htsjdk.tribble.index.tabix

Class AllRefsTabixIndexCreator

java.lang.Object

htsjdk.tribble.index.tabix.AllRefsTabixIndexCreator

All Implemented Interfaces:

IndexCreator

Direct Known Subclasses:

StreamBasedTabixIndexCreator

public class AllRefsTabixIndexCreator
extends java.lang.Object
implements IndexCreator

This is a copy of TabixIndexCreator, except sequence names are populated from the header, not from the ones that are seen. This change is needed to support index merging.

Constructor Summary

Constructors

Constructor and Description
AllRefsTabixIndexCreator(SAMSequenceDictionary sequenceDictionary, TabixFormat formatSpec)

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

Methods 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

Constructor Detail

AllRefsTabixIndexCreator

public AllRefsTabixIndexCreator(SAMSequenceDictionary sequenceDictionary,
                                TabixFormat formatSpec)

Method Detail

addFeature

public void addFeature(Feature feature,
                       long filePosition)

Description copied from interface: IndexCreator

Add a feature to the index

Specified by:

addFeature in interface IndexCreator

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

public Index finalizeIndex(long finalFilePosition)

Description copied from interface: IndexCreator

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

Specified by:

finalizeIndex in interface IndexCreator

Parameters:

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

Returns:

an index object