@Test
public void testWholeIndelReadInIsolation() {
final int firstLocus = 44367789;
// create a test version of the Reads object
ReadProperties readAttributes = createTestReadProperties();
SAMRecord indelOnlyRead =
ArtificialSAMUtils.createArtificialRead(header, "indelOnly", 0, firstLocus, 76);
indelOnlyRead.setReadBases(Utils.dupBytes((byte) 'A', 76));
indelOnlyRead.setBaseQualities(Utils.dupBytes((byte) '@', 76));
indelOnlyRead.setCigarString("76I");
List<SAMRecord> reads = Arrays.asList(indelOnlyRead);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, readAttributes);
// Traditionally, reads that end with indels bleed into the pileup at the following locus.
// Verify that the next pileup contains this read
// and considers it to be an indel-containing read.
Assert.assertTrue(
li.hasNext(),
"Should have found a whole-indel read in the normal base pileup without extended events enabled");
AlignmentContext alignmentContext = li.next();
Assert.assertEquals(
alignmentContext.getLocation().getStart(),
firstLocus,
"Base pileup is at incorrect location.");
ReadBackedPileup basePileup = alignmentContext.getBasePileup();
Assert.assertEquals(basePileup.getReads().size(), 1, "Pileup is of incorrect size");
Assert.assertSame(basePileup.getReads().get(0), indelOnlyRead, "Read in pileup is incorrect");
}
@Test(dataProvider = "LIBSTest")
public void testLIBS(LIBSTest params) {
final int locus = 44367788;
SAMRecord read =
ArtificialSAMUtils.createArtificialRead(header, "read", 0, locus, params.readLength);
read.setReadBases(Utils.dupBytes((byte) 'A', params.readLength));
read.setBaseQualities(Utils.dupBytes((byte) '@', params.readLength));
read.setCigarString(params.cigar);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(Arrays.asList(read), createTestReadProperties());
final LIBS_position tester = new LIBS_position(read);
while (li.hasNext()) {
AlignmentContext alignmentContext = li.next();
ReadBackedPileup p = alignmentContext.getBasePileup();
Assert.assertTrue(p.getNumberOfElements() == 1);
PileupElement pe = p.iterator().next();
tester.stepForwardOnGenome();
Assert.assertEquals(pe.isBeforeDeletedBase(), tester.isBeforeDeletedBase);
Assert.assertEquals(pe.isBeforeDeletionStart(), tester.isBeforeDeletionStart);
Assert.assertEquals(pe.isAfterDeletedBase(), tester.isAfterDeletedBase);
Assert.assertEquals(pe.isAfterDeletionEnd(), tester.isAfterDeletionEnd);
Assert.assertEquals(pe.isBeforeInsertion(), tester.isBeforeInsertion);
Assert.assertEquals(pe.isAfterInsertion(), tester.isAfterInsertion);
Assert.assertEquals(pe.isNextToSoftClip(), tester.isNextToSoftClip);
Assert.assertEquals(pe.getOffset(), tester.getCurrentReadOffset());
}
}
@Test
public void testIndelsInRegularPileup() {
final byte[] bases = new byte[] {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'};
final byte[] indelBases =
new byte[] {'A', 'A', 'A', 'A', 'C', 'T', 'A', 'A', 'A', 'A', 'A', 'A'};
// create a test version of the Reads object
ReadProperties readAttributes = createTestReadProperties();
SAMRecord before = ArtificialSAMUtils.createArtificialRead(header, "before", 0, 1, 10);
before.setReadBases(bases);
before.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
before.setCigarString("10M");
SAMRecord during = ArtificialSAMUtils.createArtificialRead(header, "during", 0, 2, 10);
during.setReadBases(indelBases);
during.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
during.setCigarString("4M2I6M");
SAMRecord after = ArtificialSAMUtils.createArtificialRead(header, "after", 0, 3, 10);
after.setReadBases(bases);
after.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
after.setCigarString("10M");
List<SAMRecord> reads = Arrays.asList(before, during, after);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, readAttributes);
boolean foundIndel = false;
while (li.hasNext()) {
AlignmentContext context = li.next();
ReadBackedPileup pileup = context.getBasePileup().getBaseFilteredPileup(10);
for (PileupElement p : pileup) {
if (p.isBeforeInsertion()) {
foundIndel = true;
Assert.assertEquals(p.getEventLength(), 2, "Wrong event length");
Assert.assertEquals(p.getEventBases(), "CT", "Inserted bases are incorrect");
break;
}
}
}
Assert.assertTrue(foundIndel, "Indel in pileup not found");
}
/**
* Test to make sure that reads supporting only an indel (example cigar string: 76I) are
* represented properly
*/
@Test
public void testWholeIndelReadRepresentedTest() {
final int firstLocus = 44367788, secondLocus = firstLocus + 1;
SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, secondLocus, 1);
read1.setReadBases(Utils.dupBytes((byte) 'A', 1));
read1.setBaseQualities(Utils.dupBytes((byte) '@', 1));
read1.setCigarString("1I");
List<SAMRecord> reads = Arrays.asList(read1);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, createTestReadProperties());
while (li.hasNext()) {
AlignmentContext alignmentContext = li.next();
ReadBackedPileup p = alignmentContext.getBasePileup();
Assert.assertTrue(p.getNumberOfElements() == 1);
PileupElement pe = p.iterator().next();
Assert.assertTrue(pe.isBeforeInsertion());
Assert.assertFalse(pe.isAfterInsertion());
Assert.assertEquals(pe.getEventBases(), "A");
}
SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header, "read2", 0, secondLocus, 10);
read2.setReadBases(Utils.dupBytes((byte) 'A', 10));
read2.setBaseQualities(Utils.dupBytes((byte) '@', 10));
read2.setCigarString("10I");
reads = Arrays.asList(read2);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, createTestReadProperties());
while (li.hasNext()) {
AlignmentContext alignmentContext = li.next();
ReadBackedPileup p = alignmentContext.getBasePileup();
Assert.assertTrue(p.getNumberOfElements() == 1);
PileupElement pe = p.iterator().next();
Assert.assertTrue(pe.isBeforeInsertion());
Assert.assertFalse(pe.isAfterInsertion());
Assert.assertEquals(pe.getEventBases(), "AAAAAAAAAA");
}
}
@Test
public void testXandEQOperators() {
final byte[] bases1 = new byte[] {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'};
final byte[] bases2 = new byte[] {'A', 'A', 'A', 'C', 'A', 'A', 'A', 'A', 'A', 'C'};
// create a test version of the Reads object
ReadProperties readAttributes = createTestReadProperties();
SAMRecord r1 = ArtificialSAMUtils.createArtificialRead(header, "r1", 0, 1, 10);
r1.setReadBases(bases1);
r1.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
r1.setCigarString("10M");
SAMRecord r2 = ArtificialSAMUtils.createArtificialRead(header, "r2", 0, 1, 10);
r2.setReadBases(bases2);
r2.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
r2.setCigarString("3=1X5=1X");
SAMRecord r3 = ArtificialSAMUtils.createArtificialRead(header, "r3", 0, 1, 10);
r3.setReadBases(bases2);
r3.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
r3.setCigarString("3=1X5M1X");
SAMRecord r4 = ArtificialSAMUtils.createArtificialRead(header, "r4", 0, 1, 10);
r4.setReadBases(bases2);
r4.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
r4.setCigarString("10M");
List<SAMRecord> reads = Arrays.asList(r1, r2, r3, r4);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, readAttributes);
while (li.hasNext()) {
AlignmentContext context = li.next();
ReadBackedPileup pileup = context.getBasePileup();
Assert.assertEquals(pileup.depthOfCoverage(), 4);
}
}
@BeforeClass
private void init() throws IOException {
reference = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
dictionary = reference.getSequenceDictionary();
genomeLocParser = new GenomeLocParser(dictionary);
header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test");
header.setSequenceDictionary(dictionary);
header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
readGroup = new GATKSAMReadGroupRecord(header.getReadGroup("test"));
final List<GATKSAMRecord> reads = new ArrayList<>();
for (final String contig : contigs) {
for (int i = 1; i <= numReadsPerContig; i++) {
reads.add(buildSAMRecord("read" + contig + "_" + i, contig, i));
}
}
createBAM(reads);
}
@BeforeClass
public void beforeClass() {
header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
}
/**
* Test to make sure that reads supporting only an indel (example cigar string: 76I) do not
* negatively influence the ordering of the pileup.
*/
@Test
public void testWholeIndelRead() {
final int firstLocus = 44367788, secondLocus = firstLocus + 1;
SAMRecord leadingRead =
ArtificialSAMUtils.createArtificialRead(header, "leading", 0, firstLocus, 76);
leadingRead.setReadBases(Utils.dupBytes((byte) 'A', 76));
leadingRead.setBaseQualities(Utils.dupBytes((byte) '@', 76));
leadingRead.setCigarString("1M75I");
SAMRecord indelOnlyRead =
ArtificialSAMUtils.createArtificialRead(header, "indelOnly", 0, secondLocus, 76);
indelOnlyRead.setReadBases(Utils.dupBytes((byte) 'A', 76));
indelOnlyRead.setBaseQualities(Utils.dupBytes((byte) '@', 76));
indelOnlyRead.setCigarString("76I");
SAMRecord fullMatchAfterIndel =
ArtificialSAMUtils.createArtificialRead(header, "fullMatch", 0, secondLocus, 76);
fullMatchAfterIndel.setReadBases(Utils.dupBytes((byte) 'A', 76));
fullMatchAfterIndel.setBaseQualities(Utils.dupBytes((byte) '@', 76));
fullMatchAfterIndel.setCigarString("75I1M");
List<SAMRecord> reads = Arrays.asList(leadingRead, indelOnlyRead, fullMatchAfterIndel);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, createTestReadProperties());
int currentLocus = firstLocus;
int numAlignmentContextsFound = 0;
while (li.hasNext()) {
AlignmentContext alignmentContext = li.next();
Assert.assertEquals(
alignmentContext.getLocation().getStart(),
currentLocus,
"Current locus returned by alignment context is incorrect");
if (currentLocus == firstLocus) {
List<GATKSAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
Assert.assertEquals(
readsAtLocus.size(), 1, "Wrong number of reads at locus " + currentLocus);
Assert.assertSame(
readsAtLocus.get(0),
leadingRead,
"leadingRead absent from pileup at locus " + currentLocus);
} else if (currentLocus == secondLocus) {
List<GATKSAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
Assert.assertEquals(
readsAtLocus.size(), 2, "Wrong number of reads at locus " + currentLocus);
Assert.assertSame(
readsAtLocus.get(0),
indelOnlyRead,
"indelOnlyRead absent from pileup at locus " + currentLocus);
Assert.assertSame(
readsAtLocus.get(1),
fullMatchAfterIndel,
"fullMatchAfterIndel absent from pileup at locus " + currentLocus);
}
currentLocus++;
numAlignmentContextsFound++;
}
Assert.assertEquals(
numAlignmentContextsFound, 2, "Found incorrect number of alignment contexts");
}
/**
* @author aaron
* @version 1.0
* <p>Class GenomeLocSetTest
* <p>This tests the functions of the GenomeLocSet
*/
public class GenomeLocSortedSetUnitTest extends BaseTest {
private GenomeLocSortedSet mSortedSet = null;
private SAMFileHeader header =
ArtificialSAMUtils.createArtificialSamHeader(
NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
private static final int NUMBER_OF_CHROMOSOMES = 5;
private static final int STARTING_CHROMOSOME = 1;
private static final int CHROMOSOME_SIZE = 1000;
private GenomeLocParser genomeLocParser;
private String contigOneName;
@BeforeClass
public void setup() {
genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
contigOneName = header.getSequenceDictionary().getSequence(1).getSequenceName();
}
@BeforeMethod
public void initializeSortedSet() {
mSortedSet = new GenomeLocSortedSet(genomeLocParser);
}
@Test
public void testAdd() {
GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 0, 0);
assertTrue(mSortedSet.size() == 0);
mSortedSet.add(g);
assertTrue(mSortedSet.size() == 1);
}
@Test
public void testRemove() {
assertTrue(mSortedSet.size() == 0);
GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 0, 0);
mSortedSet.add(g);
assertTrue(mSortedSet.size() == 1);
mSortedSet.remove(g);
assertTrue(mSortedSet.size() == 0);
}
@Test
public void addRegion() {
assertTrue(mSortedSet.size() == 0);
GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 1, 50);
mSortedSet.add(g);
GenomeLoc f = genomeLocParser.createGenomeLoc(contigOneName, 30, 80);
mSortedSet.addRegion(f);
assertTrue(mSortedSet.size() == 1);
}
@Test
public void addRegionsOutOfOrder() {
final String contigTwoName = header.getSequenceDictionary().getSequence(2).getSequenceName();
assertTrue(mSortedSet.size() == 0);
GenomeLoc g = genomeLocParser.createGenomeLoc(contigTwoName, 1, 50);
mSortedSet.add(g);
GenomeLoc f = genomeLocParser.createGenomeLoc(contigOneName, 30, 80);
mSortedSet.addRegion(f);
assertTrue(mSortedSet.size() == 2);
assertTrue(mSortedSet.toList().get(0).getContig().equals(contigOneName));
assertTrue(mSortedSet.toList().get(1).getContig().equals(contigTwoName));
}
@Test(expectedExceptions = IllegalArgumentException.class)
public void addThrowsException() {
assertTrue(mSortedSet.size() == 0);
GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 1, 50);
mSortedSet.add(g);
GenomeLoc f = genomeLocParser.createGenomeLoc(contigOneName, 30, 80);
mSortedSet.add(f);
}
@Test(expectedExceptions = IllegalArgumentException.class)
public void testAddDuplicate() {
assertTrue(mSortedSet.size() == 0);
GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 0, 0);
mSortedSet.add(g);
assertTrue(mSortedSet.size() == 1);
mSortedSet.add(g);
}
@Test
public void mergingOverlappingBelow() {
GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 0, 50);
GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 49, 100);
assertTrue(mSortedSet.size() == 0);
mSortedSet.add(g);
assertTrue(mSortedSet.size() == 1);
mSortedSet.addRegion(e);
assertTrue(mSortedSet.size() == 1);
Iterator<GenomeLoc> iter = mSortedSet.iterator();
GenomeLoc loc = iter.next();
assertEquals(loc.getStart(), 0);
assertEquals(loc.getStop(), 100);
assertEquals(loc.getContigIndex(), 1);
}
@Test
public void overlap() {
for (int i = 1; i < 6; i++) {
final int start = i * 10;
mSortedSet.add(genomeLocParser.createGenomeLoc(contigOneName, start, start + 1));
}
// test matches in and around interval
assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 9, 9)));
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 10, 10)));
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 11, 11)));
assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 12, 12)));
// test matches spanning intervals
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 14, 20)));
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 11, 15)));
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 30, 40)));
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 51, 53)));
// test miss
assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 12, 19)));
// test exact match after miss
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 40, 41)));
// test matches at beginning of intervals
assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 5, 6)));
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 0, 10)));
// test matches at end of intervals
assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 52, 53)));
assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 51, 53)));
assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 52, 53)));
}
@Test
public void mergingOverlappingAbove() {
GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 0, 50);
GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 49, 100);
assertTrue(mSortedSet.size() == 0);
mSortedSet.add(g);
assertTrue(mSortedSet.size() == 1);
mSortedSet.addRegion(e);
assertTrue(mSortedSet.size() == 1);
Iterator<GenomeLoc> iter = mSortedSet.iterator();
GenomeLoc loc = iter.next();
assertEquals(loc.getStart(), 0);
assertEquals(loc.getStop(), 100);
assertEquals(loc.getContigIndex(), 1);
}
@Test
public void deleteAllByRegion() {
GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 1, 100);
mSortedSet.add(e);
for (int x = 1; x < 101; x++) {
GenomeLoc del = genomeLocParser.createGenomeLoc(contigOneName, x, x);
mSortedSet = mSortedSet.subtractRegions(new GenomeLocSortedSet(genomeLocParser, del));
}
assertTrue(mSortedSet.isEmpty());
}
@Test
public void deleteSomeByRegion() {
GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 1, 100);
mSortedSet.add(e);
for (int x = 1; x < 50; x++) {
GenomeLoc del = genomeLocParser.createGenomeLoc(contigOneName, x, x);
mSortedSet = mSortedSet.subtractRegions(new GenomeLocSortedSet(genomeLocParser, del));
}
assertTrue(!mSortedSet.isEmpty());
assertTrue(mSortedSet.size() == 1);
GenomeLoc loc = mSortedSet.iterator().next();
assertTrue(loc.getStop() == 100);
assertTrue(loc.getStart() == 50);
}
@Test
public void deleteSuperRegion() {
GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 10, 20);
GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 70, 100);
mSortedSet.add(g);
mSortedSet.addRegion(e);
assertTrue(mSortedSet.size() == 2);
// now delete a region
GenomeLoc d = genomeLocParser.createGenomeLoc(contigOneName, 15, 75);
mSortedSet = mSortedSet.subtractRegions(new GenomeLocSortedSet(genomeLocParser, d));
Iterator<GenomeLoc> iter = mSortedSet.iterator();
GenomeLoc loc = iter.next();
assertTrue(loc.getStart() == 10);
assertTrue(loc.getStop() == 14);
assertTrue(loc.getContigIndex() == 1);
loc = iter.next();
assertTrue(loc.getStart() == 76);
assertTrue(loc.getStop() == 100);
assertTrue(loc.getContigIndex() == 1);
}
@Test
public void substractComplexExample() {
GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 1, 20);
mSortedSet.add(e);
GenomeLoc r1 = genomeLocParser.createGenomeLoc(contigOneName, 3, 5);
GenomeLoc r2 = genomeLocParser.createGenomeLoc(contigOneName, 10, 12);
GenomeLoc r3 = genomeLocParser.createGenomeLoc(contigOneName, 16, 18);
GenomeLocSortedSet toExclude =
new GenomeLocSortedSet(genomeLocParser, Arrays.asList(r1, r2, r3));
GenomeLocSortedSet remaining = mSortedSet.subtractRegions(toExclude);
// logger.debug("Initial " + mSortedSet);
// logger.debug("Exclude " + toExclude);
// logger.debug("Remaining " + remaining);
assertEquals(mSortedSet.coveredSize(), 20);
assertEquals(toExclude.coveredSize(), 9);
assertEquals(remaining.coveredSize(), 11);
Iterator<GenomeLoc> it = remaining.iterator();
GenomeLoc p1 = it.next();
GenomeLoc p2 = it.next();
GenomeLoc p3 = it.next();
GenomeLoc p4 = it.next();
assertEquals(genomeLocParser.createGenomeLoc(contigOneName, 1, 2), p1);
assertEquals(genomeLocParser.createGenomeLoc(contigOneName, 6, 9), p2);
assertEquals(genomeLocParser.createGenomeLoc(contigOneName, 13, 15), p3);
assertEquals(genomeLocParser.createGenomeLoc(contigOneName, 19, 20), p4);
}
private void testSizeBeforeLocX(int pos, int size) {
GenomeLoc test = genomeLocParser.createGenomeLoc(contigOneName, pos, pos);
assertEquals(
mSortedSet.sizeBeforeLoc(test), size, String.format("X pos=%d size=%d", pos, size));
}
@Test
public void testSizeBeforeLoc() {
GenomeLoc r1 = genomeLocParser.createGenomeLoc(contigOneName, 3, 5);
GenomeLoc r2 = genomeLocParser.createGenomeLoc(contigOneName, 10, 12);
GenomeLoc r3 = genomeLocParser.createGenomeLoc(contigOneName, 16, 18);
mSortedSet.addAll(Arrays.asList(r1, r2, r3));
testSizeBeforeLocX(2, 0);
testSizeBeforeLocX(3, 0);
testSizeBeforeLocX(4, 1);
testSizeBeforeLocX(5, 2);
testSizeBeforeLocX(6, 3);
testSizeBeforeLocX(10, 3);
testSizeBeforeLocX(11, 4);
testSizeBeforeLocX(12, 5);
testSizeBeforeLocX(13, 6);
testSizeBeforeLocX(15, 6);
testSizeBeforeLocX(16, 6);
testSizeBeforeLocX(17, 7);
testSizeBeforeLocX(18, 8);
testSizeBeforeLocX(19, 9);
testSizeBeforeLocX(50, 9);
testSizeBeforeLocX(50, (int) mSortedSet.coveredSize());
}
@Test
public void fromSequenceDictionary() {
mSortedSet =
GenomeLocSortedSet.createSetFromSequenceDictionary(this.header.getSequenceDictionary());
// we should have sequence
assertTrue(mSortedSet.size() == GenomeLocSortedSetUnitTest.NUMBER_OF_CHROMOSOMES);
int seqNumber = 0;
for (GenomeLoc loc : mSortedSet) {
assertTrue(loc.getStart() == 1);
assertTrue(loc.getStop() == GenomeLocSortedSetUnitTest.CHROMOSOME_SIZE);
assertTrue(loc.getContigIndex() == seqNumber);
++seqNumber;
}
assertTrue(seqNumber == GenomeLocSortedSetUnitTest.NUMBER_OF_CHROMOSOMES);
}
// -----------------------------------------------------------------------------------------------
//
// Test getOverlapping
//
// -----------------------------------------------------------------------------------------------
@DataProvider(name = "GetOverlapping")
public Object[][] makeGetOverlappingTest() throws Exception {
final GenomeLocParser genomeLocParser =
new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(b37KGReference)));
List<Object[]> tests = new ArrayList<Object[]>();
final GenomeLoc prev1 = genomeLocParser.createGenomeLoc("19", 1, 10);
final GenomeLoc prev2 = genomeLocParser.createGenomeLoc("19", 20, 50);
final GenomeLoc post1 = genomeLocParser.createGenomeLoc("21", 1, 10);
final GenomeLoc post2 = genomeLocParser.createGenomeLoc("21", 20, 50);
final int chr20Length = genomeLocParser.getContigs().getSequence("20").getSequenceLength();
for (final int regionStart : Arrays.asList(1, 10, chr20Length - 10, chr20Length)) {
for (final int regionSize : Arrays.asList(1, 10, 100)) {
final GenomeLoc region =
genomeLocParser.createGenomeLocOnContig("20", regionStart, regionStart + regionSize);
final GenomeLoc spanning =
genomeLocParser.createGenomeLocOnContig("20", regionStart - 10, region.getStop() + 10);
final GenomeLoc before_into =
genomeLocParser.createGenomeLocOnContig("20", regionStart - 10, regionStart + 1);
final GenomeLoc middle =
genomeLocParser.createGenomeLocOnContig("20", regionStart + 1, regionStart + 2);
final GenomeLoc middle_past =
genomeLocParser.createGenomeLocOnContig(
"20", region.getStop() - 1, region.getStop() + 10);
final List<GenomeLoc> potentials = new LinkedList<GenomeLoc>();
potentials.add(region);
if (spanning != null) potentials.add(spanning);
if (before_into != null) potentials.add(before_into);
if (middle != null) potentials.add(middle);
if (middle_past != null) potentials.add(middle_past);
for (final int n : Arrays.asList(1, 2, 3)) {
for (final List<GenomeLoc> regions : Utils.makePermutations(potentials, n, false)) {
tests.add(new Object[] {new GenomeLocSortedSet(genomeLocParser, regions), region});
tests.add(
new Object[] {
new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, prev1)), region
});
tests.add(
new Object[] {
new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, prev1, prev2)),
region
});
tests.add(
new Object[] {
new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, post1)), region
});
tests.add(
new Object[] {
new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, post1, post2)),
region
});
tests.add(
new Object[] {
new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, prev1, post1)),
region
});
tests.add(
new Object[] {
new GenomeLocSortedSet(
genomeLocParser, Utils.append(regions, prev1, prev2, post1, post2)),
region
});
}
}
}
}
return tests.toArray(new Object[][] {});
}
@Test(dataProvider = "GetOverlapping")
public void testGetOverlapping(final GenomeLocSortedSet intervals, final GenomeLoc region) {
final List<GenomeLoc> expectedOverlapping = intervals.getOverlappingFullSearch(region);
final List<GenomeLoc> actualOverlapping = intervals.getOverlapping(region);
Assert.assertEquals(actualOverlapping, expectedOverlapping);
Assert.assertEquals(
intervals.overlaps(region),
!expectedOverlapping.isEmpty(),
"GenomeLocSortedSet.overlaps didn't return expected result");
}
}