Merge pull request #15 from nsoranzo/master

Fix Makefile, test data and --version
ctSkennerton · 7e97dd4c1b3e246ade58b498f955885a93085b97 · ctSkennerton committed on GitHub Jul 22, 2016 · Jul 22, 2016 · 7e97dd4
2 parents c75ad1f + 43fdafd
commit 7e97dd4c1b3e246ade58b498f955885a93085b97
Unified Split

Showing with 12 additions and 13 deletions.

+5 −6 Makefile

+1 −1 minced.java

+6 −6 t/Aquifex_aeolicus_VF5.expected
diff --git 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:
diff --git 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;
diff --git 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