Package org.snpeff.snpEffect.testCases.integration

Class CompareToVep

java.lang.Object

org.snpeff.snpEffect.testCases.integration.CompareToVep

public class CompareToVep
extends java.lang.Object

Compare our results to ENSEML's Variant Effect predictor's output

Author:

pcingola

Constructor Summary

Constructors

Constructor	Description
CompareToVep(java.lang.String genomeName, boolean verbose)
CompareToVep(java.lang.String genomeName, java.lang.String[] addArgs, boolean verbose)

Method Summary

Modifier and Type	Method	Description
boolean	checkComapred()
void	compareVep(java.lang.String vcf)	Compare all VCF entries
void	setCompareHgvs()
void	setCompareHgvsDna(boolean compareHgvsDna)
void	setCompareHgvsProt(boolean compareHgvsProt)
void	setOnlyProtein(boolean onlyProtein)
void	setShiftHgvs(boolean shiftHgvs)
void	setStrict(boolean strict)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

CompareToVep

public CompareToVep(java.lang.String genomeName,
                    boolean verbose)

CompareToVep

public CompareToVep(java.lang.String genomeName,
                    java.lang.String[] addArgs,
                    boolean verbose)

Method Detail

checkComapred

public boolean checkComapred()

compareVep

public void compareVep(java.lang.String vcf)

Compare all VCF entries

setCompareHgvs

public void setCompareHgvs()

setCompareHgvsDna

public void setCompareHgvsDna(boolean compareHgvsDna)

setCompareHgvsProt

public void setCompareHgvsProt(boolean compareHgvsProt)

setOnlyProtein

public void setOnlyProtein(boolean onlyProtein)

setShiftHgvs

public void setShiftHgvs(boolean shiftHgvs)

setStrict

public void setStrict(boolean strict)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object