edu.unc.csbio.util
Class VCFReader

java.lang.Object
  extended by edu.unc.csbio.util.VCFReader

public class VCFReader
extends java.lang.Object

A VCFReader Parser conforms to VCF 4.0 (http://www.1000genomes.org/node/101)

Version:
0.1
Author:
Shunping Huang , Jack Wang

Field Summary
private static java.lang.String altFS
           
private static int altOffset
           
private static java.io.BufferedReader br
           
private static int chrOffset
           
private static java.lang.String dataFile
           
private static java.lang.String FS
           
private static int posOffset
           
private static java.lang.String REF
           
private static int refOffset
           
private static int sampleColumn
           
private static java.lang.String sampleName
           
private static int sampleOffset
           
 
Constructor Summary
VCFReader(java.lang.String _dataFile, java.lang.String _sampleName)
          Initialize the buffer, skip the meta-information lines, and get the column id of the selected sample.
 
Method Summary
 void close()
          Close the buffer
 Feature readNext()
          Read the VCF file and return the next insertion/deletion object.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

dataFile

private static java.lang.String dataFile

sampleName

private static java.lang.String sampleName

sampleColumn

private static int sampleColumn

br

private static java.io.BufferedReader br

chrOffset

private static final int chrOffset
See Also:
Constant Field Values

posOffset

private static final int posOffset
See Also:
Constant Field Values

refOffset

private static final int refOffset
See Also:
Constant Field Values

altOffset

private static final int altOffset
See Also:
Constant Field Values

sampleOffset

private static final int sampleOffset
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Constant Field Values

FS

private static final java.lang.String FS
See Also:
Constant Field Values

altFS

private static final java.lang.String altFS
See Also:
Constant Field Values

REF

private static final java.lang.String REF
See Also:
Constant Field Values
Constructor Detail

VCFReader

public VCFReader(java.lang.String _dataFile,
                 java.lang.String _sampleName)
          throws java.io.IOException
Initialize the buffer, skip the meta-information lines, and get the column id of the selected sample.

Parameters:
_dataFile - the file name of the VCF file
_sampleName - the selected sample name of the VCF file
Throws:
java.io.IOException
Method Detail

readNext

public Feature readNext()
                 throws java.io.IOException
Read the VCF file and return the next insertion/deletion object.

Returns:
A Feature object that is either a insertion or a deletion.
Throws:
java.io.IOException

close

public void close()
           throws java.io.IOException
Close the buffer

Throws:
java.io.IOException