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 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());
}
}
CoverageParams getCoverageParams(final File outFile, final List<File> mapped) throws IOException {
return CoverageParams.builder()
.outputParams(new OutputParams(outFile, false, true))
.mapped(mapped)
.genome(makeGenome())
.smoothing(0)
.ioThreads(1)
.minimumCoverageForBreadth(3)
.tsvOutput(false)
.name("CoverageParams")
.errorRates(false)
.onlyMappedRegions(false)
.filterParams(SamFilterParams.builder().create())
.create();
}
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()));
}
