Package picard.illumina.parser
Class OutputMapping
java.lang.Object
picard.illumina.parser.OutputMapping
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.
-
Constructor Summary
ConstructorsConstructorDescriptionOutputMapping
(ReadStructure readStructure) Create an OutputMapping from a readStructure, currently the outputSubstructure just references the readStructure.nonSkips Substructure -
Method Summary
Modifier and TypeMethodDescriptionRange[]
int[]
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[]
int
int
-
Constructor Details
-
OutputMapping
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 Details
-
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
- 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
- Returns:
- An iterator over the read descriptors that describe the reads to be output
-
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
-