/*
* The MIT License
*
* 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 picard.sam;
import htsjdk.samtools.util.AsciiWriter;
import htsjdk.samtools.util.BufferedLineReader;
import htsjdk.samtools.util.LineReader;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.PrintStream;
public class ViewSamTest {
/**
* Confirm that ViewSam retains whatever version number was in the input header.
*/
@Test
public void testHeaderVersion() throws Exception {
final String oldVersionHeader = "@HD\tVN:1.3\tSO:unsorted";
final File inputSam = File.createTempFile("ViewSamTest.input.", ".sam");
inputSam.deleteOnExit();
final AsciiWriter writer = new AsciiWriter(new FileOutputStream(inputSam));
writer.write(oldVersionHeader);
writer.write("\n");
writer.close();
final File viewSamOutputFile = File.createTempFile("ViewSamTest.output.", ".sam");
viewSamOutputFile.deleteOnExit();
final ViewSam viewSam = new ViewSam();
viewSam.INPUT = inputSam;
final PrintStream viewSamPrintStream = new PrintStream(viewSamOutputFile);
// TODO - Should switch over to using invocation via new PicardCommandLine() - BUT the test here is accessing class members directly.
Assert.assertEquals(viewSam.writeSamText(viewSamPrintStream), 0);
viewSamPrintStream.close();
final LineReader viewSamInputReader = new BufferedLineReader(new FileInputStream(viewSamOutputFile));
Assert.assertEquals(viewSamInputReader.readLine(), oldVersionHeader);
}
}