コード例 #1
0
  @Test(dataProvider = "loadReadsADAM", groups = "spark")
  public void readsSinkADAMTest(String inputBam, String outputDirectoryName) throws IOException {
    // Since the test requires that we not create the actual output directory in advance,
    // we instead create its parent directory and mark it for deletion on exit. This protects
    // us from naming collisions across multiple instances of the test suite.
    final File outputParentDirectory = createTempDir(outputDirectoryName + "_parent");
    final File outputDirectory = new File(outputParentDirectory, outputDirectoryName);

    JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();

    ReadsSparkSource readSource = new ReadsSparkSource(ctx);
    JavaRDD<GATKRead> rddParallelReads = readSource.getParallelReads(inputBam, null);
    SAMFileHeader header = ReadsSparkSource.getHeader(ctx, inputBam, null);

    ReadsSparkSink.writeReads(
        ctx, outputDirectory.getAbsolutePath(), rddParallelReads, header, ReadsWriteFormat.ADAM);

    JavaRDD<GATKRead> rddParallelReads2 =
        readSource.getADAMReads(outputDirectory.getAbsolutePath(), null, header);
    Assert.assertEquals(rddParallelReads.count(), rddParallelReads2.count());

    // Test the round trip
    List<GATKRead> samList = rddParallelReads.collect();
    List<GATKRead> adamList = rddParallelReads2.collect();
    Comparator<GATKRead> comparator = new ReadCoordinateComparator(header);
    samList.sort(comparator);
    adamList.sort(comparator);
    for (int i = 0; i < samList.size(); i++) {
      SAMRecord expected = samList.get(i).convertToSAMRecord(header);
      SAMRecord observed = adamList.get(i).convertToSAMRecord(header);
      // manually test equality of some fields, as there are issues with roundtrip BAM -> ADAM ->
      // BAM
      // see https://github.com/bigdatagenomics/adam/issues/823
      Assert.assertEquals(observed.getReadName(), expected.getReadName(), "readname");
      Assert.assertEquals(
          observed.getAlignmentStart(), expected.getAlignmentStart(), "getAlignmentStart");
      Assert.assertEquals(
          observed.getAlignmentEnd(), expected.getAlignmentEnd(), "getAlignmentEnd");
      Assert.assertEquals(observed.getFlags(), expected.getFlags(), "getFlags");
      Assert.assertEquals(
          observed.getMappingQuality(), expected.getMappingQuality(), "getMappingQuality");
      Assert.assertEquals(
          observed.getMateAlignmentStart(),
          expected.getMateAlignmentStart(),
          "getMateAlignmentStart");
      Assert.assertEquals(observed.getCigar(), expected.getCigar(), "getCigar");
    }
  }
コード例 #2
0
  /**
   * HACK TO CREATE GATKSAMRECORD BASED ONLY A SAMRECORD FOR TESTING PURPOSES ONLY
   *
   * @param read
   */
  public GATKSAMRecord(final SAMRecord read) {
    super(read.getHeader());
    super.setReferenceIndex(read.getReferenceIndex());
    super.setAlignmentStart(read.getAlignmentStart());
    super.setReadName(read.getReadName());
    super.setMappingQuality(read.getMappingQuality());
    // indexing bin done below
    super.setCigar(read.getCigar());
    super.setFlags(read.getFlags());
    super.setMateReferenceIndex(read.getMateReferenceIndex());
    super.setMateAlignmentStart(read.getMateAlignmentStart());
    super.setInferredInsertSize(read.getInferredInsertSize());
    SAMReadGroupRecord samRG = read.getReadGroup();
    SAMBinaryTagAndValue samAttr = GATKBin.getReadBinaryAttributes(read);
    if (samAttr == null) {
      clearAttributes();
    } else {
      setAttributes(samAttr);
    }
    if (samRG != null) {
      GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
      setReadGroup(rg);
    }

    super.setFileSource(read.getFileSource());
    super.setReadName(read.getReadName());
    super.setCigarString(read.getCigarString());
    super.setReadBases(read.getReadBases());
    super.setBaseQualities(read.getBaseQualities());
    // From SAMRecord constructor: Do this after the above because setCigarString will clear it.
    GATKBin.setReadIndexingBin(this, GATKBin.getReadIndexingBin(read));
  }