/*
* 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 htsjdk.samtools;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
/**
* Confirm that integer tag types are stored and retrieved properly.
*
* @author alecw@broadinstitute.org
*/
public class SAMIntegerTagTest {
private static final File TEST_DATA_DIR = new File("testdata/htsjdk/samtools/SAMIntegerTagTest");
private static final String BYTE_TAG = "BY";
private static final String SHORT_TAG = "SH";
private static final String INTEGER_TAG = "IN";
private static final String UNSIGNED_INTEGER_TAG = "UI";
private static final String STRING_TAG = "ST";
@Test
public void testBAM() throws Exception {
final SAMRecord rec = writeAndReadSamRecord("bam");
Assert.assertTrue(rec.getAttribute(BYTE_TAG) instanceof Integer);
Assert.assertEquals(((Number)rec.getAttribute(BYTE_TAG)).intValue(), 1);
Assert.assertTrue(rec.getAttribute(SHORT_TAG) instanceof Integer);
Assert.assertEquals(((Number)rec.getAttribute(SHORT_TAG)).intValue(), 1);
Assert.assertTrue(rec.getAttribute(INTEGER_TAG) instanceof Integer);
Assert.assertEquals(((Number)rec.getAttribute(INTEGER_TAG)).intValue(), 1);
}
@Test
public void testSAM() throws Exception {
final SAMRecord rec = writeAndReadSamRecord("sam");
Assert.assertTrue(rec.getAttribute(BYTE_TAG) instanceof Integer);
Assert.assertEquals(((Number)rec.getAttribute(BYTE_TAG)).intValue(), 1);
Assert.assertTrue(rec.getAttribute(SHORT_TAG) instanceof Integer);
Assert.assertEquals(((Number)rec.getAttribute(SHORT_TAG)).intValue(), 1);
Assert.assertTrue(rec.getAttribute(INTEGER_TAG) instanceof Integer);
Assert.assertEquals(((Number)rec.getAttribute(INTEGER_TAG)).intValue(), 1);
}
@Test(expectedExceptions = SAMException.class)
public void testUnsignedIntegerBAM() throws Exception {
SAMRecord rec = createSamRecord();
final long val = 1l + Integer.MAX_VALUE;
rec.setAttribute(UNSIGNED_INTEGER_TAG, val);
Assert.fail("Exception should have been thrown.");
}
/**
* Cannot store unsigned int in SAM text format.
*/
@Test(expectedExceptions = SAMException.class)
public void testUnsignedIntegerSAM() throws Exception {
final SAMRecord rec = createSamRecord();
final long val = 1l + Integer.MAX_VALUE;
rec.setAttribute(UNSIGNED_INTEGER_TAG, val);
}
@Test
public void testGetTypedAttributeMethods() throws Exception {
final SAMRecord rec = writeAndReadSamRecord("bam");
Assert.assertEquals(rec.getByteAttribute(INTEGER_TAG).intValue(), 1);
Assert.assertEquals(rec.getShortAttribute(INTEGER_TAG).intValue(), 1);
Assert.assertEquals(rec.getIntegerAttribute(INTEGER_TAG).intValue(), 1);
}
/**
* Should be an exception if a typed attribute call is made for the wrong type.
*/
@Test(expectedExceptions = RuntimeException.class)
public void testGetTypedAttributeForWrongType() throws Exception {
final SAMRecord rec = createSamRecord();
rec.setAttribute(STRING_TAG, "Hello, World!");
writeAndReadSamRecord("bam", rec);
rec.getIntegerAttribute(STRING_TAG);
Assert.fail("Exception should have been thrown.");
}
/**
* Should be an exception if a typed attribute call is made for a value that cannot
* be coerced into the correct type.
* This test is a little lame because a RuntimeException could be thrown for some other reason.
*/
@Test(expectedExceptions = RuntimeException.class)
public void testGetTypedAttributeOverflow() throws Exception {
final SAMRecord rec = createSamRecord();
rec.setAttribute(INTEGER_TAG, Integer.MAX_VALUE);
writeAndReadSamRecord("bam", rec);
rec.getShortAttribute(INTEGER_TAG);
Assert.fail("Exception should have been thrown.");
}
/**
* Should be an exception if a typed attribute call is made for a value that cannot
* be coerced into the correct type.
* This test is a little lame because a RuntimeException could be thrown for some other reason.
*/
@Test(expectedExceptions = RuntimeException.class)
public void testGetTypedAttributeUnerflow() throws Exception {
final SAMRecord rec = createSamRecord();
rec.setAttribute(INTEGER_TAG, Integer.MIN_VALUE);
writeAndReadSamRecord("bam", rec);
rec.getShortAttribute(INTEGER_TAG);
Assert.fail("Exception should have been thrown.");
}
/**
* Create a SAMRecord with integer tags of various sizes, write to a file, and read it back.
* @param format "sam" or "bam".
* @return The record after having being read from file.
*/
private SAMRecord writeAndReadSamRecord(final String format) throws IOException {
SAMRecord rec = createSamRecord();
rec.setAttribute(BYTE_TAG, (byte)1);
rec.setAttribute(SHORT_TAG, (short)1);
rec.setAttribute(INTEGER_TAG, 1);
rec = writeAndReadSamRecord(format, rec);
return rec;
}
/**
* Write a SAMRecord to a SAM file in the given format, and read it back.
* @param format "sam" or "bam".
* @param rec The record to write.
* @return The same record, after having being written and read back.
*/
private SAMRecord writeAndReadSamRecord(final String format, SAMRecord rec) throws IOException {
final File bamFile = File.createTempFile("htsjdk-writeAndReadSamRecord.", "." + format);
final SAMFileWriter bamWriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(rec.getHeader(), false, bamFile);
bamWriter.addAlignment(rec);
bamWriter.close();
final SAMFileReader reader = new SAMFileReader(bamFile);
rec = reader.iterator().next();
reader.close();
bamFile.delete();
return rec;
}
private SAMRecord createSamRecord() {
final SAMRecordSetBuilder builder = new SAMRecordSetBuilder(false, SAMFileHeader.SortOrder.unsorted);
builder.addFrag("readA", 20, 140, false);
return builder.iterator().next();
}
@Test(expectedExceptions = {SAMFormatException.class})
public void testBadSamStrict() {
final SAMFileReader reader = new SAMFileReader(new File(TEST_DATA_DIR, "variousAttributes.sam"));
reader.iterator().next();
Assert.fail("Should not reach.");
}
@Test(expectedExceptions = {RuntimeException.class})
public void testBadBamStrict() {
final SAMFileReader reader = new SAMFileReader(new File(TEST_DATA_DIR, "variousAttributes.bam"), true);
reader.iterator().next();
Assert.fail("Should not reach.");
}
@Test
public void testBadBamLenient() {
final SAMFileReader reader = new SAMFileReader(new File(TEST_DATA_DIR, "variousAttributes.bam"), true);
reader.setValidationStringency(ValidationStringency.LENIENT);
final SAMRecord rec = reader.iterator().next();
final Map<String, Number> expectedTags = new HashMap<String, Number>();
expectedTags.put("SB", -128);
expectedTags.put("UB", 129);
expectedTags.put("SS", 32767);
expectedTags.put("US", 65535);
expectedTags.put("SI", 2147483647);
expectedTags.put("I2", -2147483647);
expectedTags.put("UI", 4294967295L);
for (final Map.Entry<String, Number> entry : expectedTags.entrySet()) {
final Object value = rec.getAttribute(entry.getKey());
Assert.assertEquals(value, entry.getValue());
}
reader.close();
}
}