Examples with VariantReport com.hartwig.hmftools.patientreporter.variants.VariantReport used on opensource projects

Example 6 with VariantReport

use of com.hartwig.hmftools.patientreporter.variants.VariantReport in project hmftools by hartwigmedical.

the class PDFWriterTest method createTestVariants.

@NotNull
private static List<VariantReport> createTestVariants(@NotNull final PurityAdjuster purityAdjuster) {
    final VariantReport variant1 = ImmutableVariantReport.builder().gene("BRAF").variant(createTestVariant("7", 140453136, "A", "T")).transcript("ENST00000377970.6").hgvsCoding("c.1799T>A").hgvsProtein("p.Val600Glu").consequence("missense variant").cosmicID("COSM476").alleleReadCount(18).totalReadCount(99).baf("AAAB").impliedVAF(purityAdjuster.purityAdjustedVAF("7", 4, 0.18 / 0.99)).build();
    final VariantReport variant2 = ImmutableVariantReport.builder().gene("MYC").variant(createTestVariant("8", 128748854, "GG", "CA")).transcript("ENST00000377970.2").hgvsCoding("c.15_16delinsCA").hgvsProtein("p.Val6Ile").consequence("missense variant").cosmicID("").alleleReadCount(20).totalReadCount(88).impliedVAF(purityAdjuster.purityAdjustedVAF("8", 2, 0.2 / 0.88)).baf("AB").build();
    final VariantReport variant3 = ImmutableVariantReport.builder().gene("TP53").variant(createTestVariant("17", 7577111, "GCACAAA", "G")).transcript("ENST00000269305.4").hgvsCoding("c.821_826delTTTGTG").hgvsProtein("p.Val274_Cys275del").consequence("inframe deletion").alleleReadCount(20).totalReadCount(87).impliedVAF(purityAdjuster.purityAdjustedVAF("17", 3, 0.20 / 0.87)).baf("AAA").build();
    return Lists.newArrayList(variant1, variant2, variant3);
}