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 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 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);
}
}