BCF2UtilsUnitTest.java

/*
* 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 htsjdk.variant.bcf2;

import htsjdk.variant.VariantBaseTest;
import htsjdk.variant.utils.GeneralUtils;
import htsjdk.variant.vcf.VCFContigHeaderLine;
import htsjdk.variant.vcf.VCFFilterHeaderLine;
import htsjdk.variant.vcf.VCFFormatHeaderLine;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
import htsjdk.variant.vcf.VCFHeaderLineCount;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFIDHeaderLine;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.vcf.VCFSimpleHeaderLine;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.LinkedHashSet;
import java.util.List;

/**
 * Tests for BCF2Utils
 */
public final class BCF2UtilsUnitTest extends VariantBaseTest {
    @DataProvider(name = "CollapseExpandTest")
    public Object[][] makeCollapseExpandTest() {
        List<Object[]> tests = new ArrayList<Object[]>();
        tests.add(new Object[]{Arrays.asList("A"), "A", false});
        tests.add(new Object[]{Arrays.asList("A", "B"), ",A,B", true});
        tests.add(new Object[]{Arrays.asList("AB"), "AB", false});
        tests.add(new Object[]{Arrays.asList("AB", "C"), ",AB,C", true});
        tests.add(new Object[]{Arrays.asList(), "", false});
        return tests.toArray(new Object[][]{});
    }

    @Test(dataProvider = "CollapseExpandTest")
    public void testCollapseExpandTest(final List<String> in, final String expectedCollapsed, final boolean isCollapsed) {
        final String actualCollapsed = BCF2Utils.collapseStringList(in);
        Assert.assertEquals(actualCollapsed, expectedCollapsed);
        Assert.assertEquals(BCF2Utils.isCollapsedString(actualCollapsed), isCollapsed);
        if ( isCollapsed )
            Assert.assertEquals(BCF2Utils.explodeStringList(actualCollapsed), in);
    }

    @Test
    public void testCreateDictionary() {
        final List<VCFHeaderLine> inputLines = new ArrayList<VCFHeaderLine>();
        int counter = 0;
        inputLines.add(new VCFFilterHeaderLine(String.valueOf(counter++)));
        inputLines.add(new VCFFilterHeaderLine(String.valueOf(counter++)));
        inputLines.add(new VCFContigHeaderLine(Collections.singletonMap("ID", String.valueOf(counter++)), counter));
        inputLines.add(new VCFContigHeaderLine(Collections.singletonMap("ID", String.valueOf(counter++)), counter));
        inputLines.add(new VCFInfoHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
        inputLines.add(new VCFInfoHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
        inputLines.add(new VCFHeaderLine("x", "misc"));
        inputLines.add(new VCFHeaderLine("y", "misc"));
        inputLines.add(new VCFSimpleHeaderLine("GATKCommandLine","z","misc"));
        inputLines.add(new VCFFormatHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
        inputLines.add(new VCFFormatHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
        final int inputLineCounter = counter;
        final VCFHeader inputHeader = new VCFHeader(new LinkedHashSet<VCFHeaderLine>(inputLines));
        final ArrayList<String> dict = BCF2Utils.makeDictionary(inputHeader);
        final int dict_size = dict.size();
        Assert.assertEquals(7,dict_size);
    }


    @DataProvider(name = "HeaderOrderTestProvider")
    public Object[][] makeHeaderOrderTestProvider() {
        final List<VCFHeaderLine> inputLines = new ArrayList<VCFHeaderLine>();
        final List<VCFHeaderLine> extraLines = new ArrayList<VCFHeaderLine>();

        int counter = 0;
        inputLines.add(new VCFFilterHeaderLine(String.valueOf(counter++)));
        inputLines.add(new VCFFilterHeaderLine(String.valueOf(counter++)));
        inputLines.add(new VCFContigHeaderLine(Collections.singletonMap("ID", String.valueOf(counter++)), counter));
        inputLines.add(new VCFContigHeaderLine(Collections.singletonMap("ID", String.valueOf(counter++)), counter));
        inputLines.add(new VCFInfoHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
        inputLines.add(new VCFInfoHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
        inputLines.add(new VCFFormatHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
        inputLines.add(new VCFFormatHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
        final int inputLineCounter = counter;
        final VCFHeader inputHeader = new VCFHeader(new LinkedHashSet<VCFHeaderLine>(inputLines));

        extraLines.add(new VCFFilterHeaderLine(String.valueOf(counter++)));
        extraLines.add(new VCFContigHeaderLine(Collections.singletonMap("ID", String.valueOf(counter++)), counter));
        extraLines.add(new VCFInfoHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
        extraLines.add(new VCFFormatHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
        extraLines.add(new VCFHeaderLine("x", "misc"));
        extraLines.add(new VCFHeaderLine("y", "misc"));

        List<Object[]> tests = new ArrayList<Object[]>();
        for ( final int extrasToTake : Arrays.asList(0, 1, 2, 3) ) {
            final List<VCFHeaderLine> empty = Collections.emptyList();
            final List<List<VCFHeaderLine>> permutations = extrasToTake == 0
                    ? Collections.singletonList(empty)
                    : GeneralUtils.makePermutations(extraLines, extrasToTake, false);
            for ( final List<VCFHeaderLine> permutation : permutations ) {
                for ( int i = -1; i < inputLines.size(); i++ ) {
                    final List<VCFHeaderLine> allLines = new ArrayList<VCFHeaderLine>(inputLines);
                    if ( i >= 0 )
                        allLines.remove(i);
                    allLines.addAll(permutation);
                    final VCFHeader testHeader = new VCFHeader(new LinkedHashSet<VCFHeaderLine>(allLines));
                    final boolean expectedConsistent = expectedConsistent(testHeader, inputLineCounter);
                    tests.add(new Object[]{inputHeader, testHeader, expectedConsistent});
                }
            }
        }

        // sample name tests
        final List<List<String>> sampleNameTests = Arrays.asList(
                new ArrayList<String>(),
                Arrays.asList("A"),
                Arrays.asList("A", "B"),
                Arrays.asList("A", "B", "C"));
        for ( final List<String> inSamples : sampleNameTests ) {
            for ( final List<String> testSamples : sampleNameTests ) {
                final VCFHeader inputHeaderWithSamples = new VCFHeader(inputHeader.getMetaDataInInputOrder(), inSamples);

                final List<List<String>> permutations = testSamples.isEmpty()
                        ? Collections.singletonList(testSamples)
                        : GeneralUtils.makePermutations(testSamples, testSamples.size(), false);
                for ( final List<String> testSamplesPermutation : permutations ) {
                    final VCFHeader testHeaderWithSamples = new VCFHeader(inputHeader.getMetaDataInInputOrder(), testSamplesPermutation);
                    final boolean expectedConsistent = testSamples.equals(inSamples);
                    tests.add(new Object[]{inputHeaderWithSamples, testHeaderWithSamples, expectedConsistent});
                }
            }
        }

        return tests.toArray(new Object[][]{});
    }

    private static boolean expectedConsistent(final VCFHeader combinationHeader, final int minCounterForInputLines) {
        final List<Integer> ids = new ArrayList<Integer>();
        for ( final VCFHeaderLine line : combinationHeader.getMetaDataInInputOrder() ) {
            if ( line instanceof VCFIDHeaderLine) {
                ids.add(Integer.valueOf(((VCFIDHeaderLine) line).getID()));
            }
        }

        // as long as the start contains all of the ids up to minCounterForInputLines in order
        for ( int i = 0; i < minCounterForInputLines; i++ )
            if ( i >= ids.size() || ids.get(i) != i )
                return false;

        return true;
    }

    //
    // Test to make sure that we detect correctly the case where we can preserve the genotypes data in a BCF2
    // even when the header file is slightly different
    //
    @Test(dataProvider = "HeaderOrderTestProvider")
    public void testHeaderOrder(final VCFHeader inputHeader, final VCFHeader testHeader, final boolean expectedConsistent) {
        final boolean actualOrderConsistency = BCF2Utils.headerLinesAreOrderedConsistently(testHeader, inputHeader);
        Assert.assertEquals(actualOrderConsistency, expectedConsistent);
    }


    private void assertListsAreEquivalent(final List<?> a, final List<?> b) {
        Assert.assertEquals(a.size(), b.size());
        for (int i=0; i<a.size(); i++)
            Assert.assertEquals(a.get(i), b.get(i));
    }

    @DataProvider(name = "toListTestProvider")
    public Object[][] makeToListTest() {
        final List<Object[]> tests = new ArrayList<Object[]>();
        tests.add(new Object[]{Object.class, null, Collections.emptyList()});
        tests.add(new Object[]{Integer.class, 1, Arrays.asList(1)});
        tests.add(new Object[]{Integer.class, new int[]{1, 2, 3}, Arrays.asList(1, 2, 3)});
        tests.add(new Object[]{String.class, Arrays.asList("X", "Y"), Arrays.asList("X", "Y")});
        return tests.toArray(new Object[][]{});
    }

    @Test(dataProvider = "toListTestProvider")
    public void testToList(final Class<?> cls, final Object input, final List<Object> expectedOutput) {
        assertListsAreEquivalent(BCF2Utils.toList(cls, input), expectedOutput);
    }


}