ChrIndex (htsjdk 5.0.0 API)

All Known Implementing Classes:: IntervalTreeIndex.ChrIndex, LinearIndex.ChrIndex

public interface ChrIndex

Represents an index on a specific chromosome

Method Summary

Modifier and Type

Method

Description

List<Block>

getBlocks()

List<Block>

getBlocks(int start, int end)

String

getName()

void

read(LittleEndianInputStream dis)

void

write(LittleEndianOutputStream dos)

Method Details
- getName
  
  String getName()
- getBlocks
  
  List<Block> getBlocks()
  
  Returns:
  
  all blocks in ChrIndex
- getBlocks
  
  List<Block> getBlocks(int start, int end)
  
  Parameters:
  
  start - the start position, one based
  
  end - the end position, one based
  
  Returns:
  
  a list of blocks that include the region defined from start to stop. Can never return null
- write
  
  void write(LittleEndianOutputStream dos) throws IOException
  
  Throws:
  
  IOException
- read
  
  void read(LittleEndianInputStream dis) throws IOException
  
  Throws:
  
  IOException