Package net.sf.samtools.tabix

Class TabixReader

java.lang.Object

net.sf.samtools.tabix.TabixReader

All Implemented Interfaces:

java.lang.Iterable<java.lang.String>

public class TabixReader
extends java.lang.Object
implements java.lang.Iterable<java.lang.String>

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	showHeader

Constructor Summary

Constructors

Constructor	Description
TabixReader(java.lang.String fileName)
TabixReader(java.lang.String fileName, boolean debug)

Method Summary

Modifier and Type	Method	Description
protected int	chr2tid(java.lang.String chr)
void	close()
long	getFilePointer()
int	getmBc()
int	getmEc()
int	getmMeta()
int	getmPreset()
int	getmSc()
TabixIterator	iterator()
static void	main(java.lang.String[] args)
int[]	parseReg(java.lang.String reg)	Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"
TabixIterator	query(java.lang.String reg)	Return an iterator for the interval in this query Format: "chr:star-end"
TabixIterator	query(Variant variant)
void	readIndex()	Read the Tabix index from the default file.
void	readIndex(java.io.File fp)	Read the Tabix index from a file
static int	readInt(java.io.InputStream is)
java.lang.String	readLine()	Read one line from the data file.
static long	readLong(java.io.InputStream is)
void	setDebug(boolean debug)
void	setShowHeader(boolean showHeader)
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

showHeader

protected boolean showHeader

Constructor Detail

TabixReader

public TabixReader(java.lang.String fileName)
            throws java.io.IOException

Throws:

java.io.IOException

TabixReader

public TabixReader(java.lang.String fileName,
                   boolean debug)
            throws java.io.IOException

Throws:

java.io.IOException

Method Detail

main

public static void main(java.lang.String[] args)

readInt

public static int readInt(java.io.InputStream is)
                   throws java.io.IOException

Throws:

java.io.IOException

readLong

public static long readLong(java.io.InputStream is)
                     throws java.io.IOException

Throws:

java.io.IOException

chr2tid

protected int chr2tid(java.lang.String chr)

close

public void close()

getFilePointer

public long getFilePointer()

getmBc

public int getmBc()

getmEc

public int getmEc()

getmMeta

public int getmMeta()

getmPreset

public int getmPreset()

getmSc

public int getmSc()

iterator

public TabixIterator iterator()

Specified by:

iterator in interface java.lang.Iterable<java.lang.String>

parseReg

public int[] parseReg(java.lang.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, region_end] On failure, sequence_id==-1.

query

public TabixIterator query(java.lang.String reg)

Return an iterator for the interval in this query Format: "chr:star-end"

query

public TabixIterator query(Variant variant)

readIndex

public void readIndex()
               throws java.io.IOException

Read the Tabix index from the default file.

Throws:

java.io.IOException

readIndex

public void readIndex(java.io.File fp)
               throws java.io.IOException

Read the Tabix index from a file

Parameters:

fp - File pointer

Throws:

java.io.IOException

readLine

public java.lang.String readLine()
                          throws java.io.IOException

Read one line from the data file.

Throws:

java.io.IOException

setDebug

public void setDebug(boolean debug)

setShowHeader

public void setShowHeader(boolean showHeader)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object