ReportableGermlineVariantFile { @NotNull public static List<ReportableGermlineVariant> read(final String filePath) throws IOException { return fromLines(Files.readAllLines(new File(filePath).toPath())); }  @NotNull static String generateFilename(@NotNull final String basePath, @NotNull final String sample); static void write(@NotNull final String filename, @NotNull List<ReportableGermlineVariant> dataList); @NotNull static List<ReportableGermlineVariant> read(final String filePath); @NotNull static String toString(@NotNull final ReportableGermlineVariant data);  }
@Test public void canReadTestBachelorFile() throws IOException { List<ReportableGermlineVariant> germlineVariants = ReportableGermlineVariantFile.read(BACHELOR_TSV); assertEquals(1, germlineVariants.size()); ReportableGermlineVariant variant = germlineVariants.get(0); assertEquals("BRCA1", variant.gene()); assertEquals("17", variant.chromosome()); assertEquals(41276044, variant.position()); assertEquals("ACT", variant.ref()); assertEquals("A", variant.alt()); assertEquals(CodingEffect.NONSENSE_OR_FRAMESHIFT, variant.codingEffect()); assertEquals("c.68_69delAG", variant.hgvsCoding()); assertEquals("p.Glu23fs", variant.hgvsProtein()); assertEquals(45, variant.alleleReadCount()); assertEquals(97, variant.totalReadCount()); assertEquals(0.43355030873174055, variant.adjustedVaf(), EPSILON); assertEquals(3.8773, variant.adjustedCopyNumber(), EPSILON); assertFalse(variant.biallelic()); }