TabixIndex (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.tribble.index.tabix.TabixIndex

All Implemented Interfaces:

Index
```
public class TabixIndex
extends Object
implements Index
```
This class represent a Tabix index that has been built in memory or read from a file. It can be queried or written to a file.

Field Summary

Fields
Modifier and Type Field Description

static int MAGIC_NUMBER

Fields
Modifier and Type	Field	Description
`static int`	`MAGIC_NUMBER`

Constructor Summary

Constructors
Constructor	Description
`TabixIndex(TabixFormat formatSpec, List<String> sequenceNames, BinningIndexContent[] indices)`
`TabixIndex(File tabixFile)`	Convenient ctor that opens the file, wraps with with BGZF reader, and closes after reading index.
`TabixIndex(InputStream inputStream)`
`TabixIndex(Path tabixPath)`	Convenient ctor that opens the path, wraps with with BGZF reader, and closes after reading index.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`containsChromosome(String chr)`
`boolean`	`equals(Object o)`
`boolean`	`equalsIgnoreProperties(Object o)`	Returns true if this and obj are 'effectively' equivalent indices.
`List<Block>`	`getBlocks(String chr, int start, int end)`	Query the index.
`TabixFormat`	`getFormatSpec()`
`Map<String,String>`	`getProperties()`	No arbitrary properties in Tabix
`List<String>`	`getSequenceNames()`
`int`	`hashCode()`
`boolean`	`isCurrentVersion()`
`void`	`write(LittleEndianOutputStream los)`	all indexes are writable to disk
`void`	`write(Path tabixPath)`	Writes the index with BGZF.
`void`	`writeBasedOnFeaturePath(Path featurePath)`	Writes to a path with appropriate name and directory based on feature path.

Methods inherited from interface htsjdk.tribble.index.Index
write, writeBasedOnFeatureFile

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

- Field Detail
  - MAGIC_NUMBER
```
public static final int MAGIC_NUMBER
```
- Constructor Detail
  - TabixIndex
```
public TabixIndex(TabixFormat formatSpec,
                  List<String> sequenceNames,
                  BinningIndexContent[] indices)
```
    Parameters:
    
    formatSpec - Information about how to interpret the file being indexed. Unused by this class other than written to an output file.
    
    sequenceNames - Sequences in the file being indexed, in the order they appear in the file.
    
    indices - One for each element of sequenceNames
  - TabixIndex
```
public TabixIndex(InputStream inputStream)
           throws IOException
```
    Parameters:
    
    inputStream - This is expected to be buffered and be gzip-decompressing as appropriate. Caller should close input stream after ctor returns.
    
    Throws:
    
    IOException
  - TabixIndex
```
public TabixIndex(File tabixFile)
           throws IOException
```
    Convenient ctor that opens the file, wraps with with BGZF reader, and closes after reading index.
    
    Throws:
    
    IOException
  - TabixIndex
```
public TabixIndex(Path tabixPath)
           throws IOException
```
    Convenient ctor that opens the path, wraps with with BGZF reader, and closes after reading index.
    
    Throws:
    
    IOException
- Method Detail
  - getBlocks
```
public List<Block> getBlocks(String chr,
                             int start,
                             int end)
```
    Description copied from interface: Index
    
    Query the index.
    
    Specified by:
    
    getBlocks in interface Index
    
    Parameters:
    
    chr - the chromosome
    
    start - the start position, one-based, inclusive.
    
    end - the end position, one-based, inclusive.
    
    Returns:
    
    List of regions of file that are candidates for the given query.
    TODO: This method has not yet been tested, since the primary task is index writing.
  - isCurrentVersion
```
public boolean isCurrentVersion()
```
    Specified by:
    
    isCurrentVersion in interface Index
    
    Returns:
    
    true if the index is up to date, false otherwise
  - getSequenceNames
```
public List<String> getSequenceNames()
```
    Specified by:
    
    getSequenceNames in interface Index
    
    Returns:
    
    a list of the sequence names we've seen during indexing, in order
  - containsChromosome
```
public boolean containsChromosome(String chr)
```
    Specified by:
    
    containsChromosome in interface Index
    
    Parameters:
    
    chr - the chromosome (or contig) name
    
    Returns:
    
    true if we have an entry; false otherwise
  - getProperties
```
public Map<String,String> getProperties()
```
    No arbitrary properties in Tabix
    
    Specified by:
    
    getProperties in interface Index
    
    Returns:
    
    get the list of properties for this index. Returns null if no properties.
  - equalsIgnoreProperties
```
public boolean equalsIgnoreProperties(Object o)
```
    Description copied from interface: Index
    
    Returns true if this and obj are 'effectively' equivalent indices. Ignores the time stamp on the file, as this may not be the same for even identical indices
    
    Specified by:
    
    equalsIgnoreProperties in interface Index
    
    Returns:
  - getFormatSpec
```
public TabixFormat getFormatSpec()
```
  - write
```
public void write(Path tabixPath)
           throws IOException
```
    Writes the index with BGZF.
    
    Specified by:
    
    write in interface Index
    
    Parameters:
    
    tabixPath - Where to write the index.
    
    Throws:
    
    IOException - if the index is unable to write to the specified path.
  - writeBasedOnFeaturePath
```
public void writeBasedOnFeaturePath(Path featurePath)
                             throws IOException
```
    Writes to a path with appropriate name and directory based on feature path.
    
    Specified by:
    
    writeBasedOnFeaturePath in interface Index
    
    Parameters:
    
    featurePath - Path being indexed.
    
    Throws:
    
    IOException - if featureFile is not a normal file.
  - write
```
public void write(LittleEndianOutputStream los)
           throws IOException
```
    Description copied from interface: Index
    
    all indexes are writable to disk
    
    Specified by:
    
    write in interface Index
    
    Parameters:
    
    los - It is assumes that caller has done appropriate buffering and BlockCompressedOutputStream wrapping. Caller should close output stream after invoking this method.
    
    Throws:
    
    IOException
  - equals
```
public boolean equals(Object o)
```
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object

Class TabixIndex

Field Summary

Constructor Summary

Method Summary

Methods inherited from interface htsjdk.tribble.index.Index

Methods inherited from class java.lang.Object

Field Detail

MAGIC_NUMBER

Constructor Detail

TabixIndex

TabixIndex

TabixIndex

TabixIndex

Method Detail

getBlocks

isCurrentVersion

getSequenceNames

containsChromosome

getProperties

equalsIgnoreProperties

getFormatSpec

write

writeBasedOnFeaturePath

write

equals

hashCode