Added feature to intersect VCF and BED

Author: manojbhosale

.classpath

@@ -6,6 +6,11 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

.gitignore

@@ -0,0 +1 @@
+/target/

pom.xml

@@ -56,6 +56,7 @@
 
 
 	<build>
+	
 		<sourceDirectory>src</sourceDirectory>
 		<resources>
 			<resource>
@@ -64,6 +65,12 @@
 					<exclude>**/*.java</exclude>
 				</excludes>
 			</resource>
+			<resource>
+				<directory>resources</directory>
+			</resource>
+			<resource>
+				<directory>src/main/config</directory>
+			</resource>
 		</resources>
 
 
@@ -120,7 +127,7 @@
 				<artifactId>maven-clean-plugin</artifactId>
 				<version>2.5</version>
 			</plugin>
-
+			
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-jar-plugin</artifactId>

resources/50Pix.png

@@ -13,6 +13,7 @@
 import java.awt.event.ItemListener;
 import java.awt.event.KeyEvent;
 import java.io.File;
+import java.net.URL;
 
 import javax.swing.BoxLayout;
 import javax.swing.ImageIcon;
@@ -36,6 +37,7 @@
 import com.psl.automation.panels.CompareVcfPanel;
 import com.psl.automation.panels.QCComparePanel;
 import com.psl.automation.panels.TsTvMetricsPanel;
+import com.psl.automation.panels.VcfBedIntersectionPanel;
 
 public class MainGui implements ActionListener{
 	//Log4j logger
@@ -56,7 +58,10 @@ public class MainGui implements ActionListener{
 	public void createUi(){
 
 		JFrame mainFrame = new JFrame("MAutomaton");
-		ImageIcon img = new ImageIcon("C:\\Users\\manojkumar_bhosale\\Desktop\\Logo\\SoftLogo.png");
+		URL file = 
+				getClass().getClassLoader().getResource("50Pix.png");
+		ImageIcon img = new ImageIcon(file);
+		System.out.println(file);
 		mainFrame.setIconImage(img.getImage());
 		mainFrame.setSize(500, 300);
 		mainFrame.setDefaultCloseOperation(mainFrame.EXIT_ON_CLOSE);
@@ -70,11 +75,12 @@ public void createUi(){
 		BarcodeMetricsPanel bmp = new BarcodeMetricsPanel();
 		TsTvMetricsPanel tstvp = new TsTvMetricsPanel();
 		QCComparePanel qcp = new QCComparePanel();
-		
+		VcfBedIntersectionPanel vbedp = new VcfBedIntersectionPanel();
 		jtp.addTab("VCF comparator", cvp.createCompareVcfPanel());
 		jtp.addTab("HS Util", bmp.createFileConfigPanel());
 		jtp.addTab("VCF Util", tstvp.createVcfUtilPanel());
 		jtp.addTab("QC compare", qcp.createCompareQcPanel());
+		jtp.addTab("VCF BED intersect", vbedp.createIntersectVcfPanel());
 
 //		/createFileConfigPanel();
 		//createSortPanel();