Package htsjdk.tribble.index.interval
Class IntervalIndexCreator
java.lang.Object
htsjdk.tribble.index.TribbleIndexCreator
htsjdk.tribble.index.interval.IntervalIndexCreator
- All Implemented Interfaces:
IndexCreator
Creates interval indexes from a stream of features
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Field Summary
Fields inherited from class htsjdk.tribble.index.TribbleIndexCreator
properties
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Constructor Summary
ConstructorDescriptionIntervalIndexCreator
(File inputFile) IntervalIndexCreator
(File inputFile, int featuresPerInterval) IntervalIndexCreator
(Path inputPath) IntervalIndexCreator
(Path inputPath, int featuresPerInterval) -
Method Summary
Modifier and TypeMethodDescriptionvoid
addFeature
(Feature feature, long filePosition) Add a feature to the indexfinalizeIndex
(long finalFilePosition) finalize the index; create a tree index given the feature list passed in so farint
Methods inherited from class htsjdk.tribble.index.TribbleIndexCreator
addProperty, setIndexSequenceDictionary
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Field Details
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DEFAULT_FEATURE_COUNT
public static final int DEFAULT_FEATURE_COUNT- See Also:
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Constructor Details
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IntervalIndexCreator
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IntervalIndexCreator
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IntervalIndexCreator
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IntervalIndexCreator
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Method Details
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addFeature
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
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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