public void testExplosion() throws Exception {
try (TestDirectory td = new TestDirectory()) {
final File f =
FileHelper.resourceToGzFile(
"com/rtg/vcf/resources/vcfsubset.vcf", new File(td, "vcf.vcf.gz"));
final File out = new File(td, "out.vcf");
assertEquals(
"Records skipped due to invalid or incompatible sample fields: 1" + StringUtils.LS,
checkMainInitWarn(
"-i",
f.getPath(),
"-o",
out.getPath(),
"--remove-format",
"GT",
"--remove-format",
"DS",
"-Z"));
final String content = FileHelper.fileToString(out);
final String nonheader = StringUtils.grepMinusV(content, "^#");
assertTrue(nonheader.startsWith("X\t60052"));
}
}
public void testMissingSample() throws Exception {
try (TestDirectory td = new TestDirectory()) {
final File f =
FileHelper.resourceToGzFile(
"com/rtg/vcf/resources/vcfsubset.vcf", new File(td, "vcf.vcf.gz"));
final File out = new File(td, "out.vcf");
assertEquals(
"Error: Sample fields not contained in VCF header: BL RJ" + StringUtils.LS,
checkMainInitBadFlags(
"-i",
f.getPath(),
"-o",
out.getPath(),
"--keep-sample",
"HG00097",
"--keep-sample",
"HG00099",
"--keep-sample",
"BL",
"--keep-sample",
"RJ",
"-Z"));
}
}
public void testRemoveMulti() throws Exception {
try (TestDirectory td = new TestDirectory()) {
final File f =
FileHelper.resourceToGzFile(
"com/rtg/vcf/resources/vcfsubset.vcf", new File(td, "vcf.vcf.gz"));
final File out = new File(td, "out.vcf");
checkMainInitOk(
"-i",
f.getPath(),
"-o",
out.getPath(),
"--remove-samples",
"--keep-info",
"AN",
"--keep-info",
"AC",
"--keep-filter",
"YEA",
"-Z");
final String content = FileHelper.fileToString(out);
final String editedContent =
StringUtils.grepMinusV(StringUtils.grepMinusV(content, "^##RUN-ID"), "^##CL");
mNano.check("vcfsubset-multi.vcf", editedContent);
}
}
public void testKeepSamples() throws Exception {
try (TestDirectory td = new TestDirectory()) {
final File f =
FileHelper.resourceToGzFile(
"com/rtg/vcf/resources/vcfsubset.vcf", new File(td, "vcf.vcf.gz"));
final File out = new File(td, "out.vcf");
checkMainInitOk(
"-i",
f.getPath(),
"-o",
out.getPath(),
"--keep-sample",
"HG00096",
"--keep-sample",
"HG00100",
"-Z");
final String content = FileHelper.fileToString(out);
final String editedContent =
StringUtils.grepMinusV(StringUtils.grepMinusV(content, "^##RUN-ID"), "^##CL");
mNano.check("vcfsubset-keepsamples.vcf", editedContent);
}
}
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");
}
}