Better GATK version and command line output

-- Previous version emitted command lines that look like:

##HaplotypeCaller="analysis_type=HaplotypeCaller input_file=[private/testdata/reduced.readNotFullySpanningDeletion.bam] ..."

the new version provides additional information on when the GATK was run and the GATK version in a nicer format:

 ##GATKCommandLine=<ID=HaplotypeCaller,Version=2.5-206-gbc7be2b,Date="Thu Jun 20 11:09:01 EDT 2013",Epoch=1371740941197,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[private/testdata/reduced.readNotFullySpanningDeletion.bam] read_buffer_size=null phone_home=AWS ...">

 -- Additionally, the command line options are emitted sequentially in the file, so you can see a running record of how a VCF was produced, such as this example from the integration test:

 ##GATKCommandLine=<ID=HaplotypeCaller,Version=2.5-206-gbc7be2b,Date="Thu Jun 20 11:09:01 EDT 2013",Epoch=1371740941197,CommandLineOptions="lots of stuff">
 ##GATKCommandLine=<ID=SelectVariants,Version=2.5-206-gbc7be2b,Date="Thu Jun 20 11:16:23 EDT 2013",Epoch=1371741383277,CommandLineOptions="lots of stuff">

 -- Removed the ProtectedEngineFeaturesIntegrationTest
 -- Actual unit tests for these features!

protected/java/test/org/broadinstitute/sting/gatk/ProtectedEngineFeaturesIntegrationTest.java

@@ -1,93 +0,0 @@
-/*
-*  By downloading the PROGRAM you agree to the following terms of use:
-*  
-*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-*  
-*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
-*  
-*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-*  
-*  1. DEFINITIONS
-*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
-*  
-*  2. LICENSE
-*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
-*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
-*  
-*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
-*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-*  Copyright 2012 Broad Institute, Inc.
-*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
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-*/
-
-package org.broadinstitute.sting.gatk;
-
-import net.sf.samtools.util.BlockCompressedInputStream;
-import org.broad.tribble.readers.AsciiLineReader;
-import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
-import org.broadinstitute.variant.vcf.VCFCodec;
-import org.broadinstitute.variant.vcf.VCFHeader;
-import org.broadinstitute.variant.vcf.VCFHeaderLine;
-import org.testng.Assert;
-import org.testng.annotations.Test;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.util.Arrays;
-
-/**
- *
- */
-public class ProtectedEngineFeaturesIntegrationTest extends WalkerTest {
-    @Test(enabled = true)
-    public void testGATKVersionInVCF() throws Exception {
-        WalkerTestSpec spec = new WalkerTestSpec("-T UnifiedGenotyper -R " + b37KGReference + " -I "
-                + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam"
-                + " -o %s -L 20:10,000,000",
-                1, Arrays.asList(""));
-        final File vcf = executeTest("testGATKVersionInVCF", spec).first.get(0);
-        final VCFHeader header = (VCFHeader)new VCFCodec().readHeader(new AsciiLineReader(new FileInputStream(vcf)));
-        final VCFHeaderLine versionLine = header.getMetaDataLine(VariantContextWriterStub.GATK_VERSION_KEY);
-        Assert.assertNotNull(versionLine);
-        Assert.assertEquals(versionLine.getValue(), CommandLineGATK.getVersionNumber());
-    }
-
-    @Test(enabled = true)
-    public void testCompressedVCFOutputWithNT() throws Exception {
-        WalkerTestSpec spec = new WalkerTestSpec("-T UnifiedGenotyper -R " + b37KGReference + " -I "
-                + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam"
-                + " -o %s -L 20:10,000,000-10,100,000 -nt 4",
-                1, Arrays.asList("vcf.gz"), Arrays.asList(""));
-        final File vcf = executeTest("testCompressedVCFOutputWithNT", spec).first.get(0);
-        final AsciiLineReader reader = new AsciiLineReader(new BlockCompressedInputStream(vcf));
-        int nLines = 0;
-        while ( reader.readLine() != null )
-            nLines++;
-        Assert.assertTrue(nLines > 0);
-    }
-}

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -46,11 +46,15 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
+import net.sf.samtools.util.BlockCompressedInputStream;
+import org.broad.tribble.readers.AsciiLineReader;
 import org.broadinstitute.sting.WalkerTest;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.testng.Assert;
 import org.testng.annotations.Test;
 
+import java.io.File;
 import java.util.Arrays;
 import java.util.Collections;
 
@@ -302,4 +306,18 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
         executeTest("test calling on reads with Ns in CIGAR", spec);
     }
+
+    @Test(enabled = true)
+    public void testCompressedVCFOutputWithNT() throws Exception {
+        WalkerTestSpec spec = new WalkerTestSpec("-T UnifiedGenotyper -R " + b37KGReference + " -I "
+                + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam"
+                + " -o %s -L 20:10,000,000-10,100,000 -nt 4",
+                1, Arrays.asList("vcf.gz"), Arrays.asList(""));
+        final File vcf = executeTest("testCompressedVCFOutputWithNT", spec).first.get(0);
+        final AsciiLineReader reader = new AsciiLineReader(new BlockCompressedInputStream(vcf));
+        int nLines = 0;
+        while ( reader.readLine() != null )
+            nLines++;
+        Assert.assertTrue(nLines > 0);
+    }
 }

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -170,6 +170,14 @@ public class GenomeAnalysisEngine {
         this.walker = walker;
     }
 
+    /**
+     * The short name of the current GATK walker as a string
+     * @return a non-null String
+     */
+    public String getWalkerName() {
+        return getWalkerName(walker.getClass());
+    }
+
     /**
      * A processed collection of SAM reader identifiers.
      */

public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java

@@ -26,18 +26,15 @@
 package org.broadinstitute.sting.gatk.io.stubs;
 
 import net.sf.samtools.SAMSequenceDictionary;
-import org.broadinstitute.sting.gatk.CommandLineExecutable;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.variant.vcf.VCFHeader;
-import org.broadinstitute.variant.vcf.VCFHeaderLine;
 import org.broadinstitute.variant.variantcontext.VariantContext;
 import org.broadinstitute.variant.variantcontext.writer.Options;
 import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
 
 import java.io.File;
 import java.io.OutputStream;
@@ -54,7 +51,6 @@ import java.util.List;
  * @version 0.1
  */
 public class VariantContextWriterStub implements Stub<VariantContextWriter>, VariantContextWriter {
-    public final static String GATK_VERSION_KEY = "GATKVersion";
     public final static boolean UPDATE_CONTIG_HEADERS = true;
 
     /**
@@ -227,13 +223,8 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         if ( header.isWriteEngineHeaders() ) {
             // skip writing the command line header if requested
             if ( ! skipWritingCommandLineHeader && header.isWriteCommandLine() ) {
-                // write the GATK version if we have command line information enabled
+                // Always add the header line, as the current format allows multiple entries
-                vcfHeader.addMetaDataLine(getGATKVersionHeaderLine());
+                final VCFHeaderLine commandLineArgHeaderLine = GATKVCFUtils.getCommandLineArgumentHeaderLine(engine, argumentSources);
-
-                // Check for the command-line argument header line.  If not present, add it in.
-                final VCFHeaderLine commandLineArgHeaderLine = getCommandLineArgumentHeaderLine();
-                final boolean foundCommandLineHeaderLine = vcfHeader.getMetaDataLine(commandLineArgHeaderLine.getKey()) != null;
-                if ( ! foundCommandLineHeaderLine )
                 vcfHeader.addMetaDataLine(commandLineArgHeaderLine);
             }
 
@@ -280,21 +271,4 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
                 getOutputFile() != null && // that are going to disk
                 engine.getArguments().generateShadowBCF; // and we actually want to do it
     }
-
-    /**
-     * Gets the appropriately formatted header for a VCF file
-     * @return VCF file header.
-     */
-    private VCFHeaderLine getCommandLineArgumentHeaderLine() {
-        CommandLineExecutable executable = JVMUtils.getObjectOfType(argumentSources,CommandLineExecutable.class);
-        return new VCFHeaderLine(executable.getAnalysisName(), "\"" + engine.createApproximateCommandLineArgumentString(argumentSources.toArray()) + "\"");
-    }
-
-    /**
-     * Gets the GATK version header line for the VCF file
-     * @return non-null VCFHeaderLine.
-     */
-    private VCFHeaderLine getGATKVersionHeaderLine() {
-        return new VCFHeaderLine(GATK_VERSION_KEY, CommandLineGATK.getVersionNumber());
-    }
 }

public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java

@@ -30,10 +30,10 @@ import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.FeatureCodecHeader;
 import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.variant.bcf2.BCF2Codec;
 import org.broadinstitute.variant.variantcontext.VariantContext;
 import org.broadinstitute.variant.vcf.*;
 
@@ -52,6 +52,31 @@ public class GATKVCFUtils {
      */
     private GATKVCFUtils() { }
 
+    public final static String GATK_COMMAND_LINE_KEY = "GATKCommandLine";
+
+    /**
+     * Gets the appropriately formatted header for a VCF file describing this GATK run
+     *
+     * @param engine the GATK engine that holds the walker name, GATK version, and other information
+     * @param argumentSources contains information on the argument values provided to the GATK for converting to a
+     *                        command line string.  Should be provided from the data in the parsing engine.  Can be
+     *                        empty in which case the command line will be the empty string.
+     * @return VCF header line describing this run of the GATK.
+     */
+    public static VCFHeaderLine getCommandLineArgumentHeaderLine(final GenomeAnalysisEngine engine, final Collection<Object> argumentSources) {
+        if ( engine == null ) throw new IllegalArgumentException("engine cannot be null");
+        if ( argumentSources == null ) throw new IllegalArgumentException("argumentSources cannot be null");
+
+        final Map<String, String> attributes = new LinkedHashMap<>();
+        attributes.put("ID", engine.getWalkerName());
+        attributes.put("Version", CommandLineGATK.getVersionNumber());
+        final Date date = new Date();
+        attributes.put("Date", date.toString());
+        attributes.put("Epoch", Long.toString(date.getTime()));
+        attributes.put("CommandLineOptions", engine.createApproximateCommandLineArgumentString(argumentSources.toArray()));
+        return new VCFSimpleHeaderLine(GATK_COMMAND_LINE_KEY, attributes, Collections.<String>emptyList());
+    }
+
     public static <T extends Feature> Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, List<RodBinding<T>> rodBindings) {
         // Collect the eval rod names
         final Set<String> names = new TreeSet<String>();

public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk;
 
 import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMRecord;
+import org.broad.tribble.readers.AsciiLineReader;
 import org.broadinstitute.sting.WalkerTest;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -39,11 +40,16 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.VCFCodec;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.PrintStream;
 import java.util.Arrays;
 
@@ -197,6 +203,54 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
         executeTest("badCompress " + compress, spec);
     }
 
+    // --------------------------------------------------------------------------------
+    //
+    // Test that the VCF version key is what we expect
+    //
+    // --------------------------------------------------------------------------------
+    @Test(enabled = true)
+    public void testGATKVersionInVCF() throws Exception {
+        WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -R " + b37KGReference +
+                " -V " + privateTestDir + "NA12878.WGS.b37.chr20.firstMB.vcf"
+                + " -o %s -L 20:61098",
+                1, Arrays.asList(""));
+        spec.disableShadowBCF();
+        final File vcf = executeTest("testGATKVersionInVCF", spec).first.get(0);
+        final VCFHeader header = (VCFHeader)new VCFCodec().readHeader(new AsciiLineReader(new FileInputStream(vcf)));
+        final VCFHeaderLine versionLine = header.getMetaDataLine(GATKVCFUtils.GATK_COMMAND_LINE_KEY);
+        Assert.assertNotNull(versionLine);
+        Assert.assertTrue(versionLine.toString().contains("SelectVariants"));
+    }
+
+    @Test(enabled = true)
+    public void testMultipleGATKVersionsInVCF() throws Exception {
+        WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -R " + b37KGReference +
+                " -V " + privateTestDir + "gatkCommandLineInHeader.vcf"
+                + " -o %s",
+                1, Arrays.asList(""));
+        spec.disableShadowBCF();
+        final File vcf = executeTest("testMultipleGATKVersionsInVCF", spec).first.get(0);
+        final VCFHeader header = (VCFHeader)new VCFCodec().readHeader(new AsciiLineReader(new FileInputStream(vcf)));
+
+        boolean foundHC = false;
+        boolean foundSV = false;
+        for ( final VCFHeaderLine line : header.getMetaDataInInputOrder() ) {
+            if ( line.getKey().equals(GATKVCFUtils.GATK_COMMAND_LINE_KEY) ) {
+                if ( line.toString().contains("HaplotypeCaller") ) {
+                    Assert.assertFalse(foundHC);
+                    foundHC = true;
+                }
+                if ( line.toString().contains("SelectVariants") ) {
+                    Assert.assertFalse(foundSV);
+                    foundSV = true;
+                }
+            }
+        }
+
+        Assert.assertTrue(foundHC, "Didn't find HaplotypeCaller command line header field");
+        Assert.assertTrue(foundSV, "Didn't find SelectVariants command line header field");
+    }
+
     // --------------------------------------------------------------------------------
     //
     // Test that defaultBaseQualities actually works

public/java/test/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java

@@ -0,0 +1,86 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.sting.utils.variant;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Set;
+
+public class GATKVCFUtilsUnitTest extends BaseTest {
+    public static class VCFHeaderTestWalker extends RodWalker<Integer, Integer> {
+        public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return null; }
+        public Integer reduceInit() { return 0; }
+        public Integer reduce(Integer value, Integer sum) { return value + sum; }
+    }
+
+    public static class VCFHeaderTest2Walker extends VCFHeaderTestWalker {}
+
+    @Test
+    public void testAddingVCFHeaderInfo() {
+        final VCFHeader header = new VCFHeader();
+
+        final Walker walker1 = new VCFHeaderTestWalker();
+        final Walker walker2 = new VCFHeaderTest2Walker();
+
+        final GenomeAnalysisEngine testEngine1 = new GenomeAnalysisEngine();
+        testEngine1.setWalker(walker1);
+
+        final GenomeAnalysisEngine testEngine2 = new GenomeAnalysisEngine();
+        testEngine2.setWalker(walker2);
+
+        final VCFHeaderLine line1 = GATKVCFUtils.getCommandLineArgumentHeaderLine(testEngine1, Collections.EMPTY_LIST);
+        logger.warn(line1);
+        Assert.assertNotNull(line1);
+        Assert.assertEquals(line1.getKey(), GATKVCFUtils.GATK_COMMAND_LINE_KEY);
+        for ( final String field : Arrays.asList("Version", "ID", "Date", "CommandLineOptions"))
+            Assert.assertTrue(line1.toString().contains(field), "Couldn't find field " + field + " in " + line1.getValue());
+        Assert.assertTrue(line1.toString().contains("ID=" + testEngine1.getWalkerName()));
+
+        final VCFHeaderLine line2 = GATKVCFUtils.getCommandLineArgumentHeaderLine(testEngine2, Collections.EMPTY_LIST);
+        logger.warn(line2);
+
+        header.addMetaDataLine(line1);
+        final Set<VCFHeaderLine> lines1 = header.getMetaDataInInputOrder();
+        Assert.assertTrue(lines1.contains(line1));
+
+        header.addMetaDataLine(line2);
+        final Set<VCFHeaderLine> lines2 = header.getMetaDataInInputOrder();
+        Assert.assertTrue(lines2.contains(line1));
+        Assert.assertTrue(lines2.contains(line2));
+    }
+}