picard.illumina.parser

Class OutputMapping

java.lang.Object

picard.illumina.parser.OutputMapping

public class OutputMapping
extends java.lang.Object

In multiple locations we need to know what cycles are output, as of now we output all non-skip cycles, but rather than sprinkle this knowledge throughout the parser code, instead OutputMapping provides all the data a client might want about the cycles to be output including what ReadType they are.

Author:

jburke@broadinstitute.org

Constructor Summary

Constructors

Constructor and Description
OutputMapping(ReadStructure readStructure) Create an OutputMapping from a readStructure, currently the outputSubstructure just references the readStructure.nonSkips Substructure

Method Summary

Modifier and Type	Method and Description
Range[]	getCycleIndexRanges()
int[]	getOutputCycles()
java.lang.Iterable<ReadDescriptor>	getOutputDescriptors()
picard.illumina.parser.OutputMapping.TwoDIndex	getOutputIndexForCycle(int cycle) Return an index that where: index.arrayIndex - represents either the read number the cycle will be output too, or (in some cases) an array index into a two dimensional array of byte[][] where the top level array corresponds to read number index.elementIndex - represents the element a cycle will appear in inside it's give read, or the element in an array as described above
int[]	getOutputReadLengths()
ReadStructure	getOutputReadStructure()
int	getTotalOutputCycles()
int	numOutputReads()

Methods inherited from class java.lang.Object

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

Constructor Detail

OutputMapping

public OutputMapping(ReadStructure readStructure)

Create an OutputMapping from a readStructure, currently the outputSubstructure just references the readStructure.nonSkips Substructure

Parameters:

readStructure - The readStructure for the given run that we want an OutputMapping for

Method Detail

numOutputReads

public int numOutputReads()

Returns:

The number of reads that should be found in the output clusterData

getOutputCycles

public int[] getOutputCycles()

Returns:

An array of cycles in ascending order of all the cycles that should be output.

getOutputReadLengths

public int[] getOutputReadLengths()

Returns:

An ordered array of lengths, where each element represents the size of output reads respectively

getTotalOutputCycles

public int getTotalOutputCycles()

Returns:

The total number of cycles that will be output

getCycleIndexRanges

public Range[] getCycleIndexRanges()

Returns:

An ordered array of Ranges over cycle indices(cycle#-1), where each range represents a contiguous block of cycles to output, and each cycle in getOutputCycles() is in ONE AND ONLY ONE Range, all ranges are inclusive of both ends

getOutputDescriptors

public java.lang.Iterable<ReadDescriptor> getOutputDescriptors()

Returns:

An iterator over the read descriptors that describe the reads to be output

getOutputReadStructure

public ReadStructure getOutputReadStructure()

getOutputIndexForCycle

public picard.illumina.parser.OutputMapping.TwoDIndex getOutputIndexForCycle(int cycle)

Return an index that where: index.arrayIndex - represents either the read number the cycle will be output too, or (in some cases) an array index into a two dimensional array of byte[][] where the top level array corresponds to read number index.elementIndex - represents the element a cycle will appear in inside it's give read, or the element in an array as described above

Parameters:

cycle - The cycle for which we want an index

Returns:

A TwoDArrayIndex indicating where this cycle can be found