/*
* 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.SAMRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.util.AsciiWriter;
import htsjdk.samtools.util.BufferedLineReader;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.LineReader;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.cmdline.CommandLineProgramTest;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.PrintStream;
import java.util.List;
public class ViewSamTest extends CommandLineProgramTest {
@Override
public String getCommandLineProgramName() {
return ViewSam.class.getSimpleName();
}
/**
* 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.getAbsolutePath();
// create a print stream to this file
final PrintStream viewSamPrintStream = new PrintStream(viewSamOutputFile);
// make sure the command line call exited successfully
Assert.assertEquals(viewSam.writeSamText(viewSamPrintStream), 0);
viewSamPrintStream.close();
final LineReader viewSamInputReader = new BufferedLineReader(new FileInputStream(viewSamOutputFile));
Assert.assertEquals(viewSamInputReader.readLine(), oldVersionHeader);
}
/**
* Confirm that ViewSam only outputs records that overlap intervals in a provided interval file.
*/
@Test
public void testIntervals() throws Exception {
// a SAM file designed to test intervals against
final File inputSam = new File("testdata/picard/sam/viewsam_intervals_test.sam");
// an interval file containing the intervals to run against the SAM
final File inputIntervalsFile = new File("testdata/picard/sam/viewsam_intervals_test.interval_list");
// create temp output file that ViewSam call get written to
final File viewSamOutputFile = File.createTempFile("ViewSamTest.output.", ".sam");
viewSamOutputFile.deleteOnExit();
final ViewSam viewSam = new ViewSam();
viewSam.INPUT = inputSam.getAbsolutePath();
viewSam.INTERVAL_LIST = inputIntervalsFile;
// create a print stream to this file
final PrintStream viewSamPrintStream = new PrintStream(viewSamOutputFile);
// make sure the command line call exited successfully
Assert.assertEquals(viewSam.writeSamText(viewSamPrintStream), 0);
viewSamPrintStream.close();
// load the interval file
final IntervalList inputIntervalsList = IntervalList.fromFile(inputIntervalsFile);
// ViewSam internally utilizes uniqued intervals, so we will compare to the same
final List<Interval> intervals = inputIntervalsList.uniqued().getIntervals();
// make a reader that is not using intervals to load the output file we wrote that
// was written by the call to ViewSam with the given interval file. This will give us
// the "filtered" file that we can compare to the intervals and ensure that only
// overlapped records were written
final SamReader samReader = SamReaderFactory.makeDefault().open(viewSamOutputFile);
// make sure the intervals file caused at least one match to be found
boolean foundMatches = false;
for (final SAMRecord samRecord : samReader) {
// make an interval representing this SAM record
final Interval samRecordInterval = new Interval(samRecord.getContig(), samRecord.getStart(), samRecord.getEnd());
// go through and look to see whether this SAM interval overlaps a filtering interval
boolean samRecordIntervalOverlaps = false;
for (final Interval interval : intervals) {
if (interval.intersects(samRecordInterval)) {
samRecordIntervalOverlaps = true;
// mark that we have found at least one SAM record that overlaps an interval
foundMatches = true;
break;
}
}
// if this SAM record does not overlap an interval, it should not have been written
Assert.assertTrue(samRecordIntervalOverlaps, "SAM record written out was not overlapped by an interval.");
}
// we should have at least one SAM record written to ensure interval filtering worked correctly
Assert.assertTrue(foundMatches, "No SAM records overlapped the given intervals.");
}
}