/**
* Construct an artificial SAM file reader with the given SAM file header
*
* @param customHeader Header that should be returned by calls to getFileHeader() on this reader
* @param reads Reads to use as backing data source.
*/
public ArtificialSAMFileReader(SAMFileHeader customHeader, SAMRecord... reads) {
super(createEmptyInputStream(), true);
this.customHeader = customHeader;
this.genomeLocParser = new GenomeLocParser(customHeader.getSequenceDictionary());
this.reads = Arrays.asList(reads);
}
public List<String> getSequenceNames() {
if (sequenceNames == null) {
SAMFileHeader header = getFileHeader();
if (header == null) {
return null;
}
sequenceNames = new ArrayList();
List<SAMSequenceRecord> records = header.getSequenceDictionary().getSequences();
if (records.size() > 0) {
for (SAMSequenceRecord rec : header.getSequenceDictionary().getSequences()) {
String chr = rec.getSequenceName();
sequenceNames.add(chr);
}
}
}
return sequenceNames;
}
@Override
protected void setup(final SAMFileHeader header, final File samFile) {
final String outext =
(null != FILE_EXTENSION) ? FILE_EXTENSION : ""; // Add a file extension if desired
preAdapterSummaryOut =
new File(OUTPUT + SequencingArtifactMetrics.PRE_ADAPTER_SUMMARY_EXT + outext);
preAdapterDetailsOut =
new File(OUTPUT + SequencingArtifactMetrics.PRE_ADAPTER_DETAILS_EXT + outext);
baitBiasSummaryOut =
new File(OUTPUT + SequencingArtifactMetrics.BAIT_BIAS_SUMMARY_EXT + outext);
baitBiasDetailsOut =
new File(OUTPUT + SequencingArtifactMetrics.BAIT_BIAS_DETAILS_EXT + outext);
IOUtil.assertFileIsWritable(preAdapterSummaryOut);
IOUtil.assertFileIsWritable(preAdapterDetailsOut);
IOUtil.assertFileIsWritable(baitBiasSummaryOut);
IOUtil.assertFileIsWritable(baitBiasDetailsOut);
for (final SAMReadGroupRecord rec : header.getReadGroups()) {
samples.add(getOrElse(rec.getSample(), UNKNOWN_SAMPLE));
libraries.add(getOrElse(rec.getLibrary(), UNKNOWN_LIBRARY));
}
if (INTERVALS != null) {
IOUtil.assertFileIsReadable(INTERVALS);
intervalMask =
new IntervalListReferenceSequenceMask(IntervalList.fromFile(INTERVALS).uniqued());
}
if (DB_SNP != null) {
IOUtil.assertFileIsReadable(DB_SNP);
dbSnpMask = new DbSnpBitSetUtil(DB_SNP, header.getSequenceDictionary());
}
// set record-level filters
final List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
filters.add(new FailsVendorReadQualityFilter());
filters.add(new NotPrimaryAlignmentFilter());
filters.add(new DuplicateReadFilter());
filters.add(new AlignedFilter(true)); // discard unmapped reads
filters.add(new MappingQualityFilter(MINIMUM_MAPPING_QUALITY));
if (!INCLUDE_UNPAIRED) {
final int effectiveMaxInsertSize =
(MAXIMUM_INSERT_SIZE == 0) ? Integer.MAX_VALUE : MAXIMUM_INSERT_SIZE;
filters.add(new InsertSizeFilter(MINIMUM_INSERT_SIZE, effectiveMaxInsertSize));
}
recordFilter = new AggregateFilter(filters);
// set up the artifact counters
final String sampleAlias = StringUtil.join(",", new ArrayList<String>(samples));
for (final String library : libraries) {
artifactCounters.put(
library, new ArtifactCounter(sampleAlias, library, CONTEXT_SIZE, TANDEM_READS));
}
}
@Override
protected void setupPipeline(Pipeline pipeline) {
// Load the reads.
final ReadsDataflowSource readsDataflowSource = new ReadsDataflowSource(bam, pipeline);
final SAMFileHeader readsHeader = readsDataflowSource.getHeader();
final List<SimpleInterval> intervals =
intervalArgumentCollection.intervalsSpecified()
? intervalArgumentCollection.getIntervals(readsHeader.getSequenceDictionary())
: IntervalUtils.getAllIntervalsForReference(readsHeader.getSequenceDictionary());
final PCollectionView<SAMFileHeader> headerSingleton =
ReadsDataflowSource.getHeaderView(pipeline, readsHeader);
final PCollection<GATKRead> initialReads = readsDataflowSource.getReadPCollection(intervals);
// Apply MarkDuplicates to produce updated GATKReads.
final PCollection<GATKRead> markedReads =
initialReads.apply(new MarkDuplicates(headerSingleton));
// Load the Variants and the Reference and join them to reads.
final VariantsDataflowSource variantsDataflowSource =
new VariantsDataflowSource(baseRecalibrationKnownVariants, pipeline);
Map<String, String> referenceNameToIdTable =
RefAPISource.buildReferenceNameToIdTable(pipeline.getOptions(), referenceName);
RefAPIMetadata refAPIMetadata = new RefAPIMetadata(referenceName, referenceNameToIdTable);
final PCollection<KV<GATKRead, ReadContextData>> readsWithContext =
AddContextDataToRead.add(markedReads, refAPIMetadata, variantsDataflowSource);
// Apply BQSR.
final PCollection<RecalibrationTables> recalibrationReports =
readsWithContext.apply(new BaseRecalibratorStub(headerSingleton));
final PCollectionView<RecalibrationTables> mergedRecalibrationReport =
recalibrationReports.apply(View.<RecalibrationTables>asSingleton());
final PCollection<GATKRead> finalReads =
markedReads.apply(new ApplyBQSRStub(headerSingleton, mergedRecalibrationReport));
SmallBamWriter.writeToFile(pipeline, finalReads, readsHeader, output);
}
private SAMFileHeader makeHeader() {
final SAMFileHeader header = new SAMFileHeader();
final SAMSequenceDictionary dict = header.getSequenceDictionary();
dict.addSequence(new SAMSequenceRecord("chr20", 62435964));
return header;
}
@BeforeClass
public void init() {
header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000000);
genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
}
@BeforeClass
public void beforeClass() {
header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
loc = genomeLocParser.createGenomeLoc("chr1", 1);
}