ExperimentalCodec(final BitInputStream coreBlockInputStream, final BitOutputStream coreBlockOutputStream) { super(coreBlockInputStream, coreBlockOutputStream); final String subclass = this.getClass().getName(); final String warning = String.format( "Using the experimental codec %s which is untested and scheduled for removal from the CRAM spec", subclass); final Log log = Log.getInstance(ExperimentalCodec.class); log.warn(warning); } }
ExperimentalEncoding(final EncodingID encodingID) { super(encodingID); final String subclass = this.getClass().getName(); final String warning = String.format( "Using the experimental encoding %s which is untested and scheduled for removal from the CRAM spec", subclass); final Log log = Log.getInstance(ExperimentalEncoding.class); log.warn(warning); } }
ExperimentalEncoding(final EncodingID encodingID) { super(encodingID); final String subclass = this.getClass().getName(); final String warning = String.format( "Using the experimental encoding %s which is untested and scheduled for removal from the CRAM spec", subclass); final Log log = Log.getInstance(ExperimentalEncoding.class); log.warn(warning); } }
ExperimentalCodec(final BitInputStream coreBlockInputStream, final BitOutputStream coreBlockOutputStream) { super(coreBlockInputStream, coreBlockOutputStream); final String subclass = this.getClass().getName(); final String warning = String.format( "Using the experimental codec %s which is untested and scheduled for removal from the CRAM spec", subclass); final Log log = Log.getInstance(ExperimentalCodec.class); log.warn(warning); } }
/** * Describes the state of a tile being processed. It is either not yet completely read, or read. */ private enum TileProcessingState { NOT_DONE_READING, DONE_READING }
/** * Describes the state of a tile being processed. It is either not yet completely read, or read. */ private enum TileProcessingState { NOT_DONE_READING, DONE_READING }
BAMIndexer.createIndex(reader, outputIndex.toFile(), Log.getInstance(BamManager.class)); } else { if (reader.type().equals(SamReader.Type.CRAM_TYPE)) { CRAMBAIIndexer.createIndex(streamFor, outputIndex.toFile(), Log.getInstance(BamManager.class), ValidationStringency.DEFAULT_STRINGENCY); } else {
@BeforeTest public void setUp(){ progress = new ProgressLogger(Log.getInstance(WgsMetricsProcessorImpl.class)); }
@Test public void testKeeperAtEndWithinCliqueOfAllOpticalDuplicates() { final Log log = Log.getInstance(OpticalDuplicateFinderTest.class); final OpticalDuplicateFinder finder = new OpticalDuplicateFinder(OpticalDuplicateFinder.DEFAULT_READ_NAME_REGEX, 15, log); final List<PhysicalLocation> locs = Arrays.asList( loc(1, 10, 0), loc(1, 20, 0), loc(1, 30, 0) ); assertEquals(finder.findOpticalDuplicates(locs, locs.get(2)), new boolean[] {true, true, false}); }
@Test public void testKeeper() { final Log log = Log.getInstance(OpticalDuplicateFinderTest.class); final OpticalDuplicateFinder finder = new OpticalDuplicateFinder(OpticalDuplicateFinder.DEFAULT_READ_NAME_REGEX, 100, log); final List<PhysicalLocation> locs = Arrays.asList( loc(7, 1500, 1500), loc(7, 1501, 1501), loc(5, 1500, 1500), loc(7, 1490, 1502), loc(7, 2500, 2500), loc(7, 10, 10) ); assertEquals(finder.findOpticalDuplicates(locs, null ), new boolean[] {true, true, false, false, false, false}); assertEquals(finder.findOpticalDuplicates(locs, locs.get(0)), new boolean[] {false, true, false, true, false, false}); assertEquals(finder.findOpticalDuplicates(locs, locs.get(1)), new boolean[] {true, false, false, true, false, false}); assertEquals(finder.findOpticalDuplicates(locs, locs.get(3)), new boolean[] {true, true, false, false, false, false}); for (int i=0; i<100; ++i) { final Random random = new Random(i); final List<PhysicalLocation> shuffled = new ArrayList<>(locs); final List<PhysicalLocation> keepers = Arrays.asList(locs.get(0), locs.get(1), locs.get(3)); final PhysicalLocation keeper = keepers.get(random.nextInt(keepers.size())); Collections.shuffle(shuffled); int opticalDupeCount = countTrue(finder.findOpticalDuplicates(shuffled, keeper)); Assert.assertEquals(opticalDupeCount, 2); } }
/** * Tests the case where the "keeper" record is not in the list that is passed to the OpticalDuplicateFinder. This can happen * when there are, e.g. FR and RF reads, which can all be molecular duplicates of one another, but cannot be duplicates of one * another and are thus partitioned into two sets for optical duplicate checking. */ @Test public void testKeeperNotInList() { final Log log = Log.getInstance(OpticalDuplicateFinderTest.class); final OpticalDuplicateFinder finder = new OpticalDuplicateFinder(OpticalDuplicateFinder.DEFAULT_READ_NAME_REGEX, 100, log); final List<PhysicalLocation> locs = Arrays.asList( loc(1, 100, 100), loc(1, 101, 101), loc(1, 99, 99), loc(1, 99, 102) ); Assert.assertEquals(countTrue(finder.findOpticalDuplicates(locs, loc(7, 5000, 5000))), 3); }
@Test public void testKeeperOrderDependence() { final Log log = Log.getInstance(OpticalDuplicateFinderTest.class); final OpticalDuplicateFinder finder = new OpticalDuplicateFinder(OpticalDuplicateFinder.DEFAULT_READ_NAME_REGEX, 100, log); final List<PhysicalLocation> locs = Arrays.asList( loc(1, 100, 190), loc(1, 100, 280), loc(1, 100, 370), loc(1, 100, 460) ); final List<PhysicalLocation> locsReordered = Arrays.asList( loc(1, 100, 190), loc(1, 100, 460), loc(1, 100, 370), loc(1, 100, 280) ); Assert.assertEquals(countTrue(finder.findOpticalDuplicates(locs, locs.get(0))), 3); Assert.assertEquals(countTrue(finder.findOpticalDuplicates(locsReordered, locsReordered.get(0))), 3); }
protected int doWork() { IOUtil.assertFileIsReadable(INPUT); IOUtil.assertFileIsWritable(OUTPUT); final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT); final SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(reader.getFileHeader(), true, OUTPUT, REFERENCE_SEQUENCE); if (CREATE_INDEX && writer.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) { throw new PicardException("Can't CREATE_INDEX unless sort order is coordinate"); } final ProgressLogger progress = new ProgressLogger(Log.getInstance(SamFormatConverter.class)); for (final SAMRecord rec : reader) { writer.addAlignment(rec); progress.record(rec); } CloserUtil.close(reader); writer.close(); return 0; } }
protected int doWork() { IOUtil.assertFileIsReadable(INPUT); IOUtil.assertFileIsWritable(OUTPUT); final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT); final SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(reader.getFileHeader(), true, OUTPUT, REFERENCE_SEQUENCE); if (CREATE_INDEX && writer.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) { throw new PicardException("Can't CREATE_INDEX unless sort order is coordinate"); } final ProgressLogger progress = new ProgressLogger(Log.getInstance(SamFormatConverter.class)); for (final SAMRecord rec : reader) { writer.addAlignment(rec); progress.record(rec); } CloserUtil.close(reader); writer.close(); return 0; } }
private void standardReheader(final SAMFileHeader replacementHeader) { final SamReader recordReader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).validationStringency(ValidationStringency.SILENT).open(INPUT); if (replacementHeader.getSortOrder() != recordReader.getFileHeader().getSortOrder()) { throw new PicardException("Sort orders of INPUT (" + recordReader.getFileHeader().getSortOrder().name() + ") and HEADER (" + replacementHeader.getSortOrder().name() + ") do not agree."); } final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(replacementHeader, true, OUTPUT); final ProgressLogger progress = new ProgressLogger(Log.getInstance(ReplaceSamHeader.class)); for (final SAMRecord rec : recordReader) { rec.setHeader(replacementHeader); writer.addAlignment(rec); progress.record(rec); } writer.close(); CloserUtil.close(recordReader); }
private void standardReheader(final SAMFileHeader replacementHeader) { final SamReader recordReader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).validationStringency(ValidationStringency.SILENT).open(INPUT); if (replacementHeader.getSortOrder() != recordReader.getFileHeader().getSortOrder()) { throw new PicardException("Sort orders of INPUT (" + recordReader.getFileHeader().getSortOrder().name() + ") and HEADER (" + replacementHeader.getSortOrder().name() + ") do not agree."); } final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(replacementHeader, true, OUTPUT); final ProgressLogger progress = new ProgressLogger(Log.getInstance(ReplaceSamHeader.class)); for (final SAMRecord rec : recordReader) { rec.setHeader(replacementHeader); writer.addAlignment(rec); progress.record(rec); } writer.close(); CloserUtil.close(recordReader); }
final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT); final CloseableIterator<SAMRecord> it = reader.iterator(); final ProgressLogger progress = new ProgressLogger(Log.getInstance(CleanSam.class));
final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT); final CloseableIterator<SAMRecord> it = reader.iterator(); final ProgressLogger progress = new ProgressLogger(Log.getInstance(CleanSam.class));
final ProgressLogger progress = new ProgressLogger(Log.getInstance(MakeSitesOnlyVcf.class), 10000);
final ProgressLogger progress = new ProgressLogger(Log.getInstance(MakeSitesOnlyVcf.class), 10000);