/
FillGapsTaskUtilsTest.java
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/
FillGapsTaskUtilsTest.java
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package org.opencb.opencga.storage.hadoop.variant.gaps;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.hadoop.conf.Configuration;
import org.junit.Test;
import org.opencb.biodata.models.variant.Variant;
import org.opencb.biodata.models.variant.protobuf.VcfSliceProtos;
import org.opencb.opencga.storage.core.metadata.StudyConfiguration;
import org.opencb.opencga.storage.hadoop.variant.GenomeHelper;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.ListIterator;
import static junit.framework.TestCase.assertFalse;
import static junit.framework.TestCase.assertTrue;
/**
* Created on 15/02/18.
*
* @author Jacobo Coll <jacobo167@gmail.com>
*/
public class FillGapsTaskUtilsTest {
@Test
public void testGetOverlappingVariants() {
FillGapsTask a = new FillGapsTask(new StudyConfiguration(1, "a"), new GenomeHelper(new Configuration()), true);
VcfSliceProtos.VcfSlice vcfSlice = buildVcfSlice("17:29113:T:C", "17:29185:A:G", "17:29190-29189::AAAAAAAA", "17:29464:G:");
List<Variant> variants = Arrays.asList(
new Variant("1:29180:CAGAGACAGC:AAGAAACAGCAAAAAAAAAA"),
new Variant("1:29180:C:A"),
new Variant("1:29180::CAGAGA"),
new Variant("1:29181:A:G"),
new Variant("1:29193:A:G"),
new Variant("1:29198:A:G")
);
ListIterator<VcfSliceProtos.VcfRecord> iterator = vcfSlice.getRecordsList().listIterator();
for (Variant variant : variants) {
ArrayList<Pair<VcfSliceProtos.VcfSlice, VcfSliceProtos.VcfRecord>> list = new ArrayList<>();
a.getOverlappingVariants(variant, 1, vcfSlice, iterator, list);
System.out.println(variant + " iteratorIdx : " + iterator.nextIndex());
}
}
@Test
public void testGetOverlappingVariants2() {
FillGapsTask a = new FillGapsTask(new StudyConfiguration(1, "a"), new GenomeHelper(new Configuration()), true);
VcfSliceProtos.VcfSlice vcfSlice = buildVcfSlice(
"2:182562574-182562573::T",
"2:182562574-182562573::TT",
"2:182562574-182562576:TTT:"
);
List<Variant> variants = Arrays.asList(
new Variant("2:182562571:CTG:"),
new Variant("2:182562572:TGT:"),
new Variant("2:182562572:TG:"),
new Variant("2:182562572::T"),
new Variant("2:182562573:G:T"),
new Variant("2:182562574:TTTT:"),
new Variant("2:182562574:TTT:"),
new Variant("2:182562574:TT:"),
new Variant("2:182562574:T:"),
new Variant("2:182562574::T"),
new Variant("2:182562574::TT"),
new Variant("2:182562575:T:C"),
new Variant("2:182562575:T:G"),
new Variant("2:182562576:T:A"),
new Variant("2:182562576:T:C"),
new Variant("2:182562594:G:A"),
new Variant("2:182562613:G:A"),
new Variant("2:182562674:A:G"),
new Variant("2:182562683:A:G"),
new Variant("2:182562890:A:G"),
new Variant("2:182562947:C:A")
);
ListIterator<VcfSliceProtos.VcfRecord> iterator = vcfSlice.getRecordsList().listIterator();
for (Variant variant : variants) {
ArrayList<Pair<VcfSliceProtos.VcfSlice, VcfSliceProtos.VcfRecord>> list = new ArrayList<>();
a.getOverlappingVariants(variant, 1, vcfSlice, iterator, list);
System.out.println(variant + " iteratorIdx : " + iterator.nextIndex());
}
}
private VcfSliceProtos.VcfSlice buildVcfSlice(String... variants) {
Variant variant = new Variant(variants[0]);
int position = (variant.getStart() / 1000) * 1000;
VcfSliceProtos.VcfSlice.Builder vcfSlice = VcfSliceProtos.VcfSlice.newBuilder()
.setChromosome(variant.getChromosome())
.setPosition(position);
for (String s : variants) {
variant = new Variant(s);
vcfSlice.addRecords(VcfSliceProtos.VcfRecord.newBuilder()
.setRelativeStart(variant.getStart() - position)
.setRelativeEnd(variant.getEnd() - position)
.setReference(variant.getReference())
.setAlternate(variant.getAlternate())
.build());
}
return vcfSlice.build();
}
@Test
public void testOverlapsWith() {
assertTrue(FillGapsTask.overlapsWith(new Variant("1:100:T:-"), "1", 100, 100));
Variant variant = new Variant("1:100:-:T");
assertTrue(FillGapsTask.overlapsWith(variant, "1", variant.getStart(), variant.getEnd()));
variant = new Variant("1:100:-:TTTTT");
assertFalse(FillGapsTask.overlapsWith(variant, "1", 102, 102));
}
@Test
public void testIsRegionAfterVariantStart() {
assertTrue(FillGapsTask.isRegionAfterVariantStart(100, 100, new Variant("1:100:-:T")));
assertFalse(FillGapsTask.isRegionAfterVariantStart(100, 100, new Variant("1:100:A:T")));
assertTrue(FillGapsTask.isRegionAfterVariantStart(101, 101, new Variant("1:100:A:T")));
assertFalse(FillGapsTask.isRegionAfterVariantStart(99, 99, new Variant("1:100:AAA:GGG")));
assertFalse(FillGapsTask.isRegionAfterVariantStart(100, 100, new Variant("1:100:AAA:GGG")));
assertFalse(FillGapsTask.isRegionAfterVariantStart(101, 100, new Variant("1:100:AAA:GGG")));
assertTrue(FillGapsTask.isRegionAfterVariantStart(101, 101, new Variant("1:100:AAA:GGG")));
assertTrue(FillGapsTask.isRegionAfterVariantStart(102, 102, new Variant("1:100:AAA:GGG")));
assertTrue(FillGapsTask.isRegionAfterVariantStart(103, 103, new Variant("1:100:AAA:GGG")));
}
}