Add CSV Reader

seppinho · Dec 7, 2018 · 0b3cac9 · 0b3cac9
1 parent af5de7b
commit 0b3cac9
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Showing 2 changed files with 60 additions and 4 deletions.
diff --git a/pom.xml b/pom.xml
@@ -99,6 +99,7 @@
 									<include>com.github.samtools:htsjdk:*:*</include>
 									<include>genepi:haplogrep:*:*</include>
 									<include>commons-cli:commons-cli:*:*</include>
+									<include>au.com.bytecode:opencsv*:*</include>
 								</includes>
 							</artifactSet>
 						</configuration>
@@ -107,14 +108,71 @@
 			</plugin>
 		</plugins>
 	</build>
-	
+
 	<dependencies>
 
+		<dependency>
+			<groupId>net.sf.json-lib</groupId>
+			<artifactId>json-lib</artifactId>
+			<version>2.4</version>
+			<classifier>jdk15</classifier>
+		</dependency>
+
+		<dependency>
+			<groupId>jdom</groupId>
+			<artifactId>jdom</artifactId>
+			<version>1.1</version>
+		</dependency>
+
+		<dependency>
+			<groupId>com.esotericsoftware.yamlbeans</groupId>
+			<artifactId>yamlbeans</artifactId>
+			<version>1.09</version>
+		</dependency>
+
+		<dependency>
+			<groupId>jaxen</groupId>
+			<artifactId>jaxen</artifactId>
+			<version>1.1.6</version>
+		</dependency>
+
+		<dependency>
+			<groupId>jdom</groupId>
+			<artifactId>jdom</artifactId>
+			<version>1.1</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.json</groupId>
+			<artifactId>json</artifactId>
+			<version>20180130</version>
+		</dependency>
+
+		<dependency>
+			<groupId>genepi</groupId>
+			<artifactId>genepi-io</artifactId>
+			<version>1.0.10</version>
+		</dependency>
+
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.12</version>
+			<scope>test</scope>
+		</dependency>
+
 		<dependency>
 			<groupId>genepi</groupId>
 			<artifactId>haplogrep</artifactId>
 			<version>2.0.6</version>
 		</dependency>
 
+		<dependency>
+			<groupId>au.com.bytecode</groupId>
+			<artifactId>opencsv</artifactId>
+			<version>2.4</version>
+		</dependency>
+
+
 	</dependencies>
 </project>
diff --git a/src/main/java/genepi/haplogrep/main/Haplogrep.java b/src/main/java/genepi/haplogrep/main/Haplogrep.java
@@ -11,16 +11,14 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.UUID;
 import contamination.objects.Sample;
-import phylotree.Annotation;
 import util.ExportUtils;
 import core.SampleFile;
 import core.TestSample;
 
 public class Haplogrep extends Tool {
 
-	public static String VERSION = "v2.1.16";
+	public static String VERSION = "v2.1.17";
 
 	public Haplogrep(String[] args) {
 		super(args);