TabixUtils (htsjdk 4.3.0 API)

java.lang.Object

htsjdk.tribble.util.TabixUtils

public class TabixUtils extends Object

classes that have anything to do with tabix

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

static class

TabixUtils.TIndex

static class

TabixUtils.TIntv

static class

TabixUtils.TPair64
Field Summary

Fields

Modifier and Type

Field

Description

static final String

STANDARD_INDEX_EXTENSION

Deprecated.
Use since June 2019 FileExtensions.TABIX_INDEX instead.
Constructor Summary

Constructors

Constructor

Description

TabixUtils()
Method Summary

Modifier and Type

Method

Description

static SAMSequenceDictionary

getSequenceDictionary(File tabixIndex)

Generates the SAMSequenceDictionary from the given tabix index file

static boolean

less64(long u, long v)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- STANDARD_INDEX_EXTENSION
  
  @Deprecated public static final String STANDARD_INDEX_EXTENSION
  
  Deprecated.
  Use since June 2019 FileExtensions.TABIX_INDEX instead.
  See Also:
  
  Constant Field Values
Constructor Details
- TabixUtils
  
  public TabixUtils()
Method Details
- less64
  
  public static boolean less64(long u, long v)
- getSequenceDictionary
  
  public static SAMSequenceDictionary getSequenceDictionary(File tabixIndex)
  
  Generates the SAMSequenceDictionary from the given tabix index file
  
  Parameters:
  
  tabixIndex - the tabix index file
  
  Returns:
  
  non-null sequence dictionary