org.molgenis.data.annotation.core.resources.impl.tabix

Class TabixReader

java.lang.Object

org.molgenis.data.annotation.core.resources.impl.tabix.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
net.sf.samtools.util.BlockCompressedInputStream	blockCompressedInputStream
String	filename
HashMap<String,Integer>	mChr2tid

Constructor Summary

Constructors

Constructor and Description
TabixReader(String filename) The constructor

Method Summary

Modifier and Type	Method and Description
TabixReader.Iterator	query(int internalChromosomeID, int beginPosition, int endPosition)
TabixReader.Iterator	query(String queryString)
void	readIndex(File file) Read the Tabix index from a file
void	readIndex(String fileName) Read the Tabix index from the default 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

filename

public String filename

blockCompressedInputStream

public net.sf.samtools.util.BlockCompressedInputStream blockCompressedInputStream

mChr2tid

public HashMap<String,Integer> mChr2tid

Constructor Detail

TabixReader

public TabixReader(String filename)
            throws IOException

The constructor

Parameters:

filename - 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 file)
               throws IOException

Read the Tabix index from a file

Parameters:

file - File pointer

Throws:

IOException

readIndex

public void readIndex(String fileName)
               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

query

public TabixReader.Iterator query(int internalChromosomeID,
                                  int beginPosition,
                                  int endPosition)

query

public TabixReader.Iterator query(String queryString)