htsjdk.tribble.index

Interface IndexCreator

All Known Implementing Classes:

DynamicIndexCreator, IntervalIndexCreator, LinearIndexCreator, TabixIndexCreator, TribbleIndexCreator

public interface IndexCreator

An interface for creating indexes

Method Summary

Modifier and Type	Method and Description
void	addFeature(Feature feature, long filePosition) Add a feature to the index
Index	finalizeIndex(long finalFilePosition) Create the index, given the stream of features passed in to this point
default void	setIndexSequenceDictionary(SAMSequenceDictionary dict) Set the sequence dictionary for the index.

Method Detail

addFeature

void addFeature(Feature feature,
                long filePosition)

Add a feature to the index

Parameters:

feature - the feature, of which start, end, and contig must be filled in

filePosition - the current file position, at the beginning of the specified feature

finalizeIndex

Index finalizeIndex(long finalFilePosition)

Create the index, given the stream of features passed in to this point

Parameters:

finalFilePosition - the final file position, for indexes that have to close out with the final position

Returns:

an index object

setIndexSequenceDictionary

default void setIndexSequenceDictionary(SAMSequenceDictionary dict)

Set the sequence dictionary for the index. Default implementation does nothing.

Parameters:

dict - the dictionary to add to the index.