WgsMetricsProcessorImplTest.java

/*
 * The MIT License
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 * 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
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 * furnished to do so, subject to the following conditions:
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 * The above copyright notice and this permission notice shall be included in
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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);
    }
}