Package org.snpeff.snpEffect.testCases.integration

Class TestCasesHgvsBase

java.lang.Object

org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase

Direct Known Subclasses:

TestCasesHgvsExon, TestCasesHgvsIntron

public class TestCasesHgvsBase
extends java.lang.Object

Test random SNP changes

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
protected char[]	chromoBases
protected java.lang.String	chromoSequence
protected Chromosome	chromosome
protected Config	config
protected boolean	debug
protected Gene	gene
protected Genome	genome
protected java.util.Random	rand
protected SnpEffectPredictor	snpEffectPredictor
protected Transcript	transcript
protected boolean	verbose

Constructor Summary

Constructors

Constructor	Description
TestCasesHgvsBase()

Method Summary

Modifier and Type	Method	Description
protected int	exonBase(char[] bases, int pos, int direction)	Count how many bases are there until the exon
protected void	init()
protected void	initRand()
protected void	initSnpEffPredictor(boolean addUtrs, boolean onlyPlusStrand)	Create a predictor
protected java.lang.String	intronHgsv(char[] bases, int j, int pos, java.lang.String refStr, java.lang.String altStr)	Intronic HGS notation
void	snpEffect(java.lang.String genomeVer, java.lang.String vcfFile)	Run SnpEff on VCF file

Methods inherited from class java.lang.Object

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

Field Detail

debug

protected boolean debug

verbose

protected boolean verbose

rand

protected java.util.Random rand

config

protected Config config

genome

protected Genome genome

chromosome

protected Chromosome chromosome

gene

protected Gene gene

transcript

protected Transcript transcript

snpEffectPredictor

protected SnpEffectPredictor snpEffectPredictor

chromoSequence

protected java.lang.String chromoSequence

chromoBases

protected char[] chromoBases

Constructor Detail

TestCasesHgvsBase

public TestCasesHgvsBase()

Method Detail

exonBase

protected int exonBase(char[] bases,
                       int pos,
                       int direction)

Count how many bases are there until the exon

init

protected void init()

initRand

protected void initRand()

initSnpEffPredictor

protected void initSnpEffPredictor(boolean addUtrs,
                                   boolean onlyPlusStrand)

Create a predictor

intronHgsv

protected java.lang.String intronHgsv(char[] bases,
                                      int j,
                                      int pos,
                                      java.lang.String refStr,
                                      java.lang.String altStr)

Intronic HGS notation

snpEffect

public void snpEffect(java.lang.String genomeVer,
                      java.lang.String vcfFile)

Run SnpEff on VCF file