Updates to documentation.

AUTHORS

@@ -1,3 +1,4 @@
-Daniel Mapleson <daniel.mapleson@tgac.ac.uk>
-Luca Venturini <luca.venturini@tgac.ac.uk>
-David Swarbreck <david.swarbreck@tgac.ac.uk>
+Daniel Mapleson <daniel.mapleson@earlham.ac.uk>
+David Swarbreck <david.swarbreck@earlham.ac.uk>
+Luca Venturini <luca.venturini@earlham.ac.uk>
+

configure.ac

@@ -4,7 +4,7 @@
 
 # Autoconf setup
 AC_PREREQ([2.68])
-AC_INIT([portcullis],[0.17.2],[daniel.mapleson@tgac.ac.uk],[portcullis],[http://www.tgac.ac.uk])
+AC_INIT([portcullis],[0.17.3],[daniel.mapleson@tgac.ac.uk],[portcullis],[http://www.tgac.ac.uk])
 AC_CONFIG_SRCDIR([src/portcullis.cc])
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CONFIG_MACRO_DIR([m4])

doc/source/conf.py

@@ -53,9 +53,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.17.2'
+version = '0.17.3'
 # The full version, including alpha/beta/rc tags.
-release = '0.17.2'
+release = '0.17.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/installation.rst

@@ -4,14 +4,14 @@ Installation
 ============
 
 Portcullis is primarily a C++ application with some python scripts.  We use the 
-GNU build system ``Autotools`` to assist with package management and to make the 
+GNU build system *Autotools* to assist with package management and to make the 
 software portable across UNIX type operating systems.  Installation of portcullis
 therefore follows a similar incantation to other autotools based projects::
 
-  ```./configure; make; sudo make install;```
+  ./configure && make && sudo make install
 
 However, there are a few caveats.  If you cloned the software directly from the 
-git repository you must first run "./autogen.sh" to create the configure and make 
+git repository you must first run ``./autogen.sh`` to create the configure and make 
 files for your project.  If you downloaded a source code distribution tarball those
 scripts are already present so you can skip this step.
 
@@ -32,48 +32,48 @@ guide separately for instructions on how to do this.  Should you install these d
 into non-standard locations you can direct portcullis to them by using the following
 options when running the configure script.
 
-  - ```--with-boost``` - for specifying a custom boost installation directory
-  - ```--with-zlib``` - for specifying a custom zlib installation directory
+  - ``--with-boost`` - for specifying a custom boost installation directory
+  - ``--with-zlib`` - for specifying a custom zlib installation directory
 
-Note there is not option for specifying a custom pthreads or samtools location.  
-We assume pthreads is correctly installed and configured for your system already.  In most cases
-it will be.  For samtools, we just require the executable to be on the path.
+Note there is not option for specifying a custom *pthreads* or *samtools* location.  
+We assume *pthreads* is correctly installed and configured for your system already.  In most cases
+it will be.  For *samtools*, we just require the executable to be on the path.
 
-If the user has sphinx installed then documentation will also be built along with
-the software.  If sphinx is not detected then the documentation building stage is
+If the user has *sphinx* installed then documentation will also be built along with
+the software.  If *sphinx* is not detected then the documentation building stage is
 skipped and documentation won't be available locally, although it can still be 
 found at: https://portcullis.readthedocs.org/en/latest/
 
-Boost is statically linked and doesn't need to be available at runtime.  zlib and pthreads are 
-dynamically linked so will need to be on your LD_LIBRARY_PATH,
+Boost is statically linked and doesn't need to be available at runtime.  *zlib* and *pthreads* are 
+dynamically linked so will need to be on your ``LD_LIBRARY_PATH``,
 or in one of the automatically searched lib directories in order for portcullis 
 to dynamically link them at runtime.  No other non-system libraries need linking at runtime.
 
 
 Internal Dependencies
 ---------------------
 
-Portcullis contains HTSlib and Ranger (a random forest implementation)  in the source tree.  The user does
-not need to do anything special to handle htslib and ranger as these are automatically
+Portcullis contains *HTSlib* and *Ranger* (a random forest implementation)  in the source tree.  The user does
+not need to do anything special to handle *htslib* and *ranger* as these are automatically
 built and managed inside portcullis.
 
 
 Compilation and Installation
 ----------------------------
 
-First change into the portcullis root directory and run ```./configure```, providing
-any options you feel are appropriate.  By default the installation directory is "/usr/local", 
+First change into the portcullis root directory and run ``./configure``, providing
+any options you feel are appropriate.  By default the installation directory is ``/usr/local``, 
 so the portcullis executable would be found at "/usr/local/bin" by default.  If you
 want to change this use the ``--prefix`` option as previously described.  For a full
-list of configuration options type ```./configure --help```.
+list of configuration options type ``./configure --help``.
 
-Next compile the software.  This can be done by typing ```make```.  The compiles
+Next compile the software.  This can be done by typing ``make``.  The compiles
 all internal dependencies and portcullis itself.
 
 To check the code compiled correct and is operating as expected you can optionally
-type  ```make check``` to runs some tests.  This includes unit tests for HTSlib, 
+type  ``make check`` to runs some tests.  This includes unit tests for HTSlib, 
 which are embedded in the portcullis source tree.  To run only portcullis 
-unit tests go into the ``tests`` subdirectory and run ```make check``` there.
+unit tests go into the ``tests`` subdirectory and run ``make check`` there.
 
 Finally to install the compiled code to the specified (or default) installation
-directory type ```make install```.
+directory type ``make install``.

doc/source/quickstart.rst

@@ -3,7 +3,7 @@
 Quickstart
 ==========
 
-For the impatient, just use ```portcullis full -t <threads> <genome> (<bam>)+``` 
+For the impatient, just use ``portcullis full -t <threads> <genome> (<bam>)+`` 
 to get up and running.  This runs the following subtools in order:
 
 * Prepare

doc/source/using.rst

@@ -4,9 +4,9 @@ Using Portcullis
 ================
 
 Portcullis is a C++11 program containing a number of subtools which can be used in
-isolation or as part of a pipeline.  Typing ```portcullis --help``` will show a
+isolation or as part of a pipeline.  Typing ``portcullis --help`` will show a
 list of the available subtools.  Each subtool has its own help system which you 
-can access by typing ```portcullis <subtool> --help```.  
+can access by typing ``portcullis <subtool> --help``.  
 
 The list of subtools present in portcullis are listed below in order.  A more detailed
 description of each subtool follows in the subsequent sections:
@@ -151,8 +151,8 @@ for deriving a custom filter profile.  The rules can be combined
 using logic operations (and / or / not, etc) and applied to the full set of input 
 junctions.
 
-Here's an example set of rules that must all be satisfied to pass this filter:
-::
+Here's an example set of rules that must all be satisfied to pass this filter::
+
     {
             "parameters": {
                     "M4-nb_rel_aln": {