/** 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); } }