/** annovar: RGS21 chr1:192335275->TAAT */
@Test
public void testUTR3Var116() throws AnnotationException {
byte chr = 1;
int pos = 192335275;
String ref = "-";
String alt = "TAAT";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("RGS21(uc001gsh.3:c.*21_22insTAAT)", annot);
}
}
/** annovar: ANGPTL3 chr1:63070540TAATGTGGT>- */
@Test
public void testUTR3Var44() throws AnnotationException {
byte chr = 1;
int pos = 63070540;
String ref = "TAATGTGGT";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("ANGPTL3(uc001das.2:c.*52_60delTAATGTGGT)", annot);
}
}
/** annovar: C19orf55 chr19:36259494C>A */
@Test
public void testUTR3Var1183() throws AnnotationException {
byte chr = 19;
int pos = 36259494;
String ref = "C";
String alt = "A";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("C19orf55(uc021usz.1:c.*47C>A)", annot);
}
}
/**
* annovar: WIBG chr12:56295548TAAG>-
* <...1sif.1:c.*105_108del[CTTA,uc001sie.1:c.*105_108delCTTA])> but was:
* <...1sif.1:c.*105_108del[TAAG,uc001sie.1:c.*105_108delTAAG])>
*/
@Test
public void testUTR3Var843() throws AnnotationException {
byte chr = 12;
int pos = 56295548;
String ref = "TAAG";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("WIBG(uc001sie.1:c.*105_108delCTTA,uc001sif.1:c.*105_108delCTTA)", annot);
}
}
/** annovar: SLC14A2 chr18:43262532C>A */
@Test
public void testUTR3Var1131() throws AnnotationException {
byte chr = 18;
int pos = 43262532;
String ref = "C";
String alt = "A";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("SLC14A2(uc002lbe.3:c.*48C>A,uc010dnj.3:c.*48C>A)", annot);
}
}
/** annovar: SLC22A20 chr11:64993200->GCAA */
@Test
public void testUTR3Var767() throws AnnotationException {
byte chr = 11;
int pos = 64993200;
String ref = "-";
String alt = "GCAA";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("SLC22A20(uc021qlg.1:c.*33_34insGCAA)", annot);
}
}
/** annovar: DPPA3 chr12:7869698->CCCG */
@Test
public void testUTR3Var815() throws AnnotationException {
byte chr = 12;
int pos = 7869698;
String ref = "-";
String alt = "CCCG";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("DPPA3(uc001qtf.3:c.*25_26insCCCG)", annot);
}
}
/** annovar: PRPH2 chr6:42666020G>A */
@Test
public void testUTR3Var448() throws AnnotationException {
byte chr = 6;
int pos = 42666020;
String ref = "G";
String alt = "A";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("PRPH2(uc003osk.3:c.*13C>T)", annot);
}
}
/** annovar: ULBP3 chr6:150385730T>G minus strand */
@Test
public void testUTR3Var472() throws AnnotationException {
byte chr = 6;
int pos = 150385730;
String ref = "T";
String alt = "G";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("ULBP3(uc011eej.1:c.*13A>C,uc003qns.3:c.*13A>C)", annot);
}
}
/** annovar: SLC6A3 chr5:1393761->GG Minus strand! */
@Test
public void testUTR3Var360() throws AnnotationException {
byte chr = 5;
int pos = 1393761;
String ref = "-";
String alt = "GG";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("SLC6A3(uc003jck.3:c.*1089_1090insCC)", annot);
}
}
/** annovar: ATP10B chr5:160039687T>C */
@Test
public void testUTR3Var390() throws AnnotationException {
byte chr = 5;
int pos = 160039687;
String ref = "T";
String alt = "C";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("ATP10B(uc003lyn.3:c.*52A>G)", annot);
}
}
/** annovar: FRG1 chr4:190884289->GACA */
@Test
public void testUTR3Var352() throws AnnotationException {
byte chr = 4;
int pos = 190884289;
String ref = "-";
String alt = "GACA";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("FRG1(uc003izs.3:c.*5_6insGACA)", annot);
}
}
/**
* annovar: AK308309 chr4:119435320CAAGAA>- expected:<AK308309(uc010[1]my.1:c.*99_104delCAA...>
* but was:<AK308309(uc010[i]my.1:c.*99_104delCAA...>
*/
@Test
public void testUTR3Var338() throws AnnotationException {
byte chr = 4;
int pos = 119435320;
String ref = "CAAGAA";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("AK308309(uc010imy.1:c.*99_104delCAAGAA)", annot);
}
}
/** annovar: TPRG1 chr3:189038648T>C */
@Test
public void testUTR3Var298() throws AnnotationException {
byte chr = 3;
int pos = 189038648;
String ref = "T";
String alt = "C";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("TPRG1(uc003frw.2:c.*39T>C,uc003frv.2:c.*39T>C)", annot);
}
}
/** annovar: AGAP11 chr10:88769678->TGC */
@Test
public void testUTR3Var697() throws AnnotationException {
byte chr = 10;
int pos = 88769678;
String ref = "-";
String alt = "TGC";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("AGAP11(uc001kee.2:c.*16_17insTGC,uc031pwm.1:c.*16_17insTGC)", annot);
}
}
/** annovar: WBSCR22 chr7:73118196T>C */
@Test
public void testUTR3Var511() throws AnnotationException {
byte chr = 7;
int pos = 73118196;
String ref = "T";
String alt = "C";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("WBSCR22(uc003tyw.1:c.*337T>C)", annot);
}
}
/** annovar: LOC440040 chr11:49831603G>- */
@Test
public void testUTR3Var755() throws AnnotationException {
byte chr = 11;
int pos = 49831603;
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("LOC440040(uc009ymb.3:c.*317delG,uc010rhy.2:c.*317delG)", annot);
}
}
/** annovar: HGF chr7:81372156A>G minus strand */
@Test
public void testUTR3Var513() throws AnnotationException {
byte chr = 7;
int pos = 81372156;
String ref = "A";
String alt = "G";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("HGF(uc003uhn.1:c.*102T>C,uc003uho.1:c.*102T>C)", annot);
}
}
/** annovar: KDELC2 chr11:108345515->A minus strand */
@Test
public void testUTR3Var787() throws AnnotationException {
byte chr = 11;
int pos = 108345515;
String ref = "-";
String alt = "A";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("KDELC2(uc001pki.2:c.*39_40insT,uc001pkj.2:c.*39_40insT)", annot);
}
}
/** annovar: THAP3 chr1:6693165->TA */
@Test
public void testUTR3Var7() throws AnnotationException {
byte chr = 1;
int pos = 6693165;
String ref = "-";
String alt = "TA";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("THAP3(uc001aod.3:c.*28_29insTA,uc001aoc.3:c.*28_29insTA)", annot);
}
}
/** annovar: UNQ5810 chr16:19315621C>G */
@Test
public void testNcRnaExonicVar495() throws AnnotationException {
byte chr = 16;
int pos = 19315621;
String ref = "C";
String alt = "G";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("CLEC19A(uc002dga.5:c.*81C>G)", annot);
}
}
/** annovar: FAM75D3 chr9:84563495->CTAC */
@Test
public void testUTR3Var608() throws AnnotationException {
byte chr = 9;
int pos = 84563495;
String ref = "-";
String alt = "CTAC";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("SPATA31D3(uc010mpt.2:c.*573_574insCTAC)", annot);
}
}
/** annovar: ATP5G1 chr17:46973146G>- */
@Test
public void testUTR3Var1100() throws AnnotationException {
byte chr = 17;
int pos = 46973146;
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("ATP5G1(uc002iog.3:c.*15delG,uc002ioh.3:c.*15delG)", annot);
}
}
/** annovar: ROR2 chr9:94456643G>C minus strand */
@Test
public void testUTR3Var611() throws AnnotationException {
byte chr = 9;
int pos = 94456643;
String ref = "G";
String alt = "C";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("ROR2(uc004ari.1:c.*1C>G)", annot);
}
}
/** annovar: FZR1 chr19:3534842G>A */
@Test
public void testUTR3Var1146() throws AnnotationException {
byte chr = 19;
int pos = 3534842;
String ref = "G";
String alt = "A";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("FZR1(uc010dtk.2:c.*8G>A,uc002lxv.2:c.*8G>A,uc002lxt.2:c.*8G>A)", annot);
}
}
/** annovar: DDX31 chr9:135470176C>G minus strand */
@Test
public void testUTR3Var643() throws AnnotationException {
byte chr = 9;
int pos = 135470176;
String ref = "C";
String alt = "G";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("DDX31(uc010mzu.1:c.*77G>C,uc004cbq.1:c.*77G>C)", annot);
}
}
/** annovar: C19orf40 chr19:33467620T>C */
@Test
public void testUTR3Var1174() throws AnnotationException {
byte chr = 19;
int pos = 33467620;
String ref = "T";
String alt = "C";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("C19orf40(uc002nud.4:c.*32T>C)", annot);
}
}
/** annovar: WDFY4 chr10:50190799C>T */
@Test
public void testUTR3Var681() throws AnnotationException {
byte chr = 10;
int pos = 50190799;
String ref = "C";
String alt = "T";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("WDFY4(uc001jha.4:c.*179C>T)", annot);
}
}
/** annovar: MIA chr19:41283365C>G */
@Test
public void testUTR3Var1192() throws AnnotationException {
byte chr = 19;
int pos = 41283365;
String ref = "C";
String alt = "G";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("MIA(uc021uuu.1:c.*40C>G,uc002opb.4:c.*40C>G)", annot);
}
}
/** annovar: XCL1 chr1:168550535A>G */
@Test
public void testUTR3Var99() throws AnnotationException {
byte chr = 1;
int pos = 168550535;
String ref = "A";
String alt = "G";
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.UTR3, varType);
String annot = ann.getVariantAnnotation();
Assert.assertEquals("XCL1(uc001gfo.2:c.*77A>G)", annot);
}
}
