picard.illumina.parser

Class ReadStructure

java.lang.Object

picard.illumina.parser.ReadStructure

public class ReadStructure
extends java.lang.Object

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 "28T8M8B8S28T" then those bases should be split into 4 reads: read one should be 28 cycles of template, read two should be 8 cycles of molecular barcode, read three should be 8 cycles of sample barcode, 8 cycles are skipped, read four 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

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	ReadStructure.Substructure Represents a subset of ReadDescriptors in the containing ReadStructure, they ARE NOT necessarily contiguous in the containing ReadStructure but they ARE in the order they appear in the containing ReadStructure

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<ReadDescriptor>	descriptors
ReadStructure.Substructure	molecularBarcode
ReadStructure.Substructure	nonSkips
static java.lang.String	PARAMETER_DOC
int[]	readLengths
ReadStructure.Substructure	sampleBarcodes
ReadStructure.Substructure	skips
ReadStructure.Substructure	templates
int	totalCycles

Constructor Summary

Constructors

Constructor and Description
ReadStructure(java.util.List<ReadDescriptor> collection) Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors.
ReadStructure(java.lang.String readStructureString) Converts readStructureString into a List and calls the primary constructor using this List as it's argument.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object thatObj)
int	getNumDescriptors()
int	hashCode()
java.lang.String	toString() Converts this object into a String using rules complementary to the single string constructor above.

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

PARAMETER_DOC

public static final java.lang.String PARAMETER_DOC

See Also:

Constant Field Values

descriptors

public final java.util.List<ReadDescriptor> descriptors

totalCycles

public final int totalCycles

readLengths

public final int[] readLengths

sampleBarcodes

public final ReadStructure.Substructure sampleBarcodes

templates

public final ReadStructure.Substructure templates

molecularBarcode

public final ReadStructure.Substructure molecularBarcode

skips

public final ReadStructure.Substructure skips

nonSkips

public final ReadStructure.Substructure nonSkips

Constructor Detail

ReadStructure

public ReadStructure(java.util.List<ReadDescriptor> collection)

Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors.

Parameters:

collection - A collection of ReadDescriptors that describes this ReadStructure

ReadStructure

public ReadStructure(java.lang.String readStructureString)

Converts readStructureString into a List and calls the primary constructor using this List as it's argument.

Parameters:

readStructureString - A string of the format ... describing this read structure

Method Detail

getNumDescriptors

public int getNumDescriptors()

toString

public java.lang.String toString()

Converts this object into a String using rules complementary to the single string constructor above.

Overrides:

toString in class java.lang.Object

Returns:

A string of the form ... with one per ReadDescriptor in descriptors.

equals

public boolean equals(java.lang.Object thatObj)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object