@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");
}
}
/**
* 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));
}