Package htsjdk.tribble.index.linear
Class LinearIndexCreator
- java.lang.Object
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- htsjdk.tribble.index.TribbleIndexCreator
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- htsjdk.tribble.index.linear.LinearIndexCreator
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- All Implemented Interfaces:
IndexCreator
public class LinearIndexCreator extends TribbleIndexCreator
For creating a LinearIndex from a stream of features.
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Field Summary
Fields Modifier and Type Field Description static int
DEFAULT_BIN_WIDTH
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Fields inherited from class htsjdk.tribble.index.TribbleIndexCreator
properties
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Constructor Summary
Constructors Constructor Description LinearIndexCreator(File inputFile)
LinearIndexCreator(File inputFile, int binSize)
LinearIndexCreator(Path inputPath)
LinearIndexCreator(Path inputPath, int binSize)
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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 indexint
defaultBinSize()
the current default bin sizeIndex
finalizeIndex(long finalFilePosition)
finalize the index; producing an index objectint
getBinSize()
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Methods inherited from class htsjdk.tribble.index.TribbleIndexCreator
addProperty, setIndexSequenceDictionary
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Method Detail
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addFeature
public void addFeature(Feature feature, long filePosition)
add a feature to the index- Parameters:
feature
- the feature, from which we use the contig, start, and stopfilePosition
- the position of the file at the BEGINNING of the current feature
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finalizeIndex
public Index finalizeIndex(long finalFilePosition)
finalize the index; producing an index object- Parameters:
finalFilePosition
- the final file position, for indexes that have to close out with the final position- Returns:
- an Index object
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defaultBinSize
public int defaultBinSize()
the current default bin size- Returns:
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getBinSize
public int getBinSize()
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