Package picard.illumina.parser
Class OutputMapping
- java.lang.Object
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- picard.illumina.parser.OutputMapping
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public class OutputMapping extends 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.
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Constructor Summary
Constructors Constructor Description OutputMapping(ReadStructure readStructure)
Create an OutputMapping from a readStructure, currently the outputSubstructure just references the readStructure.nonSkips Substructure
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Range[]
getCycleIndexRanges()
int[]
getOutputCycles()
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 aboveint[]
getOutputReadLengths()
ReadStructure
getOutputReadStructure()
int
getTotalOutputCycles()
int
numOutputReads()
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Constructor Detail
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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
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Method Detail
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numOutputReads
public int numOutputReads()
- Returns:
- The number of reads that should be found in the output clusterData
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getOutputCycles
public int[] getOutputCycles()
- Returns:
- An array of cycles in ascending order of all the cycles that should be output.
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getOutputReadLengths
public int[] getOutputReadLengths()
- Returns:
- An ordered array of lengths, where each element represents the size of output reads respectively
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getTotalOutputCycles
public int getTotalOutputCycles()
- Returns:
- The total number of cycles that will be output
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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
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getOutputDescriptors
public Iterable<ReadDescriptor> getOutputDescriptors()
- Returns:
- An iterator over the read descriptors that describe the reads to be output
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getOutputReadStructure
public ReadStructure getOutputReadStructure()
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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
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