Package 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 Object implements IndexCreator
This is a copy ofTabixIndexCreator
, 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 Description AllRefsTabixIndexCreator(SAMSequenceDictionary sequenceDictionary, TabixFormat formatSpec)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addFeature(Feature feature, long filePosition)
Add a feature to the indexIndex
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 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
-
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 interfaceIndexCreator
- Parameters:
finalFilePosition
- the final file position, for indexes that have to close out with the final position- Returns:
- an index object
-
-