net.sf.snver.pileup.core
Class CoreAnalysis

java.lang.Object
  net.sf.snver.pileup.core.CoreAnalysis

public class CoreAnalysis
extends java.lang.Object

Core analysis algorithm

Created by IntelliJ IDEA. User: weicheng hu Date: 10/29/11 Time: 10:42 PM

Field Summary

int

failed

Constructor Summary

CoreAnalysis()

Method Summary

void	analyze(SnverMeta meta, java.util.Properties properties, java.io.PrintWriter out, java.io.PrintWriter log) Evaluate SnverMeta for output
void	close() Close the file handler
static CoreAnalysis	getInstance() Get singleton instance
double	getpValue(SnverMeta meta, int n) Deprecated.
double	getpValue(SnverMeta meta, java.util.Properties properties) Calculate P value
static boolean	makeInstance(java.util.Properties properties) Make the singleton instance for CoreAnalysis
void	print(SnverMeta meta, java.util.Properties properties, java.io.PrintWriter out) Print meta information into vcf file
static void	printCountHeader(java.io.PrintWriter out) Print the count file Header for debug
static void	printHeader(java.io.PrintWriter out, java.lang.String name) Print the vcf header
void	printoutIndividual(java.lang.String chr, java.lang.String pos, java.lang.String ref, double pvalue, java.lang.String alt, int altCount, int depth, double fisher, double sp, int altfor, int altrev, int reffor, int refrev, double gt0, double gt1, double gt2, java.io.PrintWriter out) Print for individual vcf file
boolean	test(SnverMeta meta, java.util.Properties properties, java.io.PrintWriter errorLog) Check for SnverMeta is satisfied with conditions

Methods inherited from class java.lang.Object

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

Field Detail

failed

public int failed

Constructor Detail

CoreAnalysis

public CoreAnalysis()

Method Detail

printoutIndividual

public void printoutIndividual(java.lang.String chr,
                               java.lang.String pos,
                               java.lang.String ref,
                               double pvalue,
                               java.lang.String alt,
                               int altCount,
                               int depth,
                               double fisher,
                               double sp,
                               int altfor,
                               int altrev,
                               int reffor,
                               int refrev,
                               double gt0,
                               double gt1,
                               double gt2,
                               java.io.PrintWriter out)

Print for individual vcf file

Parameters:

chr - String

pos - int

ref - char

pvalue - double

alt - char

altCount - int

depth - int

fisher - double

sp - double

altfor - int

altrev - int

reffor - int

refrev - int

gt0 - double

gt1 - double

gt2 - double

out - PrintWriter

close

public void close()

Close the file handler

makeInstance

public static boolean makeInstance(java.util.Properties properties)

Make the singleton instance for CoreAnalysis

Parameters:

properties - Properties

Returns:

boolean

getInstance

public static CoreAnalysis getInstance()
                                throws java.io.FileNotFoundException

Get singleton instance

Returns:

CoreAnalysis

Throws:

java.io.FileNotFoundException

printHeader

public static void printHeader(java.io.PrintWriter out,
                               java.lang.String name)

Print the vcf header

Parameters:

out - PrintWriter

name - String

printCountHeader

public static void printCountHeader(java.io.PrintWriter out)

Print the count file Header for debug

Parameters:

out - PrintWriter

print

public void print(SnverMeta meta,
                  java.util.Properties properties,
                  java.io.PrintWriter out)

Print meta information into vcf file

Parameters:

meta - SnverMeta

out - PrintWriter

analyze

public void analyze(SnverMeta meta,
                    java.util.Properties properties,
                    java.io.PrintWriter out,
                    java.io.PrintWriter log)
             throws org.apache.commons.math.MathException

Evaluate SnverMeta for output

Parameters:

meta - SnverMeta

out - PrintWriter

Throws:

org.apache.commons.math.MathException - Error in Calculation

test

public boolean test(SnverMeta meta,
                    java.util.Properties properties,
                    java.io.PrintWriter errorLog)
             throws org.apache.commons.math.MathException

Check for SnverMeta is satisfied with conditions

Parameters:

meta - SnverMeta

Returns:

boolean

Throws:

org.apache.commons.math.MathException - Error in Calculation

getpValue

public double getpValue(SnverMeta meta,
                        java.util.Properties properties)

Calculate P value

Parameters:

meta - SnverMeta

Returns:

double

getpValue

@Deprecated
public double getpValue(SnverMeta meta,
                                   int n)

Deprecated.

Calculate P value with specific n

Parameters:

meta - SnverMeta

n - int

Returns:

double