/*
* The MIT License
*
* Copyright (c) 2014 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.samtools.util;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.variant.vcf.VCFFileReader;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.LinkedList;
import java.util.List;
import java.util.SortedSet;
import java.util.TreeSet;
/**
* Tests the IntervalList class
*/
public class IntervalListTest {
final SAMFileHeader fileHeader;
final IntervalList list1, list2, list3;
public IntervalListTest() {
fileHeader = IntervalList.fromFile(new File("testdata/htsjdk/samtools/intervallist/IntervalListchr123_empty.interval_list")).getHeader();
fileHeader.setSortOrder(SAMFileHeader.SortOrder.unsorted);
list1 = new IntervalList(fileHeader);
list2 = new IntervalList(fileHeader);
list3 = new IntervalList(fileHeader);
list1.add(new Interval("1", 1, 100)); //de-facto: 1:1-200 1:202-300 2:100-150 2:200-300
list1.add(new Interval("1", 101, 200));
list1.add(new Interval("1", 202, 300));
list1.add(new Interval("2", 200, 300));
list1.add(new Interval("2", 100, 150));
list2.add(new Interval("1", 50, 150)); //de-facto 1:50-150 1:301-500 2:1-150 2:250-270 2:290-400
list2.add(new Interval("1", 301, 500));
list2.add(new Interval("2", 1, 150));
list2.add(new Interval("2", 250, 270));
list2.add(new Interval("2", 290, 400));
list3.add(new Interval("1", 25, 400)); //de-facto 1:25-400 2:200-600 3:50-470
list3.add(new Interval("2", 200, 600));
list3.add(new Interval("3", 50, 470));
}
@DataProvider(name = "intersectData")
public Object[][] intersectData() {
final IntervalList intersect123 = new IntervalList(fileHeader);
final IntervalList intersect12 = new IntervalList(fileHeader);
final IntervalList intersect13 = new IntervalList(fileHeader);
final IntervalList intersect23 = new IntervalList(fileHeader);
intersect123.add(new Interval("1", 50, 150));
intersect123.add(new Interval("2", 250, 270));
intersect123.add(new Interval("2", 290, 300));
intersect12.add(new Interval("1", 50, 150));
intersect12.add(new Interval("2", 100, 150));
intersect12.add(new Interval("2", 250, 270));
intersect12.add(new Interval("2", 290, 300));
intersect13.add(new Interval("1", 25, 200));
intersect13.add(new Interval("1", 202, 300));
intersect13.add(new Interval("2", 200, 300));
intersect23.add(new Interval("1", 50, 150));
intersect23.add(new Interval("1", 301, 400));
intersect23.add(new Interval("2", 250, 270));
intersect23.add(new Interval("2", 290, 400));
return new Object[][]{
new Object[]{Arrays.asList(list1, list2, list3), intersect123},
new Object[]{Arrays.asList(list1, list2), intersect12},
new Object[]{Arrays.asList(list2, list1), intersect12},
new Object[]{Arrays.asList(list2, list3), intersect23},
new Object[]{Arrays.asList(list3, list2), intersect23},
new Object[]{Arrays.asList(list1, list3), intersect13},
new Object[]{Arrays.asList(list3, list1), intersect13}
};
}
@Test(dataProvider = "intersectData")
public void testIntersectIntervalLists(final List<IntervalList> lists, final IntervalList list) {
Assert.assertEquals(
CollectionUtil.makeCollection(IntervalList.intersection(lists).iterator()),
CollectionUtil.makeCollection(list.iterator()));
}
@DataProvider(name = "mergeData")
public Object[][] mergeData() {
final IntervalList merge123 = new IntervalList(fileHeader);
final IntervalList merge12 = new IntervalList(fileHeader);
final IntervalList merge23 = new IntervalList(fileHeader);
final IntervalList merge13 = new IntervalList(fileHeader);
merge123.add(new Interval("1", 1, 100)); //de-facto: 1:1-200 1:202-300 2:100-150 2:200-300
merge123.add(new Interval("1", 101, 200));
merge123.add(new Interval("1", 202, 300));
merge123.add(new Interval("2", 200, 300));
merge123.add(new Interval("2", 100, 150));
merge123.add(new Interval("1", 50, 150)); //de-facto 1:50-150 1:301-500 2:1-150 2:250-270 2:290-400
merge123.add(new Interval("1", 301, 500));
merge123.add(new Interval("2", 1, 150));
merge123.add(new Interval("2", 250, 270));
merge123.add(new Interval("2", 290, 400));
merge123.add(new Interval("1", 25, 400)); //de-facto 1:25-400 2:200-600 3:50-470
merge123.add(new Interval("2", 200, 600));
merge123.add(new Interval("3", 50, 470));
merge12.add(new Interval("1", 1, 100)); //de-facto: 1:1-200 1:202-300 2:100-150 2:200-300
merge12.add(new Interval("1", 101, 200));
merge12.add(new Interval("1", 202, 300));
merge12.add(new Interval("2", 200, 300));
merge12.add(new Interval("2", 100, 150));
merge12.add(new Interval("1", 50, 150)); //de-facto 1:50-150 1:301-500 2:1-150 2:250-270 2:290-400
merge12.add(new Interval("1", 301, 500));
merge12.add(new Interval("2", 1, 150));
merge12.add(new Interval("2", 250, 270));
merge12.add(new Interval("2", 290, 400));
merge23.add(new Interval("1", 50, 150)); //de-facto 1:50-150 1:301-500 2:1-150 2:250-270 2:290-400
merge23.add(new Interval("1", 301, 500));
merge23.add(new Interval("2", 1, 150));
merge23.add(new Interval("2", 250, 270));
merge23.add(new Interval("2", 290, 400));
merge23.add(new Interval("1", 25, 400)); //de-facto 1:25-400 2:200-600 3:50-470
merge23.add(new Interval("2", 200, 600));
merge23.add(new Interval("3", 50, 470));
merge13.add(new Interval("1", 1, 100)); //de-facto: 1:1-200 1:202-300 2:100-150 2:200-300
merge13.add(new Interval("1", 101, 200));
merge13.add(new Interval("1", 202, 300));
merge13.add(new Interval("2", 200, 300));
merge13.add(new Interval("2", 100, 150));
merge13.add(new Interval("1", 25, 400)); //de-facto 1:25-400 2:200-600 3:50-470
merge13.add(new Interval("2", 200, 600));
merge13.add(new Interval("3", 50, 470));
return new Object[][]{
new Object[]{Arrays.asList(list1, list2, list3), merge123},
new Object[]{Arrays.asList(list1, list2), merge12},
new Object[]{Arrays.asList(list2, list3), merge23},
new Object[]{Arrays.asList(list1, list3), merge13}
};
}
@Test(dataProvider = "mergeData")
public void testMergeIntervalLists(final List<IntervalList> lists, final IntervalList list) {
Assert.assertEquals(
CollectionUtil.makeCollection(IntervalList.concatenate(lists).iterator()),
CollectionUtil.makeCollection(list.iterator()));
}
@DataProvider(name = "unionData")
public Object[][] unionData() {
final IntervalList union123 = new IntervalList(fileHeader);
final IntervalList union12 = new IntervalList(fileHeader);
final IntervalList union13 = new IntervalList(fileHeader);
final IntervalList union23 = new IntervalList(fileHeader);
union123.add(new Interval("1", 1, 500));
union123.add(new Interval("2", 1, 150));
union123.add(new Interval("2", 200, 600));
union123.add(new Interval("3", 50, 470));
union12.add(new Interval("1", 1, 200));
union12.add(new Interval("1", 202, 500));
union12.add(new Interval("2", 1, 150));
union12.add(new Interval("2", 200, 400));
union23.add(new Interval("1", 25, 500));
union23.add(new Interval("2", 1, 150));
union23.add(new Interval("2", 200, 600));
union23.add(new Interval("3", 50, 470));
union13.add(new Interval("1", 1, 400));
union13.add(new Interval("2", 100, 150));
union13.add(new Interval("2", 200, 600));
union13.add(new Interval("3", 50, 470));
return new Object[][]{
new Object[]{Arrays.asList(list1, list2, list3), union123},
new Object[]{Arrays.asList(list1, list2), union12},
new Object[]{Arrays.asList(list1, list2), union12},
new Object[]{Arrays.asList(list2, list3), union23},
new Object[]{Arrays.asList(list2, list3), union23},
new Object[]{Arrays.asList(list1, list3), union13},
new Object[]{Arrays.asList(list1, list3), union13}
};
}
@Test(dataProvider = "unionData", enabled = true)
public void testUnionIntervalLists(final List<IntervalList> lists, final IntervalList list) {
Assert.assertEquals(
CollectionUtil.makeCollection(IntervalList.union(lists).iterator()),
CollectionUtil.makeCollection(list.iterator()));
}
@DataProvider(name = "invertData")
public Object[][] invertData() {
final IntervalList invert1 = new IntervalList(fileHeader);
final IntervalList invert2 = new IntervalList(fileHeader);
final IntervalList invert3 = new IntervalList(fileHeader);
final IntervalList full = new IntervalList(fileHeader);
final IntervalList fullChopped = new IntervalList(fileHeader);
final IntervalList empty = new IntervalList(fileHeader);
invert1.add(new Interval("1", 201, 201));
invert1.add(new Interval("1", 301, fileHeader.getSequence("1").getSequenceLength()));
invert1.add(new Interval("2", 1, 99));
invert1.add(new Interval("2", 151, 199));
invert1.add(new Interval("2", 301, fileHeader.getSequence("2").getSequenceLength()));
invert1.add(new Interval("3", 1, fileHeader.getSequence("3").getSequenceLength()));
invert2.add(new Interval("1", 1, 49));
invert2.add(new Interval("1", 151, 300));
invert2.add(new Interval("1", 501, fileHeader.getSequence("1").getSequenceLength()));
invert2.add(new Interval("2", 151, 249));
invert2.add(new Interval("2", 271, 289));
invert2.add(new Interval("2", 401, fileHeader.getSequence("2").getSequenceLength()));
invert2.add(new Interval("3", 1, fileHeader.getSequence("3").getSequenceLength()));
invert3.add(new Interval("1", 1, 24));
invert3.add(new Interval("1", 401, fileHeader.getSequence("1").getSequenceLength()));
invert3.add(new Interval("2", 1, 199));
invert3.add(new Interval("2", 601, fileHeader.getSequence("2").getSequenceLength()));
invert3.add(new Interval("3", 1, 49));
invert3.add(new Interval("3", 471, fileHeader.getSequence("3").getSequenceLength()));
for (final SAMSequenceRecord samSequenceRecord : fileHeader.getSequenceDictionary().getSequences()) {
full.add(new Interval(samSequenceRecord.getSequenceName(), 1, samSequenceRecord.getSequenceLength()));
fullChopped.add(new Interval(samSequenceRecord.getSequenceName(), 1, samSequenceRecord.getSequenceLength() / 2));
fullChopped.add(new Interval(samSequenceRecord.getSequenceName(), samSequenceRecord.getSequenceLength() / 2 + 1, samSequenceRecord.getSequenceLength()));
}
return new Object[][]{
new Object[]{list1, invert1},
new Object[]{list2, invert2},
new Object[]{list3, invert3},
new Object[]{full, empty},
new Object[]{empty, full},
new Object[]{fullChopped, empty}
};
}
@Test(dataProvider = "invertData")
public void testInvertSquared(final IntervalList list, @SuppressWarnings("UnusedParameters") final IntervalList ignored) throws Exception {
final IntervalList inverseSquared = IntervalList.invert(IntervalList.invert(list));
final IntervalList originalClone = new IntervalList(list.getHeader());
for (final Interval interval : list) {
originalClone.add(interval);
}
Assert.assertEquals(
CollectionUtil.makeCollection(inverseSquared.iterator()),
CollectionUtil.makeCollection(originalClone.uniqued().iterator()));
}
@Test(dataProvider = "invertData")
public void testInvert(final IntervalList list, final IntervalList inverse) throws Exception {
Assert.assertEquals(
CollectionUtil.makeCollection(IntervalList.invert(list).iterator()),
CollectionUtil.makeCollection(inverse.iterator()));
}
@DataProvider(name = "subtractSingletonData")
public Object[][] subtractSingletonData() {
final IntervalList subtract1_from_2 = new IntervalList(fileHeader);
final IntervalList subtract2_from_3 = new IntervalList(fileHeader);
final IntervalList subtract1_from_3 = new IntervalList(fileHeader);
final IntervalList subtract3_from_1 = new IntervalList(fileHeader);
subtract1_from_2.add(new Interval("1", 301, 500));
subtract1_from_2.add(new Interval("2", 1, 99));
subtract1_from_2.add(new Interval("2", 301, 400));
subtract2_from_3.add(new Interval("1", 25, 49));
subtract2_from_3.add(new Interval("1", 151, 300));
subtract2_from_3.add(new Interval("2", 200, 249));
subtract2_from_3.add(new Interval("2", 271, 289));
subtract2_from_3.add(new Interval("2", 401, 600));
subtract2_from_3.add(new Interval("3", 50, 470));
subtract1_from_3.add(new Interval("1", 201, 201));
subtract1_from_3.add(new Interval("1", 301, 400));
subtract1_from_3.add(new Interval("2", 301, 600));
subtract1_from_3.add(new Interval("3", 50, 470));
subtract3_from_1.add(new Interval("1", 1, 49)); //de-facto 1:25-400 2:200-600 3:50-470
subtract3_from_1.add(new Interval("2", 100, 150));
return new Object[][]{
new Object[]{list2, list1, subtract1_from_2},
new Object[]{list3, list2, subtract2_from_3},
new Object[]{list3, list1, subtract1_from_3},
};
}
@DataProvider(name = "subtractData")
public Object[][] subtractData() {
final IntervalList subtract12_from_3 = new IntervalList(fileHeader);
subtract12_from_3.add(new Interval("1", 201, 201));
subtract12_from_3.add(new Interval("2", 401, 600));
subtract12_from_3.add(new Interval("3", 50, 470));
return new Object[][]{
new Object[]{CollectionUtil.makeList(list3), CollectionUtil.makeList(list1, list2), subtract12_from_3},
};
}
@Test(dataProvider = "subtractData")
public void testSubtractIntervalLists(final List<IntervalList> fromLists, final List<IntervalList> whatLists, final IntervalList list) {
Assert.assertEquals(
CollectionUtil.makeCollection(IntervalList.subtract(fromLists, whatLists).iterator()),
CollectionUtil.makeCollection(list.iterator()));
}
@Test(dataProvider = "subtractSingletonData")
public void testSubtractSingletonIntervalLists(final IntervalList fromLists, final IntervalList whatLists, final IntervalList list) {
Assert.assertEquals(
CollectionUtil.makeCollection(IntervalList.subtract(fromLists, whatLists).iterator()),
CollectionUtil.makeCollection(list.iterator()));
}
@Test(dataProvider = "subtractSingletonData")
public void testSubtractSingletonasListIntervalList(final IntervalList fromLists, final IntervalList whatLists, final IntervalList list) {
Assert.assertEquals(
CollectionUtil.makeCollection(IntervalList.subtract(Collections.singletonList(fromLists), Collections.singletonList(whatLists)).iterator()),
CollectionUtil.makeCollection(list.iterator()));
}
@DataProvider(name = "VCFCompData")
public Object[][] VCFCompData() {
return new Object[][]{
new Object[]{"testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTest.vcf", "testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestComp.interval_list", false},
new Object[]{"testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTest.vcf", "testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestCompInverse.interval_list", true},
new Object[]{"testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf", "testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManualComp.interval_list", false},
new Object[]{"testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf", "testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestCompInverseManual.interval_list", true}
};
}
@Test(dataProvider = "VCFCompData")
public void testFromVCF(final String vcf, final String compInterval, final boolean invertVCF) {
final File vcfFile = new File(vcf);
final File compIntervalFile = new File(compInterval);
final IntervalList compList = IntervalList.fromFile(compIntervalFile);
final IntervalList list = invertVCF ? IntervalList.invert(VCFFileReader.fromVcf(vcfFile)) : VCFFileReader.fromVcf(vcfFile);
compList.getHeader().getSequenceDictionary().assertSameDictionary(list.getHeader().getSequenceDictionary());
final Collection<Interval> intervals = CollectionUtil.makeCollection(list.iterator());
final Collection<Interval> compIntervals = CollectionUtil.makeCollection(compList.iterator());
//assert that the intervals correspond
Assert.assertEquals(intervals, compIntervals);
final List<String> intervalNames = new LinkedList<String>();
final List<String> compIntervalNames = new LinkedList<String>();
for (final Interval interval : intervals) {
intervalNames.add(interval.getName());
}
for (final Interval interval : compIntervals) {
compIntervalNames.add(interval.getName());
}
//assert that the names match
Assert.assertEquals(intervalNames, compIntervalNames);
}
@DataProvider
public Object[][] testFromSequenceData() {
return new Object[][]{
new Object[]{"testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestComp.interval_list", "1", 249250621},
new Object[]{"testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestComp.interval_list", "2", 243199373},
new Object[]{"testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestComp.interval_list", "3", 198022430},
};
}
@Test(dataProvider = "testFromSequenceData")
public void testFromSequenceName(final String intervalList, final String referenceName, final Integer length) {
final IntervalList intervals = IntervalList.fromFile(new File(intervalList));
final IntervalList test = IntervalList.fromName(intervals.getHeader(), referenceName);
Assert.assertEquals(test.getIntervals(), CollectionUtil.makeList(new Interval(referenceName, 1, length)));
}
@Test
public void testMerges() {
SortedSet<Interval> intervals = new TreeSet<Interval>() {{
add(new Interval("1", 500, 600, false, "foo"));
add(new Interval("1", 550, 650, false, "bar"));
add(new Interval("1", 625, 699, false, "splat"));
}};
Interval out = IntervalList.merge(intervals, false);
Assert.assertEquals(out.getStart(), 500);
Assert.assertEquals(out.getEnd(), 699);
intervals.add(new Interval("1", 626, 629, false, "whee"));
out = IntervalList.merge(intervals, false);
Assert.assertEquals(out.getStart(), 500);
Assert.assertEquals(out.getEnd(), 699);
}
}