package jannovar.annotation;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.HashMap;
/* serialization */
import java.io.ObjectInputStream;
import java.io.FileInputStream;
import java.io.IOException;
import jannovar.exception.JannovarException;
import jannovar.io.SerializationManager;
import jannovar.io.UCSCKGParser;
import jannovar.common.Constants;
import jannovar.common.VariantType;
import jannovar.reference.TranscriptModel;
import jannovar.reference.Chromosome;
import jannovar.annotation.Annotation;
import jannovar.annotation.AnnotationList;
import jannovar.exome.Variant;
import jannovar.exception.AnnotationException;
import org.junit.Test;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Assert;
/**
* This class is intended to perform unuit testing on variants that
* are intergenic.
*/
public class DeletionAnnotationTest implements Constants {
private static HashMap<Byte,Chromosome> chromosomeMap = null;
@SuppressWarnings (value="unchecked")
@BeforeClass
public static void setUp() throws IOException, JannovarException {
ArrayList<TranscriptModel> kgList=null;
java.net.URL url = SynonymousAnnotationTest.class.getResource(UCSCserializationTestFileName);
String path = url.getPath();
SerializationManager manager = new SerializationManager();
kgList = manager.deserializeKnownGeneList(path);
chromosomeMap = Chromosome.constructChromosomeMapWithIntervalTree(kgList);
}
@AfterClass public static void releaseResources() {
chromosomeMap = null;
System.gc();
}
/**
*<P>
* annovar: MST1P9:uc010ock.2:exon2:c.117_121del:p.39_41del
* The protein annotations are not accurate.
* chr1:17087544GCTGT>-
* The deletion goes from 17,087,544-17,087,548, on the rc it is ACAGC
* The gene is on the minus strand
* the deletion affects 3 codons.
* GTG-CTG-TAG
* Or reverse-complement
* CTA-CAG-CAC: the deletion A-CAG-C
* the deletion thus does not change the first amino acid, (CT*****A->CTA=Leu)
* Leu-Gln-His (i.e., LQH)
* The mutation changes TELQHLL -> TELPAT,
* i.e., the Q at position 40 is changed to a P followed by frameshift.
* NM_001271733.1:c.117_121del
* Mutalzyer:
* NM_001271733.1(MST1L_v001):c.119_123del
* NM_001271733.1(MST1L_i001):p.(Gln40Profs*18)
* Thus, we want p.Q40Pfs
*</P>
*/
@Test public void testFSDeletionVar2() throws AnnotationException, JannovarException {
byte chr = 1;
int pos = 17087544;
String ref = "GCTGT";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("MST1L(uc010ock.3:exon2:c.117_121del:p.Q40Pfs)",annot);
}
}
/**
*<P>
* annovar: OR14A16:uc001idm.1:exon1:c.486_488del:p.162_163del,
* chr1:247978544GAG>-
*</P>
*/
@Test public void testFSDeletionVar4() throws AnnotationException, JannovarException {
byte chr = 1;
int pos = 247978544;
String ref = "GAG";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.NON_FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("OR14A16(uc001idm.1:exon1:c.486_488del:p.162_163del)",annot);
}
}
///**
// *<P>
// * annovar: SRGAP2:uc009xbt.3:exon7:c.816delT:p.I272fs,SRGAP2:uc001hdy.3:exon7:c.1047delT:p.I349fs,SRGAP2:uc010prv.1:exon6:c.819delT:p.I273fs,SRGAP2:uc010pru.2:exon7:c.1044delT:p.I348fs,SRGAP2:uc001hdx.3:exon7:c.1047delT:p.I349fs,SRGAP2:uc010prt.1:exon7:c.816delT:p.I272fs,
// * chr1:206579885T>-
// *</P>
// --- Works in principle, some of the UCSC transcripts have divergent nucleotides.
//@Test public void testFSDeletionVar3() throws AnnotationException {
// byte chr = 1;
// int pos = 206579885;
// String ref = "T";
// String alt = "-";
// Chromosome c = chromosomeMap.get(chr);
// if (c==null) {
// Assert.fail("Could not identify chromosome \"" + chr + "\"");
// } else {
// AnnotationList ann =c.getAnnotationList(pos,ref,alt);
// byte varType = ann.getVarType();
// Assert.assertEquals(FS_DELETION,varType);
// String annot = ann.getVariantAnnotation();
// Assert.assertEquals("SRGAP2(uc010prt.1:exon7:c.816delT:p.I272fs,uc009xbt.3:exon7:c.816delT:p.I272fs,uc010prv.1:exon6:c.819delT:p.I273fs,uc010pru.2:exon7:c.1044delT:p.I348fs,uc001hdy.3:exon7:c.1047delT:p.I349fs,uc001hdx.3:exon7:c.1047delT:p.I349fs)",annot);
// }
//}
//*/
/**
*<P>
* annovar: ZNF852:uc011azx.2:exon4:c.1472_1473del:p.491_491del,
* Annovar is inaccurate here.
* chr3:44540796TC>-
* wt: GGAGAAAAACCTTATGAATGTATTGAGT
* mt: GGAAAAACCTTATGAATGTATTGAGT
* wt: GEKNLMNVLS
* mt: GEKPYECIE
* Thus, p.N494Pfs
*</P>
*/
@Test public void testFSDeletionVar6() throws AnnotationException, JannovarException {
byte chr = 3;
int pos = 44540796;
String ref = "TC";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("ZNF852(uc011azx.2:exon4:c.1472_1473del:p.N494Pfs)",annot);
}
}
/**
*<P>
* annovar: OR5H6:uc003dsi.1:exon1:c.369_377del:p.123_126del,
* chr3:97983497TGTAACCAC>-
*</P>
*/
@Test public void testFSDeletionVar8() throws AnnotationException , JannovarException {
byte chr = 3;
int pos = 97983497;
String ref = "TGTAACCAC";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.NON_FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("OR5H6(uc003dsi.1:exon1:c.369_377del:p.123_126del)",annot);
}
}
/**
*<P>
* annovar: OR5K2:uc011bgx.2:exon1:c.275_285del:p.92_95del (wrong)
* chr3:98216799TTTCCCTCTAT>-
* Mutalzyer:
* NM_001004737.1(OR5K2_v001):c.275_285del
* NM_001004737.1(OR5K2_i001):p.(Ile92Argfs*26)
* Thus p.I92Rfs
*</P>
*/
@Test public void testFSDeletionVar9() throws AnnotationException , JannovarException {
byte chr = 3;
int pos = 98216799;
String ref = "TTTCCCTCTAT";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("OR5K2(uc011bgx.2:exon1:c.275_285del:p.I92Rfs)",annot);
}
}
/**
*<P>
* annovar: PCDHA7:uc003lhq.2:exon1:c.1503_1507del:p.501_503del,PCDHA7:uc011dac.2:exon1:c.1503_1507del:p.501_503del,
* chr5:140215471GCGCG>-
* Thus = NM_031852.1:c.1503_1507del
* Mutalyzer:
* NM_031852.1(PCDHA7_v001):c.1503_1507del
* NM_031852.1(PCDHA7_i001):p.(Glu501Aspfs*96)
* Thus p.E501Dfs
*</P>
*/
@Test public void testFSDeletionVar10() throws AnnotationException, JannovarException {
byte chr = 5;
int pos = 140215471;
String ref = "GCGCG";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("PCDHA7(uc003lhq.2:exon1:c.1503_1507del:p.E501Dfs,uc011dac.2:exon1:c.1503_1507del:p.E501Dfs)",annot);
}
}
/**
*<P>
* annovar: PCDHB18:uc003ljc.1:exon1:c.1219_1221del:p.407_407del,
* chr5:140615504GTC>-
*</P>
*/
@Test public void testFSDeletionVar11() throws AnnotationException , JannovarException {
byte chr = 5;
int pos = 140615504;
String ref = "GTC";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.NON_FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("PCDHB18(uc003ljc.1:exon1:c.1219_1221del:p.407_407del)",annot);
}
}
/**
*<P>
* annovar: OR2B2:uc011dkw.2:exon1:c.985delA:p.T329fs,
* chr6:27879113T>-
*</P>
*/
@Test public void testFSDeletionVar12() throws AnnotationException, JannovarException {
byte chr = 6;
int pos = 27879113;
String ref = "T";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("OR2B2(uc011dkw.2:exon1:c.985delA:p.T329fs)",annot);
}
}
/**
*<P>
* annovar: KCNK17:uc003ooo.3:exon2:c.318_320del:p.106_107del,KCNK17:uc003oop.3:exon2:c.318_320del:p.106_107del,
* chr6:39278701AAG>-
*</P>
*/
@Test public void testFSDeletionVar13() throws AnnotationException, JannovarException {
byte chr = 6;
int pos = 39278701;
String ref = "AAG";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.NON_FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("KCNK17(uc003ooo.3:exon2:c.318_320del:p.106_107del,uc003oop.3:exon2:c.318_320del:p.106_107del)",annot);
}
}
/**
*<P>
* annovar: KIAA2026:uc010mht.3:exon4:c.1539_1541del:p.513_514del,KIAA2026:uc003zjq.4:exon8:c.4014_4016del:p.1338_1339del,
* chr9:5921980GTT>-
*</P>
*/
@Test public void testFSDeletionVar14() throws AnnotationException , JannovarException {
byte chr = 9;
int pos = 5921980;
String ref = "GTT";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.NON_FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("KIAA2026(uc010mht.3:exon4:c.1539_1541del:p.513_514del,uc003zjq.4:exon8:c.4014_4016del:p.1338_1339del)",annot);
}
}
/**
*<P>
* annovar: AGAP6:uc001jix.4:exon8:c.791_792del:p.264_264del,
* chr10:51768676AA>-
* NM_001077665.2:c.791_792del
* Mutalyzer:
* NM_001077665.2(AGAP6_v001):c.791_792del
* NM_001077665.2(AGAP6_i001):p.(Lys264Argfs*10)
* Thus p.K264Rfs
*</P>
*/
@Test public void testFSDeletionVar16() throws AnnotationException , JannovarException {
byte chr = 10;
int pos = 51768676;
String ref = "AA";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("AGAP6(uc001jix.4:exon8:c.791_792del:p.K264Rfs)",annot);
}
}
/**
*<P>
* annovar: AGAP6:uc001jix.4:exon8:c.890_892del:p.297_298del,
* chr10:51768775TGA>-
*</P>
*/
@Test public void testFSDeletionVar17() throws AnnotationException , JannovarException {
byte chr = 10;
int pos = 51768775;
String ref = "TGA";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.NON_FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("AGAP6(uc001jix.4:exon8:c.890_892del:p.297_298del)",annot);
}
}
/**
*<P>
* annovar: OR5M1:uc001nja.1:exon1:c.423_426del:p.141_142del,
* chr11:56380553GACA>-
* Thus NM_001004740:c.423_426del
* Mutalzyer
* NM_001004740(OR5M1_v001):c.429_432del
* NM_001004740(OR5M1_i001):p.(Cys143Trpfs*19)
* Thus p.C143Wfs
*</P>
*/
@Test public void testFSDeletionVar18() throws AnnotationException , JannovarException {
byte chr = 11;
int pos = 56380553;
String ref = "GACA";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("OR5M1(uc001nja.1:exon1:c.423_426del:p.C143Wfs)",annot);
}
}
/**
*<P>
* annovar: FAM90A1:uc001quh.2:exon5:c.376delC:p.P126fs,FAM90A1:uc001qui.2:exon6:c.376delC:p.P126fs,
* chr12:8376101G>-
*</P>
*/
@Test public void testFSDeletionVar19() throws AnnotationException , JannovarException{
byte chr = 12;
int pos = 8376101;
String ref = "G";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("FAM90A1(uc001qui.2:exon6:c.376delC:p.P126fs,uc001quh.2:exon5:c.376delC:p.P126fs)",annot);
}
}
/**
*<P>
* annovar: SETD8:uc001uew.3:exon5:c.542_543del:p.181_181del,
* chr12:123880924TT>-
* NM_020382:c.542_543del
* Mutalyzer:
* NM_020382(SETD8_v001):c.542_543del
* NM_020382(SETD8_i001):p.(Leu181Hisfs*20)
* THus p.L181Hfs
*</P>
*/
@Test public void testFSDeletionVar21() throws AnnotationException , JannovarException{
byte chr = 12;
int pos = 123880924;
String ref = "TT";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("SETD8(uc001uew.3:exon5:c.542_543del:p.L181Hfs)",annot);
}
}
/**
*<P>
* annovar: FAM194B:uc001vam.1:exon2:c.398_415del:p.133_139del,FAM194B:uc001val.2:exon3:c.398_415del:p.133_139del,
* chr13:46170726ACTCTTCCTCCTCCAGAT>-
* expected:<FAM194B(uc001va[m.1:exon2:c.398_415del:p.133_139del,uc001val.2:exon3]:c.398_415del:p.133_...>
* but was:<FAM194B(uc001va[l.2:exon3:c.398_415del:p.133_139del,uc001vam.1:exon2]:c.398_415del:p.133_...>
* (order changed)
* expected:<FAM194B(uc001va[l.2:exon3:c.398_415del:p.133_139del,uc001vam.1:exon2]:c.398_415del:p.133_...> but was:
* <FAM194B(uc001va[m.1:exon2:c.398_415del:p.133_139del,uc001val.2:exon3]:c.398_415del:p.133_...>
*</P>
*/
@Test public void testFSDeletionVar22() throws AnnotationException , JannovarException{
byte chr = 13;
int pos = 46170726;
String ref = "ACTCTTCCTCCTCCAGAT";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.NON_FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("FAM194B(uc001val.2:exon3:c.398_415del:p.133_139del,uc001vam.1:exon2:c.398_415del:p.133_139del)",annot);
}
}
/**
*<P>
* annovar: CCDC33:uc002axo.3:exon2:c.100_102del:p.34_34del,
* chr15:74536404AAG>-
*</P>
*/
@Test public void testFSDeletionVar23() throws AnnotationException , JannovarException {
byte chr = 15;
int pos = 74536404;
String ref = "AAG";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.NON_FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("CCDC33(uc002axo.4:exon2:c.100_102del:p.34_34del)",annot);
}
}
/**
*<P>
* annovar: CCDC33:uc002axo.3:exon2:c.100_102del:p.34_34del,
* chr15:74536404AAG>-
*</P>
*/
@Test public void testFSDeletionVar24() throws AnnotationException , JannovarException{
byte chr = 15;
int pos = 74536404;
String ref = "AAG";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.NON_FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("CCDC33(uc002axo.4:exon2:c.100_102del:p.34_34del)",annot);
}
}
/**
*<P>
* annovar: LOC645752:uc010bky.2:exon14:c.832_834del:p.278_278del,
* chr15:78208899CTC>-
*</P>
*/
@Test public void testFSDeletionVar25() throws AnnotationException , JannovarException {
byte chr = 15;
int pos = 78208899;
String ref = "CTC";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.NON_FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("LOC645752(uc010bky.2:exon14:c.832_834del:p.278_278del)",annot);
}
}
/**
*<P>
* annovar: SENP3:uc002ghm.3:exon8:c.1307delA:p.K436fs,
* chr17:7470288A>-
*</P>
*/
@Test public void testFSDeletionVar26() throws AnnotationException, JannovarException {
byte chr = 17;
int pos = 7470288;
String ref = "A";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("SENP3(uc002ghm.3:exon8:c.1307delA:p.K436fs)",annot);
}
}
/**
*<P>
* annovar: ATAD5:uc002hfs.1:exon2:c.861_866del:p.287_289del,ATAD5:uc002hft.1:exon1:c.552_557del:p.184_186del,
* chr17:29161960GTCAAT>-
*</P>
*/
@Test public void testFSDeletionVar28() throws AnnotationException , JannovarException{
byte chr = 17;
int pos = 29161960;
String ref = "GTCAAT";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.NON_FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("ATAD5(uc002hft.1:exon1:c.552_557del:p.184_186del,uc002hfs.1:exon2:c.861_866del:p.287_289del)",annot);
}
}
/**
*<P>
* annovar: DCAF7:uc002jbc.3:exon6:c.560delG:p.G187fs,
* chr17:61660895G>-
*</P>
*/
@Test public void testFSDeletionVar29() throws AnnotationException , JannovarException {
byte chr = 17;
int pos = 61660895;
String ref = "G";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("DCAF7(uc002jbc.4:exon6:c.560delG:p.G187fs)",annot);
}
}
/**
*<P>
* annovar: DEFB126:uc002wcx.3:exon2:c.317_318del:p.106_106del,
* chr20:126314CC>-
* Mutalzyer:
* NM_030931(DEFB126_v001):c.317_318del
* NM_030931(DEFB126_i001):p.(Pro106Argfs*27)
* p.P106Rfs
*/
@Test public void testFSDeletionVar32() throws AnnotationException , JannovarException {
byte chr = 20;
int pos = 126314;
String ref = "CC";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("DEFB126(uc002wcx.3:exon2:c.317_318del:p.P106Rfs)",annot);
}
}
/**
*<P>
* annovar: PLAC4:uc002yyz.3:exon1:c.70_88del:p.24_30del,
* chr21:42551468GTGTCAGGGTGAGTGAGGG>-
* minus strand
* Mutalyzer:
* NM_182832(PLAC4_v001):c.72_90del
* NM_182832(PLAC4_i001):p.(Ser25Hisfs*78)
* Thus p.S25Hfs
*</P>
*/
@Test public void testFSDeletionVar33() throws AnnotationException , JannovarException {
byte chr = 21;
int pos = 42551468;
String ref = "GTGTCAGGGTGAGTGAGGG";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("PLAC4(uc002yyz.3:exon1:c.70_88del:p.S25Hfs)",annot);
}
}
/**
*<P>
* annovar: ZNF135:uc010yhq.2:exon5:c.1992_1997del:p.664_666del,ZNF135:uc002qre.3:exon5:c.1956_1961del:p.652_654del,ZNF135:uc002qrg.3:exon4:c.2028_2033del:p.676_678del,ZNF135:uc002qrd.2:exon5:c.1152_1157del:p.384_386del,ZNF135:uc010yhr.2:exon3:c.1419_1424del:p.473_475del,ZNF135:uc002qrf.3:exon5:c.1830_1835del:p.610_612del,
* chr19:58579808CCAGAG>-
*</P>
*/
@Test public void testFSDeletionVar31() throws AnnotationException , JannovarException{
byte chr = 19;
int pos = 58579808;
String ref = "CCAGAG";
String alt = "-";
Chromosome c = chromosomeMap.get(chr);
if (c==null) {
Assert.fail("Could not identify chromosome \"" + chr + "\"");
} else {
AnnotationList ann =c.getAnnotationList(pos,ref,alt);
VariantType varType = ann.getVariantType();
Assert.assertEquals(VariantType.NON_FS_DELETION,varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("ZNF135(uc002qrd.2:exon5:c.1152_1157del:p.384_386del,uc010yhr.2:exon3:c.1419_1424del:p.473_475del,uc002qrf.3:exon5:c.1830_1835del:p.610_612del,uc002qre.3:exon5:c.1956_1961del:p.652_654del,uc010yhq.2:exon5:c.1992_1997del:p.664_666del,uc002qrg.3:exon4:c.2028_2033del:p.676_678del)",annot);
}
}
}