picard.illumina

Class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD>

java.lang.Object

picard.illumina.IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD>

Type Parameters:

CLUSTER_OUTPUT_RECORD - The class to which a ClusterData is converted in preparation for writing.

public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD>
extends java.lang.Object

Manages the conversion of Illumina basecalls into some output format. Creates multiple threads to manage reading, sorting and writing efficiently. Output is written in queryname output. Optionally demultiplexes indexed reads into separate outputs by barcode.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	IlluminaBasecallsConverter.ClusterDataConverter<OUTPUT_RECORD>
static interface	IlluminaBasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD>

Field Summary

Fields

Modifier and Type	Field and Description
static IlluminaDataType[]	DATA_TYPES_NO_BARCODE
static java.util.Comparator<java.lang.Integer>	TILE_NUMBER_COMPARATOR A comparator for tile numbers, which are not necessarily ordered by the number's value.

Constructor Summary

Constructors

Constructor and Description
IlluminaBasecallsConverter(java.io.File basecallsDir, java.io.File barcodesDir, int lane, ReadStructure readStructure, java.util.Map<java.lang.String,? extends IlluminaBasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap, boolean demultiplex, int maxReadsInRamPerTile, java.util.List<java.io.File> tmpDirs, int numProcessors, boolean forceGc, java.lang.Integer firstTile, java.lang.Integer tileLimit, java.util.Comparator<CLUSTER_OUTPUT_RECORD> outputRecordComparator, htsjdk.samtools.util.SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype, java.lang.Class<CLUSTER_OUTPUT_RECORD> outputRecordClass, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, boolean applyEamssFiltering, boolean includeNonPfReads, boolean ignoreUnexpectedBarcodes)
IlluminaBasecallsConverter(java.io.File basecallsDir, int lane, ReadStructure readStructure, java.util.Map<java.lang.String,? extends IlluminaBasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap, boolean demultiplex, int maxReadsInRamPerTile, java.util.List<java.io.File> tmpDirs, int numProcessors, boolean forceGc, java.lang.Integer firstTile, java.lang.Integer tileLimit, java.util.Comparator<CLUSTER_OUTPUT_RECORD> outputRecordComparator, htsjdk.samtools.util.SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype, java.lang.Class<CLUSTER_OUTPUT_RECORD> outputRecordClass, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, boolean applyEamssFiltering, boolean includeNonPfReads, boolean ignoreUnexpectedBarcodes)

Method Summary

Modifier and Type	Method and Description
void	doTileProcessing() Do the work, i.e.
IlluminaDataProviderFactory	getFactory() In case caller needs to get some info from factory.
void	setConverter(IlluminaBasecallsConverter.ClusterDataConverter<CLUSTER_OUTPUT_RECORD> converter) Must be called before doTileProcessing.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DATA_TYPES_NO_BARCODE

public static final IlluminaDataType[] DATA_TYPES_NO_BARCODE

TILE_NUMBER_COMPARATOR

public static final java.util.Comparator<java.lang.Integer> TILE_NUMBER_COMPARATOR

A comparator for tile numbers, which are not necessarily ordered by the number's value.

Constructor Detail

IlluminaBasecallsConverter

public IlluminaBasecallsConverter(java.io.File basecallsDir,
                                  int lane,
                                  ReadStructure readStructure,
                                  java.util.Map<java.lang.String,? extends IlluminaBasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap,
                                  boolean demultiplex,
                                  int maxReadsInRamPerTile,
                                  java.util.List<java.io.File> tmpDirs,
                                  int numProcessors,
                                  boolean forceGc,
                                  java.lang.Integer firstTile,
                                  java.lang.Integer tileLimit,
                                  java.util.Comparator<CLUSTER_OUTPUT_RECORD> outputRecordComparator,
                                  htsjdk.samtools.util.SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype,
                                  java.lang.Class<CLUSTER_OUTPUT_RECORD> outputRecordClass,
                                  BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
                                  boolean applyEamssFiltering,
                                  boolean includeNonPfReads,
                                  boolean ignoreUnexpectedBarcodes)

Parameters:

basecallsDir - Where to read basecalls from.

lane - What lane to process.

readStructure - How to interpret each cluster.

barcodeRecordWriterMap - Map from barcode to CLUSTER_OUTPUT_RECORD writer. If demultiplex is false, must contain one writer stored with key=null.

demultiplex - If true, output is split by barcode, otherwise all are written to the same output stream.

maxReadsInRamPerTile - Configures number of reads each tile will store in RAM before spilling to disk.

tmpDirs - For SortingCollection spilling.

numProcessors - Controls number of threads. If <= 0, the number of threads allocated is available cores - numProcessors.

forceGc - Force explicit GC periodically. This is good for causing memory maps to be released.

firstTile - (For debugging) If non-null, start processing at this tile.

tileLimit - (For debugging) If non-null, process no more than this many tiles.

outputRecordComparator - For sorting output records within a single tile.

codecPrototype - For spilling output records to disk.

outputRecordClass - Inconveniently needed to create SortingCollections.

includeNonPfReads - If true, will include ALL reads (including those which do not have PF set)

ignoreUnexpectedBarcodes - If true, will ignore reads whose called barcode is not found in barcodeRecordWriterMap, otherwise will throw an exception

IlluminaBasecallsConverter

public IlluminaBasecallsConverter(java.io.File basecallsDir,
                                  java.io.File barcodesDir,
                                  int lane,
                                  ReadStructure readStructure,
                                  java.util.Map<java.lang.String,? extends IlluminaBasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap,
                                  boolean demultiplex,
                                  int maxReadsInRamPerTile,
                                  java.util.List<java.io.File> tmpDirs,
                                  int numProcessors,
                                  boolean forceGc,
                                  java.lang.Integer firstTile,
                                  java.lang.Integer tileLimit,
                                  java.util.Comparator<CLUSTER_OUTPUT_RECORD> outputRecordComparator,
                                  htsjdk.samtools.util.SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype,
                                  java.lang.Class<CLUSTER_OUTPUT_RECORD> outputRecordClass,
                                  BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
                                  boolean applyEamssFiltering,
                                  boolean includeNonPfReads,
                                  boolean ignoreUnexpectedBarcodes)

Parameters:

basecallsDir - Where to read basecalls from.

barcodesDir - Where to read barcodes from (optional; use basecallsDir if not specified).

lane - What lane to process.

readStructure - How to interpret each cluster.

barcodeRecordWriterMap - Map from barcode to CLUSTER_OUTPUT_RECORD writer. If demultiplex is false, must contain one writer stored with key=null.

demultiplex - If true, output is split by barcode, otherwise all are written to the same output stream.

maxReadsInRamPerTile - Configures number of reads each tile will store in RAM before spilling to disk.

tmpDirs - For SortingCollection spilling.

numProcessors - Controls number of threads. If <= 0, the number of threads allocated is available cores - numProcessors.

forceGc - Force explicit GC periodically. This is good for causing memory maps to be released.

firstTile - (For debugging) If non-null, start processing at this tile.

tileLimit - (For debugging) If non-null, process no more than this many tiles.

outputRecordComparator - For sorting output records within a single tile.

codecPrototype - For spilling output records to disk.

outputRecordClass - Inconveniently needed to create SortingCollections.

includeNonPfReads - If true, will include ALL reads (including those which do not have PF set)

ignoreUnexpectedBarcodes - If true, will ignore reads whose called barcode is not found in barcodeRecordWriterMap, otherwise will throw an exception

Method Detail

setConverter

public void setConverter(IlluminaBasecallsConverter.ClusterDataConverter<CLUSTER_OUTPUT_RECORD> converter)

Must be called before doTileProcessing. This is not passed in the ctor because often the IlluminaDataProviderFactory is needed in order to construct the converter.

Parameters:

converter - Converts ClusterData to CLUSTER_OUTPUT_RECORD

getFactory

public IlluminaDataProviderFactory getFactory()

In case caller needs to get some info from factory.

doTileProcessing

public void doTileProcessing()

Do the work, i.e. create a bunch of threads to read, sort and write. setConverter() must be called before calling this method.