public void testBadArgs() throws Exception {
try (TestDirectory dir = new TestDirectory("sdf2fasta")) {
final ArrayList<InputStream> al = new ArrayList<>();
final FastaSequenceDataSource ds = new FastaSequenceDataSource(al, new DNAFastaSymbolTable());
final SequencesWriter sw = new SequencesWriter(ds, dir, 300000, PrereadType.UNKNOWN, false);
sw.processSequences();
checkHandleFlagsErr("-i", dir.toString(), "-o", "junithi", "-l", "-1");
}
}
public void testValidUse2() throws Exception {
try (TestDirectory dir = new TestDirectory("sdf2fasta")) {
createPreread(">x" + StringUtils.LS + "actgn" + StringUtils.LS, new File(dir, "left"));
createPreread(">x" + StringUtils.LS + "actgn" + StringUtils.LS, new File(dir, "right"));
final String pathpr = dir.getPath();
runCommandWithNamedOutput(JUNITOUT, pathpr, "ACTGN", "ACTGN");
runCommandWithNamedOutput(JUNITOUT + ".FA", pathpr, "ACTGN", "ACTGN");
runCommandWithNamedOutput(JUNITOUT + ".fasta", pathpr, "ACTGN", "ACTGN");
}
}
public void testValidUse() throws Exception {
try (TestDirectory dir = new TestDirectory("sdf2fasta")) {
createPreread(">x" + StringUtils.LS + "actgn" + StringUtils.LS, dir);
final String pathpr = dir.getPath();
try {
runCommandWithNamedOutput(JUNITOUT, pathpr, "ACTGN");
runCommandWithNamedOutput(JUNITOUT + ".FA", pathpr, "ACTGN");
runCommandWithNamedOutput(JUNITOUT + ".fasta", pathpr, "ACTGN");
runCommandLineLength2(pathpr);
} finally {
FileHelper.deleteAll(dir);
}
createPrereadProtein(dir);
runCommandWithNamedOutput(JUNITOUT, pathpr, "X*ARNDCQEGHILKMFPSTWYV");
}
}
public void testValidation() throws Exception {
try (TestDirectory main = new TestDirectory()) {
final File in =
FileHelper.resourceToGzFile(
"com/rtg/vcf/resources/vcfsubset.vcf", new File(main, "vcf.vcf.gz"));
final File foo = new File(main, "foo");
final File out = new File(main, "out.vcf.gz");
final File out2 = new File(main, "out.vcf");
String err = checkHandleFlagsErr("-i", foo.getPath(), "-o", out.getPath());
TestUtils.containsAll(TestUtils.unwrap(err), "Given file ", " does not exist.");
err = checkHandleFlagsErr("-i", main.getPath(), "-o", out.getPath());
TestUtils.containsAll(TestUtils.unwrap(err), main.getPath() + "\" is a directory");
assertTrue(out.createNewFile());
err = checkHandleFlagsErr("-i", in.getPath(), "-o", new File(main, "out.vcf").getPath());
TestUtils.containsAll(
TestUtils.unwrap(err), "The file \"" + out.getPath() + "\" already exists");
assertTrue(out2.createNewFile());
err = checkHandleFlagsErr("-i", in.getPath(), "-o", out2.getPath(), "--no-gzip");
TestUtils.containsAll(
TestUtils.unwrap(err), "The file \"" + out2.getPath() + "\" already exists");
err =
checkHandleFlagsErr(
"-i",
in.getPath(),
"-o",
new File(main, "newout.gz").getPath(),
"--remove-infos",
"--remove-info",
"blah");
TestUtils.containsAll(
TestUtils.unwrap(err),
"Only one of --remove-infos, --remove-info, or --keep-info can be set");
err =
checkHandleFlagsErr(
"-i",
in.getPath(),
"-o",
new File(main, "newout.gz").getPath(),
"--remove-infos",
"--keep-info",
"blah");
TestUtils.containsAll(
TestUtils.unwrap(err),
"Only one of --remove-infos, --remove-info, or --keep-info can be set");
err =
checkHandleFlagsErr(
"-i",
in.getPath(),
"-o",
new File(main, "newout.gz").getPath(),
"--remove-info",
"feh",
"--keep-info",
"blah");
TestUtils.containsAll(
TestUtils.unwrap(err),
"Only one of --remove-infos, --remove-info, or --keep-info can be set");
err =
checkHandleFlagsErr(
"-i",
in.getPath(),
"-o",
new File(main, "newout.gz").getPath(),
"--remove-filters",
"--remove-filter",
"blah");
TestUtils.containsAll(
TestUtils.unwrap(err),
"Only one of --remove-filters, --remove-filter, or --keep-filter can be set");
err =
checkHandleFlagsErr(
"-i",
in.getPath(),
"-o",
new File(main, "newout.gz").getPath(),
"--remove-filters",
"--keep-filter",
"blah");
TestUtils.containsAll(
TestUtils.unwrap(err),
"Only one of --remove-filters, --remove-filter, or --keep-filter can be set");
err =
checkHandleFlagsErr(
"-i",
in.getPath(),
"-o",
new File(main, "newout.gz").getPath(),
"--remove-filter",
"feh",
"--keep-filter",
"blah");
TestUtils.containsAll(
TestUtils.unwrap(err),
"Only one of --remove-filters, --remove-filter, or --keep-filter can be set");
err =
checkHandleFlagsErr(
"-i",
in.getPath(),
"-o",
new File(main, "newout.gz").getPath(),
"--remove-samples",
"--remove-sample",
"blah");
TestUtils.containsAll(
TestUtils.unwrap(err),
"Only one of --remove-samples, --remove-sample, or --keep-sample can be set");
err =
checkHandleFlagsErr(
"-i",
in.getPath(),
"-o",
new File(main, "newout.gz").getPath(),
"--remove-samples",
"--keep-sample",
"blah");
TestUtils.containsAll(
TestUtils.unwrap(err),
"Only one of --remove-samples, --remove-sample, or --keep-sample can be set");
err =
checkHandleFlagsErr(
"-i",
in.getPath(),
"-o",
new File(main, "newout.gz").getPath(),
"--remove-sample",
"feh",
"--keep-sample",
"blah");
TestUtils.containsAll(
TestUtils.unwrap(err),
"Only one of --remove-samples, --remove-sample, or --keep-sample can be set");
err =
checkHandleFlagsErr(
"-i",
in.getPath(),
"-o",
new File(main, "newout.gz").getPath(),
"--remove-format",
"feh",
"--keep-format",
"blah");
TestUtils.containsAll(
TestUtils.unwrap(err), "Only one of --remove-format or --keep-format can be set");
}
}