From 6a6eb1c4d423a77dab619932ea26ecd1d98287ac Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
Date: Fri, 22 Jul 2016 16:00:27 +0100
Subject: [PATCH 1/3] Update test output for release 0.2.0

---
 t/Aquifex_aeolicus_VF5.expected | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/t/Aquifex_aeolicus_VF5.expected b/t/Aquifex_aeolicus_VF5.expected
index bba930f..c504150 100644
--- a/t/Aquifex_aeolicus_VF5.expected
+++ b/t/Aquifex_aeolicus_VF5.expected
@@ -1,7 +1,7 @@
 ##gff-version 3
-gi|15282445|ref|NC_000918.1|	minced:0.1.6	CRISPR	156460	156767	5	.	.	ID=CRISPR1
-gi|15282445|ref|NC_000918.1|	minced:0.1.6	CRISPR	244561	244791	4	.	.	ID=CRISPR2
-gi|15282445|ref|NC_000918.1|	minced:0.1.6	CRISPR	279264	279555	5	.	.	ID=CRISPR3
-gi|15282445|ref|NC_000918.1|	minced:0.1.6	CRISPR	1226626	1226861	4	.	.	ID=CRISPR4
-gi|15282445|ref|NC_000918.1|	minced:0.1.6	CRISPR	1379598	1379894	5	.	.	ID=CRISPR5
-gi|15282445|ref|NC_000918.1|	minced:0.1.6	CRISPR	1418900	1419060	3	.	.	ID=CRISPR6
+gi|15282445|ref|NC_000918.1|	minced:0.2.0	CRISPR	156460	156767	5	.	.	ID=CRISPR1
+gi|15282445|ref|NC_000918.1|	minced:0.2.0	CRISPR	244561	244791	4	.	.	ID=CRISPR2
+gi|15282445|ref|NC_000918.1|	minced:0.2.0	CRISPR	279264	279555	5	.	.	ID=CRISPR3
+gi|15282445|ref|NC_000918.1|	minced:0.2.0	CRISPR	1226626	1226861	4	.	.	ID=CRISPR4
+gi|15282445|ref|NC_000918.1|	minced:0.2.0	CRISPR	1379598	1379894	5	.	.	ID=CRISPR5
+gi|15282445|ref|NC_000918.1|	minced:0.2.0	CRISPR	1418900	1419060	3	.	.	ID=CRISPR6

From 402c8e0d713f0c71e435cba1e8711aada9ee1901 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
Date: Fri, 22 Jul 2016 16:27:38 +0100
Subject: [PATCH 2/3] Fix Makefile to not rebuild .class files every time

---
 Makefile | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/Makefile b/Makefile
index 600e297..f8df66f 100644
--- a/Makefile
+++ b/Makefile
@@ -2,17 +2,16 @@ JFLAGS = -g
 JC = javac
 JAR = jar
 .SUFFIXES: .java .class
+JAVA_FILES = CRISPR.java CRISPRFinder.java CRISPRUtil.java DNASequence.java FASTAReader.java SearchUtil.java minced.java IntervalSearchTree.java
+JAVA_CLASSES = $(JAVA_FILES:.java=.class)
+.PHONY: default clean test
 
 .java.class:
 	$(JC) $(JFLAGS) $*.java
 
-CLASSES = CRISPR.java CRISPRFinder.java CRISPRUtil.java DNASequence.java FASTAReader.java SearchUtil.java minced.java IntervalSearchTree.java
+default: minced.jar
 
-default: classes minced.jar
-
-classes: $(CLASSES:.java=.class)
-
-minced.jar: classes
+minced.jar: $(JAVA_CLASSES)
 	$(JAR) cfm minced.jar MANIFEST.txt *class
 
 clean:

From 43fdafd6d842cf03723574e1580396ff3253ec3d Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
Date: Fri, 22 Jul 2016 16:33:04 +0100
Subject: [PATCH 3/3] minced --version should exit 0

There is no error.
---
 minced.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/minced.java b/minced.java
index 0ad1d1d..8b07144 100644
--- a/minced.java
+++ b/minced.java
@@ -39,7 +39,7 @@ public static void main(String[] args)
       if (args[0].equals("--version"))
       {
          printVersion();
-         System.exit(1);
+         System.exit(0);
       }
 
       int i = 0;