/*
* The MIT License
*
* Copyright (c) 2016 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
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* THE SOFTWARE.
*/
package picard.analysis;
import htsjdk.samtools.reference.ReferenceSequenceFile;
import htsjdk.samtools.reference.ReferenceSequenceFileWalker;
import htsjdk.samtools.util.AbstractLocusIterator;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.ProgressLogger;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
import static org.testng.Assert.assertEquals;
import static picard.analysis.CollectWgsMetricsTestUtils.createIntervalList;
import static picard.analysis.CollectWgsMetricsTestUtils.createReadEndsIterator;
import static picard.analysis.CollectWgsMetricsTestUtils.exampleSamOneRead;
import static picard.analysis.CollectWgsMetricsTestUtils.getReferenceSequenceFileWalker;
import static picard.analysis.CollectWgsMetricsTestUtils.createReferenceSequenceFile;
public class WgsMetricsProcessorImplTest {
private ProgressLogger progress;
@BeforeTest
public void setUp(){
progress = new ProgressLogger(Log.getInstance(WgsMetricsProcessorImpl.class));
}
@Test
public void testForProcessFile(){
AbstractLocusIterator iterator = createReadEndsIterator(exampleSamOneRead);
CollectWgsMetrics collectWgsMetrics = new CollectWgsMetrics();
FastWgsMetricsCollector collector = new FastWgsMetricsCollector(collectWgsMetrics, 100, createIntervalList());
WgsMetricsProcessorImpl wgsMetricsProcessor =
new WgsMetricsProcessorImpl(iterator, getReferenceSequenceFileWalker(), collector, progress);
wgsMetricsProcessor.processFile();
assertEquals(20, collector.counter);
}
@Test
public void testForFilteredBases(){
AbstractLocusIterator iterator = createReadEndsIterator(exampleSamOneRead);
CollectWgsMetrics collectWgsMetrics = new CollectWgsMetrics();
FastWgsMetricsCollector collector = new FastWgsMetricsCollector(collectWgsMetrics, 100, createIntervalList());
String secondReferenceString = ">ref\nNNNNNNNNNNAATATTCTTC";
ReferenceSequenceFile referenceSequenceFile = createReferenceSequenceFile(secondReferenceString);
ReferenceSequenceFileWalker refWalker = new ReferenceSequenceFileWalker(referenceSequenceFile);
WgsMetricsProcessorImpl wgsMetricsProcessor =
new WgsMetricsProcessorImpl(iterator, refWalker, collector, progress);
wgsMetricsProcessor.processFile();
assertEquals(10, collector.counter);
}
@Test
public void testForExitAfter(){
AbstractLocusIterator iterator = createReadEndsIterator(exampleSamOneRead);
CollectWgsMetrics collectWgsMetrics = new CollectWgsMetrics();
collectWgsMetrics.STOP_AFTER = 16;
AbstractWgsMetricsCollector collector = new FastWgsMetricsCollector(collectWgsMetrics, 100, null);
WgsMetricsProcessorImpl wgsMetricsProcessor =
new WgsMetricsProcessorImpl(iterator, getReferenceSequenceFileWalker(), collector, progress);
wgsMetricsProcessor.processFile();
assertEquals(15, collector.counter);
}
}