예제 #1
0
  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"));
    }
  }
예제 #2
0
  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);
    }
  }
예제 #3
0
  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);
    }
  }