update the version number

Author: ctSkennerton

CHANGES

@@ -1,5 +1,10 @@
 Revision history for MinCED
 
+0.3.2 02-Mar-2019
+        Fix a bug that was causing some string indexing errors where
+        the bounds of the CRISPR was not being updated properly when
+        a partial repeat was removed.
+
 0.3.2 01-Oct-2018
         Modify searching behaviour so that parital repeats that are at
         the edges of contigs do not prevent the extension of other repeats

README.md

@@ -56,7 +56,7 @@ The output can be large, so save it in a file:
 
 ```
 Copyright 2011      Florent ANGLY     <florent.angly@gmail.com>
-          2013-2018 Connor SKENNERTON <c.skennerton@gmail.com>
+          2013-2019 Connor SKENNERTON <c.skennerton@gmail.com>
 
 MinCED is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by

minced.java

@@ -2,7 +2,7 @@
 
 public class minced
 {
-   public static final String VERSION = "0.3.2";
+   public static final String VERSION = "0.3.3";
 	public static void main(String[] args)
    {
       //default values

t/Aquifex_aeolicus_VF5.expected

@@ -1,7 +1,7 @@
 ##gff-version 3
-gi|15282445|ref|NC_000918.1|	minced:0.3.2	repeat_region	156460	156767	5	.	.	ID=CRISPR1;rpt_type=direct;rpt_family=CRISPR;rpt_unit_seq=GTTCCTAATGTACCGTGTGGAGTTGAAACC
-gi|15282445|ref|NC_000918.1|	minced:0.3.2	repeat_region	244561	244791	4	.	.	ID=CRISPR2;rpt_type=direct;rpt_family=CRISPR;rpt_unit_seq=GTTTCAACTCCACACGGTACATTAGGAAC
-gi|15282445|ref|NC_000918.1|	minced:0.3.2	repeat_region	279264	279555	5	.	.	ID=CRISPR3;rpt_type=direct;rpt_family=CRISPR;rpt_unit_seq=GTTTTAACTCCACACGGTACATTAGAAAC
-gi|15282445|ref|NC_000918.1|	minced:0.3.2	repeat_region	1226626	1226861	4	.	.	ID=CRISPR4;rpt_type=direct;rpt_family=CRISPR;rpt_unit_seq=CGTTTCTAATGTACCGTAGAGGAGTTGAAAC
-gi|15282445|ref|NC_000918.1|	minced:0.3.2	repeat_region	1379598	1379894	5	.	.	ID=CRISPR5;rpt_type=direct;rpt_family=CRISPR;rpt_unit_seq=GTTTCAACTCCACTACGGTACATTAGGAAC
-gi|15282445|ref|NC_000918.1|	minced:0.3.2	repeat_region	1418900	1419060	3	.	.	ID=CRISPR6;rpt_type=direct;rpt_family=CRISPR;rpt_unit_seq=GTTCCTAATGTACCGTGTGGAGTTGAAAC
+gi|15282445|ref|NC_000918.1|	minced:0.3.3	repeat_region	156460	156767	5	.	.	ID=CRISPR1;rpt_type=direct;rpt_family=CRISPR;rpt_unit_seq=GTTCCTAATGTACCGTGTGGAGTTGAAACC
+gi|15282445|ref|NC_000918.1|	minced:0.3.3	repeat_region	244561	244791	4	.	.	ID=CRISPR2;rpt_type=direct;rpt_family=CRISPR;rpt_unit_seq=GTTTCAACTCCACACGGTACATTAGGAAC
+gi|15282445|ref|NC_000918.1|	minced:0.3.3	repeat_region	279264	279555	5	.	.	ID=CRISPR3;rpt_type=direct;rpt_family=CRISPR;rpt_unit_seq=GTTTTAACTCCACACGGTACATTAGAAAC
+gi|15282445|ref|NC_000918.1|	minced:0.3.3	repeat_region	1226626	1226861	4	.	.	ID=CRISPR4;rpt_type=direct;rpt_family=CRISPR;rpt_unit_seq=CGTTTCTAATGTACCGTAGAGGAGTTGAAAC
+gi|15282445|ref|NC_000918.1|	minced:0.3.3	repeat_region	1379598	1379894	5	.	.	ID=CRISPR5;rpt_type=direct;rpt_family=CRISPR;rpt_unit_seq=GTTTCAACTCCACTACGGTACATTAGGAAC
+gi|15282445|ref|NC_000918.1|	minced:0.3.3	repeat_region	1418900	1419060	3	.	.	ID=CRISPR6;rpt_type=direct;rpt_family=CRISPR;rpt_unit_seq=GTTCCTAATGTACCGTGTGGAGTTGAAAC