/*
* 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 org.broadinstitute.gatk.utils.codecs.hapmap;
import htsjdk.tribble.annotation.Strand;
import htsjdk.tribble.readers.LineIterator;
import htsjdk.tribble.readers.LineIteratorImpl;
import htsjdk.tribble.readers.LineReaderUtil;
import htsjdk.tribble.readers.PositionalBufferedStream;
import org.broadinstitute.gatk.utils.BaseTest;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
/**
* Unit tests for the HapMap codec
*/
public class HapMapUnitTest extends BaseTest {
// our sample hapmap file
private final static File hapMapFile = new File(privateTestDir + "genotypes_chr1_ASW_phase3.3_first500.hapmap");
private final static String knownLine = "rs2185539 C/T chr1 556738 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_r" +
"s2185539:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC TC TT CT CC CC CC CC CC CC CC CC CC";
/**
* test reading the header off of the file. We take in the file, read off the first line,
* close the reader, and then ask the HapMap decoder for the header with a new reader. These should
* be equal (i.e. they return the same object).
*/
@Test
public void testReadHeader() {
RawHapMapCodec codec = new RawHapMapCodec();
final LineIterator reader = getLineIterator();
try {
String header = reader.next();
Assert.assertTrue(header.equals(codec.readActualHeader(getLineIterator())));
} finally {
codec.close(reader);
}
}
@Test
public void testKnownRecordConversion() {
RawHapMapCodec codec = new RawHapMapCodec();
RawHapMapFeature feature = (RawHapMapFeature)codec.decode(knownLine);
// check that the alleles are right
Assert.assertEquals(feature.getAlleles().length,2);
Assert.assertTrue("C".equals(feature.getAlleles()[0]));
Assert.assertTrue("T".equals(feature.getAlleles()[1]));
// check the name
Assert.assertTrue("rs2185539".equals(feature.getName()));
// check the position
Assert.assertEquals(feature.getStart(),556738);
Assert.assertEquals(feature.getEnd(),556738);
// check the contig
Assert.assertTrue("chr1".equals(feature.getChr()));
// check the assembly, center, protLSID, assayLSID, panelLSID, and qccode
Assert.assertTrue("ncbi_b36".equals(feature.getAssembly()));
Assert.assertTrue("bbs".equals(feature.getCenter()));
Assert.assertTrue("urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1".equals(feature.getProtLSID()));
Assert.assertTrue("urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2185539:1".equals(feature.getAssayLSID()));
Assert.assertTrue("urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4".equals(feature.getPanelLSID()));
Assert.assertTrue("QC+".equals(feature.getQCCode()));
// check the strand
Assert.assertEquals(feature.getStrand(),Strand.POSITIVE);
// check the genotypes
int x = 0;
for (; x < feature.getGenotypes().length; x++) {
switch (x) {
case 1: Assert.assertTrue("TC".equals(feature.getGenotypes()[x])); break;
case 2: Assert.assertTrue("TT".equals(feature.getGenotypes()[x])); break;
case 3: Assert.assertTrue("CT".equals(feature.getGenotypes()[x])); break;
default: Assert.assertTrue("CC".equals(feature.getGenotypes()[x])); break;
}
}
// assert that we found the correct number of records
Assert.assertEquals(x,13);
}
@Test
public void testReadCorrectNumberOfRecords() {
// setup the record for reading our 500 line file (499 records, 1 header line)
RawHapMapCodec codec = new RawHapMapCodec();
final LineIterator reader = getLineIterator();
int count = 0;
try {
codec.readHeader(reader);
while (reader.hasNext()) {
codec.decode(reader.next());
++count;
}
} catch (IOException e) {
Assert.fail("IOException " + e.getMessage());
} finally {
codec.close(reader);
}
Assert.assertEquals(count,499);
}
@Test
public void testGetSampleNames() {
// setup the record for reading our 500 line file (499 records, 1 header line)
RawHapMapCodec codec = new RawHapMapCodec();
final LineIterator reader = getLineIterator();
String line;
try {
codec.readHeader(reader);
line = reader.next();
RawHapMapFeature feature = (RawHapMapFeature) codec.decode(line);
Assert.assertEquals(feature.getSampleIDs().length,87);
} catch (IOException e) {
Assert.fail("IOException " + e.getMessage());
} finally {
codec.close(reader);
}
}
public LineIterator getLineIterator() {
try {
return new LineIteratorImpl(LineReaderUtil.fromBufferedStream(new PositionalBufferedStream(new FileInputStream(hapMapFile))));
} catch (FileNotFoundException e) {
Assert.fail("Unable to open hapmap file : " + hapMapFile);
}
return null; // for intellij, it doesn't know that assert.fail is fatal
}
}