picard.illumina.parser

Class IlluminaDataProviderFactory

java.lang.Object

picard.illumina.parser.IlluminaDataProviderFactory

public class IlluminaDataProviderFactory
extends java.lang.Object

IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an IlluminaDataProvider, an iterator over the ClusterData for that lane, which utilizes these options.

Note: Since we tend to use IlluminaDataProviderFactory in multithreaded environments (e.g. we call makeDataProvider in a different thread per tile in IlluminaBasecallsToSam). I've made it essentially immutable. makeDataProvider/getTiles are now idempotent (well as far as IlluminaDataProviderFactory is concerned, many file handles and other things are opened when makeDataProvider is called). We may in the future want dataTypes to be provided to the makeDataProvider factory methods so configuration is not done multiple times for the same basecallDirectory in client code.

Author:

jburke@broadinstitute.org

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.Map<IlluminaFileUtil.SupportedIlluminaFormat,java.util.Set<IlluminaDataType>>	formatToDataTypes A Map of file formats to the dataTypes they will provide for this run.

Constructor Summary

Constructors

Constructor and Description
IlluminaDataProviderFactory(java.io.File basecallDirectory, java.io.File barcodesDirectory, int lane, ReadStructure readStructure, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, IlluminaDataType... dataTypesArg) Create factory with the specified options, one that favors using QSeqs over all other files
IlluminaDataProviderFactory(java.io.File basecallDirectory, int lane, ReadStructure readStructure, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, IlluminaDataType... dataTypesArg) Create factory with the specified options, one that favors using QSeqs over all other files

Method Summary

Modifier and Type	Method and Description
static java.util.Map<IlluminaFileUtil.SupportedIlluminaFormat,java.util.Set<IlluminaDataType>>	determineFormats(java.util.Set<IlluminaDataType> requestedDataTypes, IlluminaFileUtil fileUtil) For all requestedDataTypes return a map of file format to set of provided data types that covers as many requestedDataTypes as possible and chooses the most preferred available formats possible
static IlluminaFileUtil.SupportedIlluminaFormat	findPreferredFormat(IlluminaDataType dt, IlluminaFileUtil fileUtil) Given a data type find the most preferred file format even if files are not available
static java.util.Set<IlluminaDataType>	findUnmatchedTypes(java.util.Set<IlluminaDataType> requestedDataTypes, java.util.Map<IlluminaFileUtil.SupportedIlluminaFormat,java.util.Set<IlluminaDataType>> formatToMatchedTypes) Given a set of formats to data types they provide, find any requested data types that do not have a format associated with them and return them
java.util.List<java.lang.Integer>	getAvailableTiles() Return the list of tiles available for this flowcell and lane.
ReadStructure	getOutputReadStructure() Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input readStructure
IlluminaDataProvider	makeDataProvider() Call this method to create a ClusterData iterator over all clusters for all tiles in ascending numeric order.
IlluminaDataProvider	makeDataProvider(java.util.List<java.lang.Integer> requestedTiles) Call this method to create a ClusterData iterator over the specified tiles.
void	setApplyEamssFiltering(boolean applyEamssFiltering) Sets whether or not EAMSS filtering will be applied if parsing BCL files for bases and quality scores.

Methods inherited from class java.lang.Object

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

Field Detail

formatToDataTypes

protected final java.util.Map<IlluminaFileUtil.SupportedIlluminaFormat,java.util.Set<IlluminaDataType>> formatToDataTypes

A Map of file formats to the dataTypes they will provide for this run.

Constructor Detail

IlluminaDataProviderFactory

public IlluminaDataProviderFactory(java.io.File basecallDirectory,
                                   int lane,
                                   ReadStructure readStructure,
                                   BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
                                   IlluminaDataType... dataTypesArg)

Create factory with the specified options, one that favors using QSeqs over all other files

Parameters:

basecallDirectory - The baseCalls directory of a complete Illumina directory. Files are found by searching relative to this folder (some of them higher up in the directory tree).

lane - Which lane to iterate over.

readStructure - The read structure to which output clusters will conform. When not using QSeqs, EAMSS masking(see BclParser) is run on individual reads as found in the readStructure, if the readStructure specified does not match the readStructure implied by the sequencer's output than the quality scores output may differ than what would be found in a run's QSeq files

dataTypesArg - Which data types to read

IlluminaDataProviderFactory

public IlluminaDataProviderFactory(java.io.File basecallDirectory,
                                   java.io.File barcodesDirectory,
                                   int lane,
                                   ReadStructure readStructure,
                                   BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
                                   IlluminaDataType... dataTypesArg)

Create factory with the specified options, one that favors using QSeqs over all other files

Parameters:

basecallDirectory - The baseCalls directory of a complete Illumina directory. Files are found by searching relative to this folder (some of them higher up in the directory tree).

barcodesDirectory - The barcodesDirectory with barcode files extracted by 'ExtractIlluminaBarcodes' (optional, use basecallDirectory if not specified)

lane - Which lane to iterate over.

readStructure - The read structure to which output clusters will conform. When not using QSeqs, EAMSS masking(see BclParser) is run on individual reads as found in the readStructure, if the readStructure specified does not match the readStructure implied by the sequencer's output than the quality scores output may differ than what would be found in a run's QSeq files

dataTypesArg - Which data types to read

Method Detail

getOutputReadStructure

public ReadStructure getOutputReadStructure()

Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input readStructure

Returns:

The ReadStructure describing the output cluster data

getAvailableTiles

public java.util.List<java.lang.Integer> getAvailableTiles()

Return the list of tiles available for this flowcell and lane. These are in ascending numerical order.

Returns:

List of all tiles available for this flowcell and lane.

setApplyEamssFiltering

public void setApplyEamssFiltering(boolean applyEamssFiltering)

Sets whether or not EAMSS filtering will be applied if parsing BCL files for bases and quality scores.

makeDataProvider

public IlluminaDataProvider makeDataProvider()

Call this method to create a ClusterData iterator over all clusters for all tiles in ascending numeric order.

Returns:

An iterator for reading the Illumina basecall output for the lane specified in the ctor.

makeDataProvider

public IlluminaDataProvider makeDataProvider(java.util.List<java.lang.Integer> requestedTiles)

Call this method to create a ClusterData iterator over the specified tiles.

Returns:

An iterator for reading the Illumina basecall output for the lane specified in the constructor.

findUnmatchedTypes

public static java.util.Set<IlluminaDataType> findUnmatchedTypes(java.util.Set<IlluminaDataType> requestedDataTypes,
                                                                 java.util.Map<IlluminaFileUtil.SupportedIlluminaFormat,java.util.Set<IlluminaDataType>> formatToMatchedTypes)

Given a set of formats to data types they provide, find any requested data types that do not have a format associated with them and return them

Parameters:

requestedDataTypes - Data types that need to be provided

formatToMatchedTypes - A map of file formats to data types that will support them

Returns:

The data types that go unsupported by the formats found in formatToMatchedTypes

determineFormats

public static java.util.Map<IlluminaFileUtil.SupportedIlluminaFormat,java.util.Set<IlluminaDataType>> determineFormats(java.util.Set<IlluminaDataType> requestedDataTypes,
                                                                                                                       IlluminaFileUtil fileUtil)

For all requestedDataTypes return a map of file format to set of provided data types that covers as many requestedDataTypes as possible and chooses the most preferred available formats possible

Parameters:

requestedDataTypes - Data types to be provided

fileUtil - A file util for the lane/directory we wish to provide data for

Returns:

A Map

findPreferredFormat

public static IlluminaFileUtil.SupportedIlluminaFormat findPreferredFormat(IlluminaDataType dt,
                                                                           IlluminaFileUtil fileUtil)

Given a data type find the most preferred file format even if files are not available

Parameters:

dt - Type of desired data

fileUtil - Util for the lane/directory in which we will find data

Returns:

The file format that is "most preferred" (i.e. fastest to parse/smallest in memory)