Package picard.illumina.parser
Class ReadStructure
- java.lang.Object
-
- picard.illumina.parser.ReadStructure
-
public class ReadStructure extends Object
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)
-
-
Nested Class Summary
Nested Classes Modifier and Type Class Description class
ReadStructure.Substructure
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
Fields Modifier and Type Field Description List<ReadDescriptor>
descriptors
ReadStructure.Substructure
molecularBarcode
ReadStructure.Substructure
nonSkips
static String
PARAMETER_DOC
int[]
readLengths
ReadStructure.Substructure
sampleBarcodes
ReadStructure.Substructure
skips
ReadStructure.Substructure
templates
int
totalCycles
-
Constructor Summary
Constructors Constructor Description ReadStructure(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
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
equals(Object thatObj)
int
getNumDescriptors()
int
hashCode()
boolean
hasSampleBarcode()
String
toString()
Converts this object into a String using rules complementary to the single string constructor above.
-
-
-
Field Detail
-
PARAMETER_DOC
public static final String PARAMETER_DOC
- See Also:
- Constant Field Values
-
descriptors
public final List<ReadDescriptor> descriptors
-
totalCycles
public final int totalCycles
-
readLengths
public final int[] readLengths
-
sampleBarcodes
public final ReadStructure.Substructure sampleBarcodes
-
templates
public final ReadStructure.Substructure templates
-
molecularBarcode
public final ReadStructure.Substructure molecularBarcode
-
skips
public final ReadStructure.Substructure skips
-
nonSkips
public final ReadStructure.Substructure nonSkips
-
-
Constructor Detail
-
ReadStructure
public ReadStructure(List<ReadDescriptor> collection)
Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors.- Parameters:
collection
- A collection of ReadDescriptors that describes this ReadStructure
-
ReadStructure
public ReadStructure(String readStructureString)
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
-
-
Method Detail
-
getNumDescriptors
public int getNumDescriptors()
-
toString
public String toString()
Converts this object into a String using rules complementary to the single string constructor above.
-
hasSampleBarcode
public boolean hasSampleBarcode()
-
-