public void testOk1() throws Exception { final File map = File.createTempFile("testok1", "coverageParams"); try { FileUtils.stringToFile(SharedSamConstants.SAM9, map); assertTrue(map.isFile()); final CoverageParams ccp; final File outFile = new File(mDir, TEST_OUTPUT); assertTrue(outFile.mkdir()); final List<File> mapped = new ArrayList<>(); mapped.add(map); ccp = getCoverageParams(outFile, mapped); assertFalse(ccp.errorRates()); assertNotNull(ccp.filterParams()); assertEquals(1, ccp.ioThreads()); assertEquals(3, ccp.minimumCoverageForBreadth()); final String ccs = ccp.toString(); // System.err.println(ccs); TestUtils.containsAll(ccs, BASE_PARAMS); ccp.close(); } finally { assertTrue(map.delete()); } }
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())); }