updated version number

new major version, 1.0.0, as I've made some backwards incompatible
changes. In particular the --removeHomopolymers option has been
removed, which means that crass will likely not work on 454 data anymore.

Author: ctSkennerton

README.md

@@ -1,4 +1,4 @@
-crass -- CRisprASSembler -- version 0 subversion 3 revision 12 (0.3.12)
+crass -- CRisprASSembler -- version 1 subversion 0 revision 0 (1.0.0)
 =======================================================================
 
 CITATION
@@ -13,6 +13,7 @@ COPYRIGHT
 ---------
 
 Copyright 2011-2015 Connor Skennerton & Michael Imelfort. All rights reserved. 
+Copyright 2016      Connor Skennerton. All rights reserved. 
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -36,7 +37,7 @@ at the following locations:
 
 [Boyer-Moore Search Algorithm](http://dev-faqs.blogspot.com/2010/05/boyer-moore-algorithm.html)
 
-[Wu-Manber Search Algorithm](http://www.oneunified.net/blog/2008/03/23/)
+[Aho-Corasick Search Algorithm](https://github.com/mischasan/aho-corasick)
 
 [Levensthein String Comparison Algorithm](http://www.merriampark.com/ldcpp.htm)
 
@@ -96,17 +97,3 @@ example:
 
     $ ./configure --enable-rendering LDFLAGS="-L/usr/home/user_name/local/lib/" CPPFLAGS="-I/usr/home/user_name/local/include/" 
 
-RUNNING CRASS
--------------
-
-crass has two executables:
-
-    $ crass [-bcdhklnoswxyDSV] [--removeHomopolymers] [--logToScreen] <sequence_files>
-
-which finds CRISPR containing reads
-
-    $ crass-assemble [--velvet | --cap3] -x <file.crispr> -s <segments> -g <group> -i <input directory> [-o]
-
-which is a wrapper for genome assemblers to assemble particular branches in a spacer graph 
-
-

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.61)
-AC_INIT(crass, 0.3.12, c.skennerton@gmail.com)
+AC_INIT(crass, 1.0.0, c.skennerton@gmail.com)
 
 AC_CONFIG_AUX_DIR(build)
 AC_CONFIG_MACRO_DIR([m4])
@@ -14,9 +14,9 @@ LT_INIT
 LT_LANG([C++])
 # custom defines for config.h
 AC_DEFINE([PACKAGE_FULL_NAME],["CRisprASSembler"],[Define the full name of the package])
-AC_DEFINE([PACKAGE_MAJOR_VERSION],[0],[Define the major version of the package])
-AC_DEFINE([PACKAGE_MINOR_VERSION],[3],[Define the minor version of the package])
-AC_DEFINE([PACKAGE_REVISION],[12],[Define the revision of the package])
+AC_DEFINE([PACKAGE_MAJOR_VERSION],[1],[Define the major version of the package])
+AC_DEFINE([PACKAGE_MINOR_VERSION],[0],[Define the minor version of the package])
+AC_DEFINE([PACKAGE_REVISION],[0],[Define the revision of the package])
 
 
 # extra configure options