/*
* The MIT License
*
* Copyright (c) 2009 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.SAMFileHeader;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.SAMRecord;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import picard.cmdline.CommandLineProgramTest;
import picard.PicardException;
import java.io.File;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: ktibbett
* Date: Jul 20, 2010
* Time: 10:27:58 AM
* To change this template use File | Settings | File Templates.
*/
public class RevertSamTest extends CommandLineProgramTest {
public static final String basicSamToRevert = "testdata/picard/sam/revert_sam_basic.sam";
public static final String negativeTestSamToRevert = "testdata/picard/sam/revert_sam_negative.sam";
private static final String revertedQualities =
"11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111";
private static final String unmappedRead = "both_reads_present_only_first_aligns/2";
public String getCommandLineProgramName() {
return RevertSam.class.getSimpleName();
}
@Test(dataProvider="positiveTestData")
public void basicPositiveTests(final SAMFileHeader.SortOrder so, final boolean removeDuplicates, final boolean removeAlignmentInfo,
final boolean restoreOriginalQualities, final String sample, final String library,
final List<String> attributesToClear) throws Exception {
final File output = File.createTempFile("reverted", ".sam");
final RevertSam reverter = new RevertSam();
final String args[] = new String[5 + (so != null ? 1 : 0) + attributesToClear.size() + (sample != null ? 1 : 0) + (library != null ? 1 : 0)];
int index = 0;
args[index++] = "INPUT=" + basicSamToRevert;
args[index++] = "OUTPUT=" + output.getAbsolutePath();
if (so != null) {
args[index++] = "SORT_ORDER=" + so.name();
}
args[index++] = "REMOVE_DUPLICATE_INFORMATION=" + removeDuplicates;
args[index++] = "REMOVE_ALIGNMENT_INFORMATION=" + removeAlignmentInfo;
args[index++] = "RESTORE_ORIGINAL_QUALITIES=" + restoreOriginalQualities;
if (sample != null) {
args[index++] = "SAMPLE_ALIAS=" + sample;
}
if (library != null) {
args[index++] = "LIBRARY_NAME=" + library;
}
for (final String attr : attributesToClear) {
args[index++] = "ATTRIBUTE_TO_CLEAR=" + attr;
}
runPicardCommandLine(args);
final SAMFileReader reader = new SAMFileReader(output);
final SAMFileHeader header = reader.getFileHeader();
Assert.assertEquals(header.getSortOrder(), SAMFileHeader.SortOrder.queryname);
Assert.assertEquals(header.getProgramRecords().size(), removeAlignmentInfo ? 0 : 1);
for (final SAMReadGroupRecord rg : header.getReadGroups()) {
if (sample != null) {
Assert.assertEquals(rg.getSample(), sample);
}
else {
Assert.assertEquals(rg.getSample(), "Hi,Mom!");
}
if (library != null) {
Assert.assertEquals(rg.getLibrary(), library);
}
else {
Assert.assertEquals(rg.getLibrary(), "my-library");
}
}
for (final SAMRecord rec : reader) {
if (removeDuplicates) {
Assert.assertFalse(rec.getDuplicateReadFlag(),
"Duplicates should have been removed: " + rec.getReadName());
}
if (removeAlignmentInfo) {
Assert.assertTrue(rec.getReadUnmappedFlag(),
"Alignment info should have been removed: " + rec.getReadName());
}
if (restoreOriginalQualities && !unmappedRead.equals(
rec.getReadName() + "/" + (rec.getFirstOfPairFlag() ? "1" : "2"))) {
Assert.assertEquals(rec.getBaseQualityString(), revertedQualities);
} else {
Assert.assertNotSame(rec.getBaseQualityString(), revertedQualities);
}
for (final SAMRecord.SAMTagAndValue attr : rec.getAttributes()) {
if (removeAlignmentInfo || (!attr.tag.equals("PG") && !attr.tag.equals("NM")
&& !attr.tag.equals("MQ"))) {
Assert.assertFalse(reverter.ATTRIBUTE_TO_CLEAR.contains(attr.tag),
attr.tag + " should have been cleared.");
}
}
}
}
@DataProvider(name="positiveTestData")
public Object[][] getPostitiveTestData() {
return new Object[][] {
{null, true, true, true, null, null, Collections.EMPTY_LIST},
{SAMFileHeader.SortOrder.queryname, true, true, true, "Hey,Dad!", null, Arrays.asList("XT")},
{null, false, true, false, "Hey,Dad!", "NewLibraryName", Arrays.asList("XT")},
{null, false, false, false, null, null, Collections.EMPTY_LIST}
};
}
@Test(dataProvider="negativeTestData", expectedExceptions = {PicardException.class})
public void basicNegativeTest(final String sample, final String library) throws Exception {
final File output = File.createTempFile("bad", ".sam");
final RevertSam reverter = new RevertSam();
final String args[] = new String[2 + (sample != null ? 1 : 0) + (library != null ? 1 : 0)];
int index = 0;
args[index++] = "INPUT=" + negativeTestSamToRevert;
args[index++] = "OUTPUT=" + output.getAbsolutePath();
if (sample != null) {
args[index++] = "SAMPLE_ALIAS=" + sample;
}
if (library != null) {
args[index++] = "LIBRARY_NAME=" + library;
}
runPicardCommandLine(args);
Assert.fail("Negative test should have thrown an exception and didn't");
}
@DataProvider(name="negativeTestData")
public Object[][] getNegativeTestData() {
return new Object[][] {
{"NewSample", null},
{null, "NewLibrary"},
{"NewSample", "NewLibrary"}
};
}
}