/*
* The MIT License
*
* Copyright (c) 2014 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.SAMFileReader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMValidationError;
import htsjdk.samtools.SamFileValidator;
import htsjdk.samtools.ValidationStringency;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import picard.cmdline.CommandLineProgramTest;
import picard.sam.testers.CleanSamTester;
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.Arrays;
public class CleanSamTest extends CommandLineProgramTest {
private static final File TEST_DATA_DIR = new File("testdata/picard/sam/CleanSam");
private static final String qualityScore = "&/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0";
public String getCommandLineProgramName() {
return CleanSam.class.getSimpleName();
}
@Test(dataProvider = "testCleanSamDataProvider")
public void testCleanSam(final String samFile, final String expectedCigar) throws IOException {
final File cleanedFile = File.createTempFile(samFile + ".", ".sam");
cleanedFile.deleteOnExit();
final String[] args = new String[]{
"INPUT=" + new File(TEST_DATA_DIR, samFile).getAbsolutePath(),
"OUTPUT=" + cleanedFile.getAbsolutePath()
};
Assert.assertEquals(runPicardCommandLine(args), 0);
final SamFileValidator validator = new SamFileValidator(new PrintWriter(System.out), 8000);
validator.setIgnoreWarnings(true);
validator.setVerbose(true, 1000);
validator.setErrorsToIgnore(Arrays.asList(SAMValidationError.Type.MISSING_READ_GROUP));
SAMFileReader samReader = new SAMFileReader(cleanedFile);
samReader.setValidationStringency(ValidationStringency.LENIENT);
final SAMRecord rec = samReader.iterator().next();
samReader.close();
Assert.assertEquals(rec.getCigarString(), expectedCigar);
samReader = new SAMFileReader(cleanedFile);
final boolean validated = validator.validateSamFileVerbose(samReader, null);
samReader.close();
Assert.assertTrue(validated, "ValidateSamFile failed");
}
@DataProvider(name = "testCleanSamDataProvider")
public Object[][] testCleanSamDataProvider() {
return new Object[][]{
{"simple_fits.sam", "100M"},
{"simple_overhang.sam", "99M1S"},
{"fits_with_deletion.sam", "91M2D9M"},
{"overhang_with_deletion.sam", "91M2D8M1S"},
{"trailing_insertion.sam", "99M1I"},
{"long_trailing_insertion.sam", "90M10I"},
};
}
//identical test case using the SamFileTester to generate that SAM file on the fly
@Test(dataProvider = "testCleanSamTesterDataProvider")
public void testCleanSamTester(final String originalCigar, final String expectedCigar, final int defaultChromosomeLength, final int alignStart) throws IOException {
final CleanSamTester cleanSamTester = new CleanSamTester(expectedCigar, 100, defaultChromosomeLength);
// NB: this will add in the mate cigar, when enabled in SamPairUtil, for additional validation
cleanSamTester.addMappedPair(0, alignStart, alignStart, false, false, originalCigar, originalCigar, false, 50);
cleanSamTester.runTest();
}
@DataProvider(name = "testCleanSamTesterDataProvider")
public Object[][] testCleanSamTesterDataProvider() {
return new Object[][]{
{"100M", "100M", 101, 2}, // simple_filts.sam
{"100M", "99M1S", 101, 3}, // simple_overhang.sam
{"91M2D9M", "91M2D9M", 102, 1}, // fits_with_deletion.sam
{"91M2D9M", "91M2D8M1S", 101, 1}, // overhang_with_deletion.sam
{"99M1I", "99M1I", 101, 3}, // trailing_insertion.sam
{"90M10I", "90M10I", 101, 3} // long_trailing_insertion.sam
};
}
}