TabixReader (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.tribble.readers.TabixReader

```
public class TabixReader
extends Object
```

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static interface`	`TabixReader.Iterator`
`protected static class`	`TabixReader.TIndex`
`protected static class`	`TabixReader.TPair64`

Field Summary

Fields
Modifier and Type Field and Description

protected TabixReader.TIndex[] mIndex

Fields
Modifier and Type	Field and Description
`protected TabixReader.TIndex[]`	`mIndex`

Constructor Summary

Constructors
Constructor and Description
`TabixReader(String fn)`
`TabixReader(String fn, SeekableStream stream)`
`TabixReader(String fn, String idxFn)`
`TabixReader(String fn, String idxFn, SeekableStream stream)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`chr2tid(String chr)` return chromosome ID or -1 if it is unknown
`void`	`close()`
`Set<String>`	`getChromosomes()` return the chromosomes in that tabix file
`String`	`getSource()` return the source (filename/URL) of that reader
`static void`	`main(String[] args)`
`int[]`	`parseReg(String reg)` Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"
`TabixReader.Iterator`	`query(int tid, int beg, int end)` Return
`TabixReader.Iterator`	`query(String reg)`
`TabixReader.Iterator`	`query(String reg, int start, int end)`
`static int`	`readInt(InputStream is)`
`String`	`readLine()` Read one line from the data file.
`static String`	`readLine(InputStream is)`
`static long`	`readLong(InputStream is)`
`String`	`toString()`

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

- Field Detail
  - mIndex
```
protected TabixReader.TIndex[] mIndex
```
- Constructor Detail
  - TabixReader
```
public TabixReader(String fn)
            throws IOException
```
    Parameters:
    
    fn - File name of the data file
    
    Throws:
    
    IOException
  - TabixReader
```
public TabixReader(String fn,
                   String idxFn)
            throws IOException
```
    Parameters:
    
    fn - File name of the data file
    
    idxFn - Full path to the index file. Auto-generated if null
    
    Throws:
    
    IOException
  - TabixReader
```
public TabixReader(String fn,
                   SeekableStream stream)
            throws IOException
```
    Parameters:
    
    fn - File name of the data file (used for error messages only)
    
    stream - Seekable stream from which the data is read
    
    Throws:
    
    IOException
  - TabixReader
```
public TabixReader(String fn,
                   String idxFn,
                   SeekableStream stream)
            throws IOException
```
    Parameters:
    
    fn - File name of the data file (used for error messages only)
    
    idxFn - Full path to the index file. Auto-generated if null
    
    stream - Seekable stream from which the data is read
    
    Throws:
    
    IOException
- Method Detail
  - getSource
```
public String getSource()
```
    return the source (filename/URL) of that reader
  - readInt
```
public static int readInt(InputStream is)
                   throws IOException
```
    Throws:
    
    IOException
  - readLong
```
public static long readLong(InputStream is)
                     throws IOException
```
    Throws:
    
    IOException
  - readLine
```
public static String readLine(InputStream is)
                       throws IOException
```
    Throws:
    
    IOException
  - readLine
```
public String readLine()
                throws IOException
```
    Read one line from the data file.
    
    Throws:
    
    IOException
  - chr2tid
```
public int chr2tid(String chr)
```
    return chromosome ID or -1 if it is unknown
  - getChromosomes
```
public Set<String> getChromosomes()
```
    return the chromosomes in that tabix file
  - parseReg
```
public int[] parseReg(String reg)
```
    Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"
    
    Parameters:
    
    reg - Region string
    
    Returns:
    
    An array where the three elements are sequence_id, region_begin and region_end. On failure, sequence_id==-1.
  - query
```
public TabixReader.Iterator query(int tid,
                                  int beg,
                                  int end)
```
    Return
    
    Parameters:
    
    tid - Sequence id
    
    beg - beginning of interval, genomic coords
    
    end - end of interval, genomic coords
    
    Returns:
    
    an iterator over the lines within the specified interval
  - query
```
public TabixReader.Iterator query(String reg)
```
    Parameters:
    
    reg - A region string of the form acceptable by parseReg(String)
    
    Returns:
    
    See Also:
    
    parseReg(String)
  - query
```
public TabixReader.Iterator query(String reg,
                                  int start,
                                  int end)
```
    Parameters:
    
    reg - a chromosome
    
    start - start interval
    
    end - end interval
    
    Returns:
    
    a tabix iterator
    
    See Also:
    
    parseReg(String)
  - main
```
public static void main(String[] args)
```
  - close
```
public void close()
```
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class TabixReader

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

mIndex

Constructor Detail

TabixReader

TabixReader

TabixReader

TabixReader

Method Detail

getSource

readInt

readLong

readLine

readLine

chr2tid

getChromosomes

parseReg

query

query

query

main

close

toString