple of 1024 greater than
+1MB. Append the letter k or K to indicate kilobytes, or m or M to indicate
+megabytes.
+      </PARA>
+      <PARA>
+Use <LITERAL>-Xmxn</LITERAL> to specify the maximum size, in bytes, of the
+memory allocation pool. This value must a multiple of 1024 greater than
+2MB. Append the letter k or K to indicate kilobytes, or m or M to indicate
+megabytes.
+      </PARA>
+    </SECT2>
+
+    <SECT2 ID="BB-MODE">
+       <TITLE><LITERAL>-Dblack_belt_mode=false</LITERAL></TITLE>
+      <PARA>
+If this is set to false then warning messages are kept to a minimum.
+      </PARA>
+    </SECT2>
+
+    <SECT2 ID="JVM-OFFSET">
+       <TITLE><LITERAL>-Doffset=10000</LITERAL></TITLE>
+      <PARA>
+This sets the base position that &prog; opens at, e.g. 10000.
+      </PARA>
+    </SECT2>
+
+    <SECT2 ID="JVM-USERPLOT">
+       <TITLE><LITERAL>-Duserplot=pathToFile</LITERAL></TITLE>
+      <PARA>
+This can be used to open userplots from the command line. The paths are comma
+separated to open multiple plots (-Duserplot=-Duserplot='/pathToFile/userPlot1,/pathToFile/userPlot2').
+      </PARA>
+    </SECT2>
+
+    <SECT2 ID="JVM-NG">
+       <TITLE><LITERAL>-Dbam=pathToFile</LITERAL></TITLE>
+      <PARA>
+This can be used to open BAM files or VCF/BCF files (see <XREF LINKEND="FILEMENU-READ-BAM"> for more about the
+using these file types).
+      </PARA>
+    </SECT2>
+
+    <SECT2 ID="JVM-FWD-LINES">
+       <TITLE><LITERAL>-Dshow_forward_lines=false</LITERAL></TITLE>
+      <PARA>
+Hide/show forward frame lines.
+      </PARA>
+    </SECT2>
+
+    <SECT2 ID="JVM-BWD-LINES">
+       <TITLE><LITERAL>-Dshow_reverse_lines=false</LITERAL></TITLE>
+      <PARA>
+Hide/show reverse frame lines.
+      </PARA>
+    </SECT2>

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.
+      </PARA>
+      <PARA>
+Variant Call Format (<ULINK
+URL="http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0">VCF</ULINK>)
+files can also be read. The VCF files need to be compressed and indexed using bgzip and
+tabix respectively (see the <ULINK URL="http://samtools.sourceforge.net/tabix.shtml">tabix manual</ULINK> and
+<ULINK URL="http://sourceforge.net/projects/samtools/files/">download page</ULINK>).
+The compressed file gets read in (e.g. file.vcf.gz) and below are the commands for
+generating this from a VCF file:
+        </PARA>
+        <SYNOPSIS>
+        bgzip file.vcf
+        tabix -p vcf file.vcf.gz
+        </SYNOPSIS>
+      <PARA>
+Alternatively a Binary VCF (<ULINK URL="http://samtools.sourceforge.net/mpileup.shtml">BCF</ULINK>) can
+be indexed with BCFtools and read into Artemis or ACT.
+      </PARA>
+        <PARA>
+As with reading in multiple BAM files, it is possible to read a number of (compressed and indexed)
+VCF files by listing their full paths in a single file. They then get displayed in separate rows
+in the VCF panel.
+        </PARA>
+        <MEDIAOBJECT>
+        <IMAGEOBJECT>
+           <IMAGEDATA FORMAT="png" FILEREF="vcf.png"></IMAGEOBJECT>
+        </MEDIAOBJECT>
+        <PARA>
+For single base changes the colour represents the base it is being changed to, i.e. T black,
+G blue, A green, C red. There are options available to filter the display by the different
+types of variants. Right clicking on the VCF panel will display a pop-up menu in which
+there is a 'Filter...' menu. This opens a window with check boxes for a number of varaint types and properties that can
+be used to filter on. This can be used to show and hide synonymous, non-synonymous, deletion (grey),
+insertion (yellow), and multiple allele (orange line with a circle at the top)
+variants.  In this window there is a check box to hide the variants that do not overlap CDS features.
+There is an option to mark variants that introduce stop codons (into the CDS
+features) with a circle in the middle of the line that represents the variant. There are also options
+to filter the variants by various properties such as their quality score (QUAL) or their depth across the
+samples (DP).
+        </PARA>
+        <PARA>
+Placing the mouse over a vertical line shows an overview  of the variation as a
+tooltip. Also right clicking over a line then gives an extra option in the pop-up
+menu to show the details for that variation in a separate window. There are also
+alternative colouring schemes. It is possible to colour the variants by whether they are
+synonymous or non-synonymous or by their quality score (the lower the quality the
+more faded the variant appears).
+        </PARA>
+  </SECT2>
+