org.molgenis.data.annotation

Class TabixReader

java.lang.Object

org.molgenis.data.annotation.TabixReader

public class TabixReader
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	TabixReader.Iterator

Field Summary

Fields

Modifier and Type	Field and Description
HashMap<String,Integer>	mChr2tid
String	mFn
net.sf.samtools.util.BlockCompressedInputStream	mFp

Constructor Summary

Constructors

Constructor and Description
TabixReader(String fn) The constructor

Method Summary

Modifier and Type	Method and Description
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)
TabixReader.Iterator	query(String reg)
void	readIndex() Read the Tabix index from the default file.
void	readIndex(File fp) Read the Tabix index from a file
static int	readInt(InputStream is)
String	readLine() Read one line from the data file.
static String	readLine(InputStream is)
static long	readLong(InputStream is)

Methods inherited from class java.lang.Object

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

Field Detail

mFn

public String mFn

mFp

public net.sf.samtools.util.BlockCompressedInputStream mFp

mChr2tid

public HashMap<String,Integer> mChr2tid

Constructor Detail

TabixReader

public TabixReader(String fn)
            throws IOException

The constructor

Parameters:

fn - File name of the data file

Throws:

IOException

Method Detail

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

readIndex

public void readIndex(File fp)
               throws IOException

Read the Tabix index from a file

Parameters:

fp - File pointer

Throws:

IOException

readIndex

public void readIndex()
               throws IOException

Read the Tabix index from the default file.

Throws:

IOException

readLine

public String readLine()
                throws IOException

Read one line from the data file.

Throws:

IOException

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)

query

public TabixReader.Iterator query(String reg)