Package picard.illumina.parser
Class ReadStructure
java.lang.Object
picard.illumina.parser.ReadStructure
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)
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionclass
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
FieldsModifier and TypeFieldDescriptionfinal List
<ReadDescriptor> static final String
final int[]
final int
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Constructor Summary
ConstructorsConstructorDescriptionReadStructure
(String readStructureString) Converts readStructureString into a Listand calls the primary constructor using this List as it's argument. ReadStructure
(List<ReadDescriptor> collection) Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors. -
Method Summary
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Field Details
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PARAMETER_DOC
- See Also:
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descriptors
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totalCycles
public final int totalCycles -
readLengths
public final int[] readLengths -
sampleBarcodes
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templates
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molecularBarcode
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skips
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nonSkips
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Constructor Details
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ReadStructure
Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors.- Parameters:
collection
- A collection of ReadDescriptors that describes this ReadStructure
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ReadStructure
Converts readStructureString into a Listand calls the primary constructor using this List as it's argument. - Parameters:
readStructureString
- A string of the format... describing this read structure
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Method Details
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getNumDescriptors
public int getNumDescriptors() -
toString
Converts this object into a String using rules complementary to the single string constructor above. -
equals
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hashCode
public int hashCode() -
hasSampleBarcode
public boolean hasSampleBarcode()
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