public class TabixIndexCreator extends java.lang.Object implements IndexCreator
Constructor and Description |
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TabixIndexCreator(SAMSequenceDictionary sequenceDictionary,
TabixFormat formatSpec) |
TabixIndexCreator(TabixFormat formatSpec) |
Modifier and Type | Method and Description |
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void |
addFeature(Feature feature,
long filePosition)
Add a feature to the index
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Index |
finalizeIndex(long finalFilePosition)
Create the index, given the stream of features passed in to this point
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
setIndexSequenceDictionary
public TabixIndexCreator(SAMSequenceDictionary sequenceDictionary, TabixFormat formatSpec)
sequenceDictionary
- is not required, but if present all features added must refer to sequences in the
dictionary. It is used to optimize the memory needed to build the index.public TabixIndexCreator(TabixFormat formatSpec)
public void addFeature(Feature feature, long filePosition)
IndexCreator
addFeature
in interface IndexCreator
feature
- the feature, of which start, end, and contig must be filled infilePosition
- the current file position, at the beginning of the specified featurepublic Index finalizeIndex(long finalFilePosition)
IndexCreator
finalizeIndex
in interface IndexCreator
finalFilePosition
- the final file position, for indexes that have to close out with the final position