/*
* The MIT License
*
* Copyright (c) 2011 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 htsjdk.samtools.util;
import htsjdk.samtools.BamFileIoUtils;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.SAMFileWriter;
import htsjdk.samtools.SAMFileWriterFactory;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordIterator;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.util.Arrays;
public class IupacTest {
@Test(dataProvider = "basicDataProvider")
public void basic(final String tempFileExtension) throws Exception {
final File outputFile = File.createTempFile("iupacTest.", tempFileExtension);
outputFile.deleteOnExit();
final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(new SAMFileHeader(), false, outputFile);
final String bases1 = "=ACMGRSVTWYHKDBNA";
final String bases2 = "A=ACMGRSVTWYHKDBN"; // Test both high-order and low-order base encoding.
final byte[] quals = new byte[bases1.length()];
Arrays.fill(quals, (byte)20);
final String[] reads = {bases1, bases1.toLowerCase(), bases2, bases2.toLowerCase()};
for (int i = 0; i < reads.length; ++i) {
final SAMRecord rec = new SAMRecord(writer.getFileHeader());
rec.setReadName("read" + i);
rec.setReadUnmappedFlag(true);
rec.setReadString(reads[i]);
rec.setBaseQualities(quals);
writer.addAlignment(rec);
}
writer.close();
final SAMFileReader reader = new SAMFileReader(outputFile);
final SAMRecordIterator it = reader.iterator();
for (int i = 0; i < reads.length; ++i) {
final SAMRecord rec = it.next();
Assert.assertEquals(rec.getReadString(), reads[i].toUpperCase());
}
reader.close();
}
@DataProvider(name = "basidDataProvider")
public Object[][] basicDataProvider() {
return new Object[][] {
{BamFileIoUtils.BAM_FILE_EXTENSION},
{".sam"}
};
}
}