update

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15306 ee4ac58c-ac51-4696-9907-e4b3aa274f04

docs/act_file_menu.sgml

@@ -142,7 +142,7 @@ LINKEND="GRAPHMENU-USAGE-PLOTS"> to find out how to plot a usage graph).
     </SECT3>
   </SECT2>
 
-
+  &nextgen;
 
   <SECT2 ID="FILEMENU-EDIT-IN-ARTEMIS">
     <TITLE>Edit In Artemis ...</TITLE>

docs/act_manual.sgml

@@ -20,7 +20,9 @@
 <!ENTITY mousebuttons SYSTEM "mousebuttons.sgml">
 <!ENTITY gettingjava SYSTEM "getting_java.sgml">
 <!ENTITY unixargs SYSTEM "unix_args.sgml">
+<!ENTITY jvmopts SYSTEM "jvm_options.sgml">
 <!ENTITY options-menu SYSTEM "options_menu.sgml">
+<!ENTITY nextgen SYSTEM "next_gen.sgml">
 
 <!ENTITY % artemis-only "IGNORE">
 

docs/file_menu.sgml

@@ -71,64 +71,7 @@ the user.
     </PARA>
   </SECT2>
 
-  <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>
+  &nextgen;
 
   <SECT2 ID="FILEMENU-SAVE-DEFAULT-ENTRY">
     <TITLE>Save Default Entry</TITLE>

docs/manual.sgml

@@ -21,7 +21,9 @@
 <!ENTITY mousebuttons SYSTEM "mousebuttons.sgml">
 <!ENTITY gettingjava SYSTEM "getting_java.sgml">
 <!ENTITY unixargs SYSTEM "unix_args.sgml">
+<!ENTITY jvmopts SYSTEM "jvm_options.sgml">
 <!ENTITY options-menu SYSTEM "options_menu.sgml">
+<!ENTITY nextgen SYSTEM "next_gen.sgml">
 
 <!ENTITY % artemis-only "INCLUDE">
 

docs/requirements.sgml

@@ -4,7 +4,7 @@
 &prog; will run on any machine that has a recent version of Java.
 This version of &prog; requires Java 1.5 at least. Most of the
 development has been done using JDK v1.6 and some of the more 
-advanced features (BamView) now require 1.6. 
+advanced features (BamView and VCF/BCF View) now require 1.6. 
 Please note that the version of Java that comes with Netscape and
 Internet Explorer is not sufficient to run &prog;.  See <XREF
 LINKEND="INSTALLATION"> for details on how to get Java.

docs/unix_args.sgml

@@ -26,21 +26,6 @@ read <LITERAL>new_options</LITERAL> in the current directory as an options
 file.
       </PARA>
     </SECT2>
-
-    <SECT2 ID="UNIXARGS-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>
+     &jvmopts;
 
   </SECT1>