Package htsjdk.tribble.index.tabix
Class TabixIndexCreator
java.lang.Object
htsjdk.tribble.index.tabix.TabixIndexCreator
- All Implemented Interfaces:
IndexCreator
IndexCreator for Tabix.
Features are expected to be 1-based, inclusive.
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Constructor Summary
ConstructorsConstructorDescriptionTabixIndexCreator
(SAMSequenceDictionary sequenceDictionary, TabixFormat formatSpec) TabixIndexCreator
(TabixFormat formatSpec) -
Method Summary
Modifier and TypeMethodDescriptionvoid
addFeature
(Feature feature, long filePosition) Add a feature to the indexfinalizeIndex
(long finalFilePosition) Create the index, given the stream of features passed in to this pointMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface htsjdk.tribble.index.IndexCreator
setIndexSequenceDictionary
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Constructor Details
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TabixIndexCreator
- Parameters:
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.
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TabixIndexCreator
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Method Details
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addFeature
Description copied from interface:IndexCreator
Add a feature to the index- Specified by:
addFeature
in interfaceIndexCreator
- 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
Description copied from interface:IndexCreator
Create the index, given the stream of features passed in to this point- Specified by:
finalizeIndex
in interfaceIndexCreator
- 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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