IlluminaBasecallsToSamAdapterClippingTest.java

/*
 * 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
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 * THE SOFTWARE.
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package picard.illumina;

import htsjdk.samtools.ReservedTagConstants;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.util.CollectionUtil;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import picard.cmdline.CommandLineProgramTest;

import java.io.File;
import java.util.List;

import static picard.util.IlluminaUtil.IlluminaAdapterPair.*;


/**
 * Run IlluminaBasecallsToSam on a sample tests, then sanity-check the generated SAM file
 */
public class IlluminaBasecallsToSamAdapterClippingTest extends CommandLineProgramTest {

    private static final File TEST_DATA_DIR = new File("testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls");
    private static final String ALIAS = "myalias";
    private static final String RUN_BARCODE = "305PJAAXX080716";

    public String getCommandLineProgramName() {
        return IlluminaBasecallsToSam.class.getSimpleName();
    }

    /**
     * Run IlluminaBasecallsToSam on a few test cases, and verify that results agree with hand-checked expectation.
     */
    @Test(dataProvider="data")
    public void testBasic(final String LANE, final String readStructure,
                          final String fivePrimerAdapter, final String threePrimerAdapter,
                          final int expectedNumClippedRecords) throws Exception {
        // Create the SAM file from Gerald output
        final File samFile = File.createTempFile("." + LANE + ".illuminaBasecallsToSam", ".sam");
        samFile.deleteOnExit();
        final List<String> illuminaArgv = CollectionUtil.makeList("BASECALLS_DIR=" + TEST_DATA_DIR,
                "LANE=" + LANE,
                "RUN_BARCODE=" + RUN_BARCODE,
                "READ_STRUCTURE=" + readStructure,
                "OUTPUT=" + samFile,
                "ALIAS=" + ALIAS
        );
        if (fivePrimerAdapter != null) {
            illuminaArgv.addAll(CollectionUtil.makeList(
                "ADAPTERS_TO_CHECK=null",
                "FIVE_PRIME_ADAPTER=" + fivePrimerAdapter,
                "THREE_PRIME_ADAPTER=" + threePrimerAdapter
            ));
        }
        Assert.assertEquals(runPicardCommandLine(illuminaArgv), 0);

        // Read the file and confirm it contains what is expected
        final SamReader samReader = SamReaderFactory.makeDefault().open(samFile);

        // look for clipped adaptor attribute in lane 3 PE (2) and in lane 6 (1) non-PE
        int count = 0;
        for (final SAMRecord record : samReader) {
            if (record.getIntegerAttribute(ReservedTagConstants.XT) != null) {
                count++;
                if ((count == 1 || count == 2) && LANE.equals("2")){
                    Assert.assertEquals (114, (int)record.getIntegerAttribute(ReservedTagConstants.XT));
                } else if (count == 1 || count == 2 && LANE.equals("1")) {
                    Assert.assertEquals(68, (int) record.getIntegerAttribute(ReservedTagConstants.XT));
                }
            }
        }

        // Check the total number of clipped records
        Assert.assertEquals(count, expectedNumClippedRecords);

        samReader.close();
        samFile.delete();
    }

    @DataProvider(name="data")
    private Object[][] getIlluminaBasecallsToSamTestData(){
        return new Object[][] {
                // Use the default set of adapters
                {"1", "125T125T", null,                             null,                            32},
                {"2", "125T125T", null,                             null,                            108},

                // Use adapters that don't match
                {"1", "125T125T", "ACGTACGTACGTACGT",               "ACGTACGTACGTACGT",              0},
                {"2", "125T125T", "ACGTACGTACGTACGT",               "ACGTACGTACGTACGT",              0},

                // Add just the "nextera v2" adapters, which should not match
                {"1", "125T125T", NEXTERA_V2.get5PrimeAdapter(),    NEXTERA_V2.get3PrimeAdapter(),   0},
                {"2", "125T125T", NEXTERA_V2.get5PrimeAdapter(),    NEXTERA_V2.get3PrimeAdapter(),   0},

                // Add just the "fludigm" adapters, which should not match
                {"1", "125T125T", FLUIDIGM.get5PrimeAdapter(),      FLUIDIGM.get3PrimeAdapter(),     0},
                {"2", "125T125T", FLUIDIGM.get5PrimeAdapter(),      FLUIDIGM.get3PrimeAdapter(),     0},

                // Add just the "dual indexed" adapters, which should match
                {"1", "125T125T", DUAL_INDEXED.get5PrimeAdapter(),  DUAL_INDEXED.get3PrimeAdapter(), 32},
                {"2", "125T125T", DUAL_INDEXED.get5PrimeAdapter(),  DUAL_INDEXED.get3PrimeAdapter(), 108},

                // Add just the "indexed" adapters, which should match
                {"1", "125T125T", INDEXED.get5PrimeAdapter(),       INDEXED.get3PrimeAdapter(),      32},
                {"2", "125T125T", INDEXED.get5PrimeAdapter(),       INDEXED.get3PrimeAdapter(),      108}
        };
    }
}