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manojbhosale · Jan 2, 2019 · 57394b9 · 57394b9
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diff --git a/.classpath b/.classpath
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry including="**/*.java" kind="src" output="target/classes" path="src">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<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"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/.project b/.project
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>MAutomaton</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>
diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
@@ -0,0 +1,12 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.8
diff --git a/.settings/org.eclipse.m2e.core.prefs b/.settings/org.eclipse.m2e.core.prefs
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1
diff --git a/bin/com/psl/automation/annotation/VariationReporter.class b/bin/com/psl/automation/annotation/VariationReporter.class
diff --git a/bin/com/psl/automation/fileCompare/VCFrecord.class b/bin/com/psl/automation/fileCompare/VCFrecord.class
diff --git a/bin/com/psl/automation/main/BigTextField$1.class b/bin/com/psl/automation/main/BigTextField$1.class
diff --git a/bin/com/psl/automation/main/BigTextField.class b/bin/com/psl/automation/main/BigTextField.class
diff --git a/bin/com/psl/automation/main/FileChooserDemo$1.class b/bin/com/psl/automation/main/FileChooserDemo$1.class
diff --git a/bin/com/psl/automation/main/FileChooserDemo.class b/bin/com/psl/automation/main/FileChooserDemo.class
diff --git a/bin/com/psl/automation/main/Interval.class b/bin/com/psl/automation/main/Interval.class
diff --git a/bin/com/psl/automation/main/MainGui$1.class b/bin/com/psl/automation/main/MainGui$1.class
diff --git a/bin/com/psl/automation/main/MainGui.class b/bin/com/psl/automation/main/MainGui.class
diff --git a/bin/com/psl/automation/panels/BarcodeMetricsPanel$1.class b/bin/com/psl/automation/panels/BarcodeMetricsPanel$1.class
diff --git a/bin/com/psl/automation/panels/BarcodeMetricsPanel$2.class b/bin/com/psl/automation/panels/BarcodeMetricsPanel$2.class
diff --git a/bin/com/psl/automation/panels/BarcodeMetricsPanel.class b/bin/com/psl/automation/panels/BarcodeMetricsPanel.class
diff --git a/bin/com/psl/automation/panels/CompareVcfPanel$1.class b/bin/com/psl/automation/panels/CompareVcfPanel$1.class
diff --git a/bin/com/psl/automation/panels/CompareVcfPanel$2.class b/bin/com/psl/automation/panels/CompareVcfPanel$2.class
diff --git a/bin/com/psl/automation/panels/CompareVcfPanel$3.class b/bin/com/psl/automation/panels/CompareVcfPanel$3.class
diff --git a/bin/com/psl/automation/panels/CompareVcfPanel$4.class b/bin/com/psl/automation/panels/CompareVcfPanel$4.class
diff --git a/bin/com/psl/automation/panels/CompareVcfPanel$5.class b/bin/com/psl/automation/panels/CompareVcfPanel$5.class
diff --git a/bin/com/psl/automation/panels/CompareVcfPanel.class b/bin/com/psl/automation/panels/CompareVcfPanel.class
diff --git a/bin/com/psl/automation/panels/LiftOverUtilPanel.class b/bin/com/psl/automation/panels/LiftOverUtilPanel.class
diff --git a/bin/com/psl/automation/panels/QCComparePanel$1.class b/bin/com/psl/automation/panels/QCComparePanel$1.class
diff --git a/bin/com/psl/automation/panels/QCComparePanel$2.class b/bin/com/psl/automation/panels/QCComparePanel$2.class
diff --git a/bin/com/psl/automation/panels/QCComparePanel$3.class b/bin/com/psl/automation/panels/QCComparePanel$3.class
diff --git a/bin/com/psl/automation/panels/QCComparePanel$4.class b/bin/com/psl/automation/panels/QCComparePanel$4.class
diff --git a/bin/com/psl/automation/panels/QCComparePanel$5.class b/bin/com/psl/automation/panels/QCComparePanel$5.class
diff --git a/bin/com/psl/automation/panels/QCComparePanel.class b/bin/com/psl/automation/panels/QCComparePanel.class
diff --git a/bin/com/psl/automation/panels/TsTvMetricsPanel$1.class b/bin/com/psl/automation/panels/TsTvMetricsPanel$1.class
diff --git a/bin/com/psl/automation/panels/TsTvMetricsPanel$2.class b/bin/com/psl/automation/panels/TsTvMetricsPanel$2.class
diff --git a/bin/com/psl/automation/panels/TsTvMetricsPanel$3.class b/bin/com/psl/automation/panels/TsTvMetricsPanel$3.class
diff --git a/bin/com/psl/automation/panels/TsTvMetricsPanel.class b/bin/com/psl/automation/panels/TsTvMetricsPanel.class
diff --git a/bin/com/psl/swingexample/DigitalWatch.class b/bin/com/psl/swingexample/DigitalWatch.class
diff --git a/bin/com/psl/swingexample/DisplayGraphics.class b/bin/com/psl/swingexample/DisplayGraphics.class
diff --git a/bin/com/psl/swingexample/FirstSwingExample.class b/bin/com/psl/swingexample/FirstSwingExample.class
diff --git a/bin/com/psl/swingexample/JIFrameDemo$1.class b/bin/com/psl/swingexample/JIFrameDemo$1.class
diff --git a/bin/com/psl/swingexample/JIFrameDemo$2.class b/bin/com/psl/swingexample/JIFrameDemo$2.class
diff --git a/bin/com/psl/swingexample/JIFrameDemo.class b/bin/com/psl/swingexample/JIFrameDemo.class
diff --git a/bin/com/psl/swingexample/MainScreen.class b/bin/com/psl/swingexample/MainScreen.class
diff --git a/bin/com/psl/swingexample/MyProgress.class b/bin/com/psl/swingexample/MyProgress.class
diff --git a/bin/com/psl/swingexample/Notepad.class b/bin/com/psl/swingexample/Notepad.class
diff --git a/bin/com/psl/swingexample/OpenMenu.class b/bin/com/psl/swingexample/OpenMenu.class
diff --git a/bin/hsutils/BAMParser.class b/bin/hsutils/BAMParser.class
diff --git a/bin/hsutils/BamSorter.class b/bin/hsutils/BamSorter.class
diff --git a/bin/hsutils/TestAl.class b/bin/hsutils/TestAl.class
diff --git a/bin/liftoverutils/BedInterval.class b/bin/liftoverutils/BedInterval.class
diff --git a/bin/liftoverutils/Chain.class b/bin/liftoverutils/Chain.class
diff --git a/bin/liftoverutils/ChainException.class b/bin/liftoverutils/ChainException.class
diff --git a/bin/liftoverutils/Interval.class b/bin/liftoverutils/Interval.class
diff --git a/bin/liftoverutils/IntervalNode.class b/bin/liftoverutils/IntervalNode.class
diff --git a/bin/liftoverutils/IntervalTree.class b/bin/liftoverutils/IntervalTree.class
diff --git a/bin/liftoverutils/LiftOverDriver.class b/bin/liftoverutils/LiftOverDriver.class
diff --git a/bin/log4j.properties b/bin/log4j.properties
@@ -0,0 +1,11 @@
+# Define the root logger with appender file
+log = c:/gatKAutomator/log4j
+log4j.rootLogger = DEBUG, FILE
+
+# Define the file appender
+log4j.appender.FILE=org.apache.log4j.FileAppender
+log4j.appender.FILE.File=${log}/log.out
+
+# Define the layout for file appender
+log4j.appender.FILE.layout=org.apache.log4j.PatternLayout
+log4j.appender.FILE.layout.conversionPattern=%m%n
diff --git a/bin/qcutils/QCCompareResults.class b/bin/qcutils/QCCompareResults.class
diff --git a/bin/qcutils/QCMetricsCompare.class b/bin/qcutils/QCMetricsCompare.class
diff --git a/bin/vcfutils/CompareUtils.class b/bin/vcfutils/CompareUtils.class
diff --git a/bin/vcfutils/ComparisonResult.class b/bin/vcfutils/ComparisonResult.class
diff --git a/bin/vcfutils/TestVCFreader.class b/bin/vcfutils/TestVCFreader.class
diff --git a/bin/vcfutils/TsTvStatistics$1.class b/bin/vcfutils/TsTvStatistics$1.class
diff --git a/bin/vcfutils/TsTvStatistics$2.class b/bin/vcfutils/TsTvStatistics$2.class
diff --git a/bin/vcfutils/TsTvStatistics.class b/bin/vcfutils/TsTvStatistics.class
diff --git a/bin/vcfutils/VCFUtils.class b/bin/vcfutils/VCFUtils.class
diff --git a/bin/vcfutils/VCFrecord.class b/bin/vcfutils/VCFrecord.class
diff --git a/bin/vcfutils/VariantExceptions.class b/bin/vcfutils/VariantExceptions.class
diff --git a/bin/vcfutils/VariantTypes.class b/bin/vcfutils/VariantTypes.class
diff --git a/comparisonResults/common.vcf b/comparisonResults/common.vcf
diff --git a/comparisonResults/delNew.vcf b/comparisonResults/delNew.vcf
diff --git a/comparisonResults/delOld.vcf b/comparisonResults/delOld.vcf
diff --git a/comparisonResults/insNew.vcf b/comparisonResults/insNew.vcf
diff --git a/comparisonResults/insOld.vcf b/comparisonResults/insOld.vcf
diff --git a/comparisonResults/snpNew.vcf b/comparisonResults/snpNew.vcf
diff --git a/comparisonResults/snpOld.vcf b/comparisonResults/snpOld.vcf
diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml
@@ -0,0 +1,43 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>Automaton</groupId>
+  <artifactId>MAutomaton</artifactId>
+  <version>0.0.2-SNAPSHOT</version>
+  <build>
+    <sourceDirectory>src</sourceDirectory>
+    <resources>
+      <resource>
+        <directory>src</directory>
+        <excludes>
+          <exclude>**/*.java</exclude>
+        </excludes>
+      </resource>
+    </resources>
+    <plugins>
+      <plugin>
+        <artifactId>maven-compiler-plugin</artifactId>
+        <version>3.7.0</version>
+        <configuration>
+          <source>1.8</source>
+          <target>1.8</target>
+        </configuration>
+      </plugin>
+      <plugin>
+        <artifactId>maven-clean-plugin</artifactId>
+        <version>2.5</version>
+      </plugin>
+      <plugin>
+        <artifactId>maven-jar-plugin</artifactId>
+        <version>3.1.0</version>
+        <configuration>
+          <archive>
+            <manifest>
+              <mainClass>com.psl.automation.main.MainGui</mainClass>
+            </manifest>
+          </archive>
+        </configuration>
+      </plugin>
+    </plugins>
+  </build>
+</project>
diff --git a/pom.xml b/pom.xml
@@ -0,0 +1,90 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<groupId>Automaton</groupId>
+	<artifactId>MAutomaton</artifactId>
+	<version>0.0.2-SNAPSHOT</version>
+
+
+	<dependencies>
+		<!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpcore -->
+		<dependency>
+			<groupId>org.apache.httpcomponents</groupId>
+			<artifactId>httpcore</artifactId>
+			<version>4.4.6</version>
+		</dependency>
+		<!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpclient -->
+		<dependency>
+			<groupId>org.apache.httpcomponents</groupId>
+			<artifactId>httpclient</artifactId>
+			<version>4.2.5</version>
+		</dependency>
+
+
+		<!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpmime -->
+		<dependency>
+			<groupId>org.apache.httpcomponents</groupId>
+			<artifactId>httpmime</artifactId>
+			<version>4.2.5</version>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/com.github.samtools/htsjdk -->
+		<dependency>
+			<groupId>com.github.samtools</groupId>
+			<artifactId>htsjdk</artifactId>
+			<version>2.17.0</version>
+		</dependency>
+		<!-- https://mvnrepository.com/artifact/log4j/log4j -->
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+			<version>1.2.17</version>
+		</dependency>
+
+
+	</dependencies>
+
+
+	<build>
+		<sourceDirectory>src</sourceDirectory>
+		<resources>
+			<resource>
+				<directory>src</directory>
+				<excludes>
+					<exclude>**/*.java</exclude>
+				</excludes>
+			</resource>
+		</resources>
+
+
+
+		<plugins>
+			<plugin>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>3.7.0</version>
+				<configuration>
+					<source>1.8</source>
+					<target>1.8</target>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-clean-plugin</artifactId>
+				<version>2.5</version>
+			</plugin>
+
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-jar-plugin</artifactId>
+				<version>3.1.0</version>
+				<configuration>
+					<archive>
+						<manifest>
+							<mainClass>com.psl.automation.main.MainGui</mainClass>
+						</manifest>
+					</archive>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+</project>
diff --git a/src/com/psl/automation/annotation/Driver.java b/src/com/psl/automation/annotation/Driver.java
@@ -0,0 +1,16 @@
+package com.psl.automation.annotation;
+
+import java.io.File;
+
+public class Driver {
+
+	public static void main(String[] args) {
+		VariationReporter vr = new VariationReporter();
+		try {
+			System.out.println(vr.analyze(9606, "GCF_000001405.25", "", new File("C:\\Users\\manojkumar_bhosale\\Desktop\\TestVariationreporter\\vcf.vcf")));
+		} catch (Exception e) {
+			System.out.println(e);
+		}
+	}
+
+}
diff --git a/src/com/psl/automation/annotation/VariationReporter.java b/src/com/psl/automation/annotation/VariationReporter.java
@@ -0,0 +1,50 @@
+package com.psl.automation.annotation;
+
+import java.io.File;
+
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.ResponseHandler;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.mime.MultipartEntity;
+import org.apache.http.entity.mime.content.FileBody;
+import org.apache.http.entity.mime.content.StringBody;
+import org.apache.http.impl.client.BasicResponseHandler;
+import org.apache.http.impl.client.DefaultHttpClient;
+
+public class VariationReporter {
+
+	private String postUrl = "https://www.ncbi.nlm.nih.gov/projects/SNP/VariantAnalyzer/var_rep.cgi"; //post url
+
+    public String analyze(int organism, String src_assembly, String annot1, File annot) throws Exception {
+        String result = null;
+        HttpClient httpClient = new DefaultHttpClient(); //user agent
+        //httpClient.getParams().setParameter(CoreConnectionPNames.CONNECTION_TIMEOUT, 30000); //user agent timeout must be at least 30 sec.
+
+        HttpPost httpPost = new HttpPost(postUrl);
+        MultipartEntity multiPartEntity = new MultipartEntity();
+
+        //Setup form parameters
+        multiPartEntity.addPart("source-assembly", new StringBody(src_assembly)); //reference assembly 
+        multiPartEntity.addPart("annot1", new StringBody(annot1)); //query input as a text 
+        multiPartEntity.addPart("api_protocol_version", new StringBody("1.0")); //API version
+        //query as an input file
+        FileBody fileBody = new FileBody(annot, "application/text");
+        multiPartEntity.addPart("annot", fileBody);
+        httpPost.setEntity(multiPartEntity);
+        ResponseHandler<String> responseHandler = new BasicResponseHandler(); 
+
+        //httpPost.
+//       / httpClient
+
+        try {
+            result = httpClient.execute(httpPost, responseHandler);
+            String jobIdLine = result.substring(0, result.indexOf("\n") + 1); //first line contains job id 
+            result = jobIdLine + result.substring(result.indexOf("##")); //actual query result starts with lines beginning with '##' 
+        }
+        finally {
+            httpClient.getConnectionManager().shutdown();
+        }
+        return result;
+    }
+
+}