public class OutputMapping extends Object
Constructor | Description |
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OutputMapping(ReadStructure readStructure) |
Create an OutputMapping from a readStructure, currently the outputSubstructure just references the readStructure.nonSkips
Substructure
|
Modifier and Type | Method | Description |
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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 above
|
int[] |
getOutputReadLengths() |
|
ReadStructure |
getOutputReadStructure() |
|
int |
getTotalOutputCycles() |
|
int |
numOutputReads() |
public OutputMapping(ReadStructure readStructure)
readStructure
- The readStructure for the given run that we want an OutputMapping forpublic int numOutputReads()
public int[] getOutputCycles()
public int[] getOutputReadLengths()
public int getTotalOutputCycles()
public Range[] getCycleIndexRanges()
public Iterable<ReadDescriptor> getOutputDescriptors()
public ReadStructure getOutputReadStructure()
public picard.illumina.parser.OutputMapping.TwoDIndex getOutputIndexForCycle(int cycle)
cycle
- The cycle for which we want an index