Examples of picard.illumina.parser.ReadStructure$Substructure

picard.illumina.parser.ReadStructure
Represents a subset of ReadDescriptors in the containing ReadStructure, they ARE NOT necessarily contiguous in the containing ReadStrucure but they ARE in the order they appear in the containing ReadStructure

        /**
         * In extract illumina barcodes we NEVER want to look at the template reads, therefore replace them with skips because
         * IlluminaDataProvider and its factory will not open these nor produce ClusterData with the template reads in them, thus reducing
         * the file IO and value copying done by the data provider
         */
        readStructure = new ReadStructure(READ_STRUCTURE.replaceAll("T", "S"));
        final IlluminaDataType[] datatypes = (MINIMUM_BASE_QUALITY > 0) ?
                new IlluminaDataType[]{IlluminaDataType.BaseCalls, IlluminaDataType.PF, IlluminaDataType.QualityScores} :
                new IlluminaDataType[]{IlluminaDataType.BaseCalls, IlluminaDataType.PF};
        factory = new IlluminaDataProviderFactory(BASECALLS_DIR, LANE, readStructure, bclQualityEvaluationStrategy, datatypes);

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        IOUtil.assertDirectoryIsReadable(BASECALLS_DIR);
        if (OUTPUT == null) OUTPUT = new File(BASECALLS_DIR, String.format("LANE%s_basecalling_metrics", LANE));
        IOUtil.assertFileIsWritable(OUTPUT);


        final IlluminaDataProviderFactory factory;
        final ReadStructure readStructure = new ReadStructure(READ_STRUCTURE);
        final BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY);


        if (INPUT == null) {
            // TODO: Legacy support. Remove when INPUT is required, after all old workflows are through
            factory = new IlluminaDataProviderFactory(BASECALLS_DIR, LANE, readStructure, bclQualityEvaluationStrategy,

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            metrics.SD_PCT_PF_CLUSTERS_PER_TILE = Double.valueOf(decFormat.format(laneToPctPfClusterHistogram.getStandardDeviationBinSize(meanPctPfClustersPerTile) * 100));


            metrics.TOTAL_CLUSTERS = (long) this.tileToClusterHistogram.getSumOfValues();
            metrics.PF_CLUSTERS    = (long) this.tileToPfClusterHistogram.getSumOfValues();
            
            final ReadStructure readStructure = new ReadStructure(READ_STRUCTURE);
            int templateBaseCountPerCluster = 0;
            for (int i = 0; i < readStructure.templates.length(); i++) templateBaseCountPerCluster += readStructure.templates.get(i).length;
            metrics.TOTAL_READS = metrics.TOTAL_CLUSTERS * readStructure.templates.length();
            metrics.PF_READS = metrics.PF_CLUSTERS * readStructure.templates.length();
            metrics.TOTAL_BASES = metrics.TOTAL_CLUSTERS * templateBaseCountPerCluster;

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            barcodeSamWriterMap.put(null, buildSamFileWriter(OUTPUT, SAMPLE_ALIAS, LIBRARY_NAME, buildSamHeaderParameters(null)));
        } else {
            populateWritersFromLibraryParams();
        }


        readStructure = new ReadStructure(READ_STRUCTURE);


        final int numOutputRecords = readStructure.templates.length();


        basecallsConverter = new IlluminaBasecallsConverter<SAMRecordsForCluster>(BASECALLS_DIR, BARCODES_DIR, LANE, readStructure,
                barcodeSamWriterMap, true, MAX_READS_IN_RAM_PER_TILE/numOutputRecords, TMP_DIR, NUM_PROCESSORS, FORCE_GC,

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            LIBRARY_PARAMS = BARCODE_PARAMS;
        }


        final ArrayList<String> messages = new ArrayList<String>();


        readStructure = new ReadStructure(READ_STRUCTURE);
        if (!readStructure.barcodes.isEmpty()) {
            if (LIBRARY_PARAMS == null) {
                messages.add("BARCODE_PARAMS or LIBRARY_PARAMS is missing.  If READ_STRUCTURE contains a B (barcode)" +
                        " then either LIBRARY_PARAMS or BARCODE_PARAMS(deprecated) must be provided!");
            }

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        new CheckIlluminaDirectory().instanceMainWithExit(argv);
    }


    @Override
    protected int doWork() {
        final ReadStructure readStructure = new ReadStructure(READ_STRUCTURE);
        if (DATA_TYPES.isEmpty()) {
            DATA_TYPES.addAll(Arrays.asList(IlluminaBasecallsConverter.DATA_TYPES_NO_BARCODE));
        }


        final List<Integer> failingLanes = new ArrayList<Integer>();

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                readNameEncoder = new IlluminaReadNameEncoder(RUN_BARCODE);
                break;
        }
        
        final BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY);
        readStructure = new ReadStructure(READ_STRUCTURE);
        if (MULTIPLEX_PARAMS != null) {
            IOUtil.assertFileIsReadable(MULTIPLEX_PARAMS);
        }
        final boolean demultiplex;
        if (OUTPUT_PREFIX != null) {

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                    "MULTIPLEX_PARAMS=" + libraryParams,
                    "MACHINE_NAME=machine1",
                    "FLOWCELL_BARCODE=abcdeACXX"
            });


            final ReadStructure readStructure = new ReadStructure(readStructureString);
            for (final File outputSam : outputPrefixes) {
                for (int i = 1; i <= readStructure.templates.length(); ++i) {
                    final String filename = outputSam.getName() + "." + i + ".fastq";
                    IOUtil.assertFilesEqual(new File(outputSam.getParentFile(), filename), new File(testDataDir, filename));
                }

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        Assert.assertEquals(illuminaFields[1], "N");


        barcodeParser.close();


        // Tack on test of barcode-informed Illumina Basecall parsing
        final ReadStructure rs = new ReadStructure("25T8B25T");
        final IlluminaDataProviderFactory factory = new IlluminaDataProviderFactory(basecallsDir, lane, rs,
                new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY),
                IlluminaDataType.BaseCalls, IlluminaDataType.QualityScores, IlluminaDataType.Barcodes);
        testParsing(factory, rs, metricOne, barcodePosition);
    }

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        return outObjs;
    }


    @Test(dataProvider = "validReadStructures")
    public void testValidStructuresFromString(final String rsString, final List<ReadDescriptor> descriptors, final int numTemplates, final int numBarcodes, final int numSkips) {
        final ReadStructure readStructure = new ReadStructure(rsString);
        testReadStructure(readStructure, rsString, descriptors, numTemplates, numBarcodes, numSkips);
    }

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Related Classes of picard.illumina.parser.ReadStructure$Substructure

picard.illumina.CheckIlluminaDirectory

picard.illumina.CollectIlluminaBasecallingMetrics

picard.illumina.CollectIlluminaBasecallingMetrics$IlluminaMetricCounts

picard.illumina.ExtractIlluminaBarcodes

picard.illumina.ExtractIlluminaBarcodesTest

picard.illumina.IlluminaBasecallsToFastq

picard.illumina.IlluminaBasecallsToFastqTest

picard.illumina.IlluminaBasecallsToSam

picard.illumina.IlluminaLaneMetricsCollectorTest

picard.illumina.ReadStructureTest

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