public void testTsv() throws IOException { final File outDir = new File(mDir, "output"); final CoverageParams cp = CoverageParams.builder() .outputParams(new OutputParams(outDir, false, false)) .genome(makeGenome()) .tsvOutput(true) .create(); assertTrue(cp.tsvOutput()); assertEquals("coverage.tsv", cp.outFile().getName()); assertFalse(cp.bedOutput()); }
public void testDefaultParams() throws IOException { final File outDir = new File(mDir, "output"); final CoverageParams cp = CoverageParams.builder() .outputParams(new OutputParams(outDir, false, false)) .genome(makeGenome()) .create(); assertFalse(cp.tsvOutput()); assertTrue(cp.bedOutput()); assertFalse(cp.blockCompressed()); assertFalse(cp.onlyMappedRegions()); assertFalse(cp.errorRates()); assertEquals(0, cp.smoothing()); assertEquals(1, cp.minimumCoverageForBreadth()); assertEquals(outDir, cp.directory()); assertEquals(cp.outFile(), cp.file("coverage.bed")); assertEquals("coverage.bed", cp.outFile().getName()); final OutputStream out = cp.bedStream(); out.write("test".getBytes()); out.close(); assertTrue(cp.outFile().exists()); assertEquals("test", FileUtils.fileToString(cp.outFile())); }