diff --git a/docs/act_file_menu.sgml b/docs/act_file_menu.sgml
index d7ad525a90b9f205e0d91036e355b96803b99d62..6a5b24de77eff30ab2eea08f51688a6bcffb4b03 100644
--- a/docs/act_file_menu.sgml
+++ b/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>
diff --git a/docs/act_manual.sgml b/docs/act_manual.sgml
index 516bd61f4601649a505cfc910f6505e74ecb0575..5a593ad9cf8e24ae7c0c60c42c16f35cfa03c25c 100644
--- a/docs/act_manual.sgml
+++ b/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">
diff --git a/docs/file_menu.sgml b/docs/file_menu.sgml
index 643848d9294c7ad460249989f12b1f217019781b..b5b66a3edb821cb0255e4369936218ed59f62340 100644
--- a/docs/file_menu.sgml
+++ b/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>
diff --git a/docs/manual.sgml b/docs/manual.sgml
index 985ea60b3fcae9cc69b06cc6424a315fb42ac7eb..f34969e83b7ad3b9cf3ebcbd52fd897536b9cb54 100644
--- a/docs/manual.sgml
+++ b/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">
diff --git a/docs/requirements.sgml b/docs/requirements.sgml
index 828bfb50d18ee0533cbac1222828ec62706f4502..1f8932449fc3162f8927398d5f4199b3bf444dcc 100644
--- a/docs/requirements.sgml
+++ b/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.
diff --git a/docs/unix_args.sgml b/docs/unix_args.sgml
index 2161da4974f8d2c24010af97098a55c1cb71bd3a..4b996dfa4ee599cf91a36ca1d0c99fe928fea9b2 100644
--- a/docs/unix_args.sgml
+++ b/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>