Package picard.illumina.parser
Class ReadStructure.Substructure
java.lang.Object
picard.illumina.parser.ReadStructure.Substructure
- All Implemented Interfaces:
Iterable<ReadDescriptor>
- Enclosing class:
- ReadStructure
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
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Constructor Summary
ConstructorsConstructorDescriptionSubstructure
(List<Integer> descriptorIndices, List<Range> allRanges) Indices into the ReadStructure.descriptors for this specific substructure, indices must be in the order they appear in the descriptors list (but the indices do NOT have to be continuous) -
Method Summary
Modifier and TypeMethodDescriptionget
(int index) Range[]
int[]
int[]
int[]
int
boolean
isEmpty()
iterator()
int
length()
Create a ReadStructure from this substructure composed of only the descriptors contained in this substructure, Any ReadDescriptors not in this substructure are treated as if they don't exist (e.g.Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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Substructure
Indices into the ReadStructure.descriptors for this specific substructure, indices must be in the order they appear in the descriptors list (but the indices do NOT have to be continuous)- Parameters:
descriptorIndices
- A list of indices into ReadStructure.descriptors of the enclosing ReadStructureallRanges
- A list of ranges for all reads (not just those in this substructure) in the same order as ReadStructure.descriptors
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Method Details
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get
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isEmpty
public boolean isEmpty() -
length
public int length() -
getTotalCycles
public int getTotalCycles() -
getIndices
public int[] getIndices() -
getDescriptorLengths
public int[] getDescriptorLengths() -
getCycleIndexRanges
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iterator
- Specified by:
iterator
in interfaceIterable<ReadDescriptor>
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getCycles
public int[] getCycles() -
toReadStructure
Create a ReadStructure from this substructure composed of only the descriptors contained in this substructure, Any ReadDescriptors not in this substructure are treated as if they don't exist (e.g. if you have a readStructure (36T8S8B36T) and this substructure consists of all the non-skipped reads than toReadStructure would return (36T8B36T) in ReadStructure form
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