Examples of picard.illumina.parser.ReadStructure

picard.illumina.parser.ReadStructure
Describes the intended logical output structure of clusters of an Illumina run. (e.g. If the input data consists of 80 base clusters and we provide a read structure of "36T8B36T" then those bases should be split into 3 reads: read one should be 36 cycles of template, read two should be 8 cycles of barcode, read three should be another 36 cycle template read.) Note: In future releases, ReadStructures will be specified by clients of IlluminaDataProvider(currently read structures are detected by IlluminaDataProviderFactory via the structure of QSeq files). When working with QSeq formats, while the individual reads need not fall on QSeq end file boundaries the total number of cycles should equal the total number of cycles found in all end files for one tile. (e.g. if I have 80 reads and 3 end files per tile, those end files should have a total of 80 reads in them regardless of how many reads appear in each individual file) @author jburke@broadinstitute.org

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

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    }


    @Test(dataProvider = "invalidReadStructures", expectedExceptions = IllegalArgumentException.class)
    public void testInvalidReadStructureFromString(final String rsString, final List<ReadDescriptor> descriptors) {
        final ReadStructure readStructure = new ReadStructure(rsString);
    }

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        final ReadStructure readStructure = new ReadStructure(rsString);
    }


    @Test(dataProvider = "invalidReadStructuresFromList", expectedExceptions = IllegalArgumentException.class)
    public void testInvalidReadStructureFromList(final String rsString, final List<ReadDescriptor> descriptors) {
        final ReadStructure readStructure = new ReadStructure(descriptors);
    }

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    }


    @DataProvider(name="substructuresToReadStructureData")
    public Object [][] substructureToReadStructureData() {
        return new Object[][] {
            {new ReadStructure("10T10T").templates,      "10T10T"  },
            {new ReadStructure("10T8B10T").nonSkips,     "10T8B10T"},
            {new ReadStructure("8S10T8B8S10T").nonSkips, "10T8B10T"},
            {new ReadStructure("10T8S8S10T").skips,      "8S8S"    },
            {new ReadStructure("8B").barcodes,           "8B"      }
        };
    }

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    }


    @DataProvider(name="substructureToReadStructureNegativeData")
    public Object[][] substructureToReadStructureNegativeData() {
        return new Object[][] {
            {new ReadStructure("10T").barcodes   },
            {new ReadStructure("10S").nonSkips   },
            {new ReadStructure("10S8B").templates},
        };
    }

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    public void testWriteLaneMetrics(final String testRun) throws Exception {
        final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
        clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
        clp.RUN_DIRECTORY = new File(TEST_DIRECTORY, testRun);
        clp.OUTPUT_PREFIX = "test";
        clp.READ_STRUCTURE = new ReadStructure("101T8B101T");
        clp.doWork();


        final File laneMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaLaneMetrics.getExtension());
        final File canonicalOutputFile = buildOutputFile(TEST_DIRECTORY, testRun, IlluminaLaneMetrics.getExtension());

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        IOUtil.deleteDirectoryTree(clp.OUTPUT_DIRECTORY);    }


    @DataProvider(name = "testCollectIlluminaLaneMetrics")
    public Object[][] testCollectIlluminaLaneMetricsDataProvider() {
        return new Object[][] {
                {"A7LE0", new ReadStructure("25T8B8B25T")},
                {"C2MFAACXX", new ReadStructure("95T101T")},
                {"H7BATADXX", new ReadStructure("76T8B76T")},
                {"H7H7RADXX", new ReadStructure("101T8B8B101T")},
                {"A67HY", new ReadStructure("8B8B")}
        };
    }

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