Package htsjdk.tribble.index.interval
Class IntervalIndexCreator
- java.lang.Object
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- htsjdk.tribble.index.TribbleIndexCreator
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- htsjdk.tribble.index.interval.IntervalIndexCreator
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- All Implemented Interfaces:
IndexCreator
public class IntervalIndexCreator extends TribbleIndexCreator
Creates interval indexes from a stream of features
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Field Summary
Fields Modifier and Type Field Description static int
DEFAULT_FEATURE_COUNT
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Fields inherited from class htsjdk.tribble.index.TribbleIndexCreator
properties
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Constructor Summary
Constructors Constructor Description IntervalIndexCreator(File inputFile)
IntervalIndexCreator(File inputFile, int featuresPerInterval)
IntervalIndexCreator(Path inputPath)
IntervalIndexCreator(Path inputPath, int featuresPerInterval)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addFeature(Feature feature, long filePosition)
Add a feature to the indexIndex
finalizeIndex(long finalFilePosition)
finalize the index; create a tree index given the feature list passed in so farint
getFeaturesPerInterval()
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Methods inherited from class htsjdk.tribble.index.TribbleIndexCreator
addProperty, setIndexSequenceDictionary
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Constructor Detail
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IntervalIndexCreator
public IntervalIndexCreator(Path inputPath, int featuresPerInterval)
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IntervalIndexCreator
public IntervalIndexCreator(File inputFile, int featuresPerInterval)
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IntervalIndexCreator
public IntervalIndexCreator(File inputFile)
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IntervalIndexCreator
public IntervalIndexCreator(Path inputPath)
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Method Detail
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addFeature
public void addFeature(Feature feature, long filePosition)
Description copied from interface:IndexCreator
Add a feature to the index- Parameters:
feature
- the feature, of which start, end, and contig must be filled infilePosition
- the current file position, at the beginning of the specified feature
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finalizeIndex
public Index finalizeIndex(long finalFilePosition)
finalize the index; create a tree index given the feature list passed in so far- Parameters:
finalFilePosition
- the final file position, for indexes that have to close out with the final position- Returns:
- a Tree Index
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getFeaturesPerInterval
public int getFeaturesPerInterval()
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