Pair<Integer, Integer> adjustedRange = adjustedVariantStart(variant);
@Test public void adjustedVariantStart_SecAlt_INDEL() throws Exception { StudyConfiguration sc = new StudyConfiguration(1, "1"); VariantVcfDataWriter dw = new VariantVcfDataWriter(sc, null, null, null); Integer adjustStart = dw.adjustedVariantStart(createVariantSecAlt("1:123:A:C", "1:122:GG:-")).getLeft(); assertEquals("Adjusted start position wrong", Integer.valueOf(121), adjustStart); }
@Test public void adjustedVariantStart_SecAlt_MNV() throws Exception { StudyConfiguration sc = new StudyConfiguration(1, "1"); VariantVcfDataWriter dw = new VariantVcfDataWriter(sc, null, null, null); Integer adjustStart = dw.adjustedVariantStart(createVariantSecAlt("1:123:A:C", "1:122:GG:CC")).getLeft(); assertEquals("Adjusted start position wrong", Integer.valueOf(122), adjustStart); }