TestCasesVariantRealignment (Snp Effect 4.3t API)

java.lang.Object
- org.snpeff.snpEffect.testCases.unity.TestCasesBase
- - org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment

public class TestCasesVariantRealignment
extends TestCasesBase

Test cases for variant realignment

Field Summary
- Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
  addUtrs, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, transcript, verbose

Constructor Summary

Constructors
Constructor Description

TestCasesVariantRealignment()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`init()`
`void`	`test_01()`	Shift by one position
`void`	`test_02()`	No shift
`void`	`test_03()`	Shift by one position
`void`	`test_04_Intron()`	Shift by one position in an intron
`void`	`test_05_savant()`	Test case from Savant's poster http://www.well.ox.ac.uk/savant (Marton Munz, Elise Ruark, Nazneen Rahman, Gerton Lunter)
`void`	`test_05_savant_opposite()`
`void`	`test_06_savant()`	Same as test Savant's test case, but using variant and GenomicSequences
`void`	`test_07_savant()`	Another test case fmor Savant's poster
`void`	`test_08_reallyLongRealign()`	This test should trigger progressive realignment.
`void`	`test_09_reallyLongRealign()`	This test should trigger (AND fail) to make a progressive realignment.

Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, initRand, initSnpEffPredictor, initSnpEffPredictor, prependSequenceToFirstExon, showTranscripts

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - TestCasesVariantRealignment
```
public TestCasesVariantRealignment()
```
- Method Detail
  - init
```
protected void init()
```
    Overrides:
    
    init in class TestCasesBase
  - test_01
```
public void test_01()
```
    Shift by one position
  - test_02
```
public void test_02()
```
    No shift
  - test_03
```
public void test_03()
```
    Shift by one position
  - test_04_Intron
```
public void test_04_Intron()
```
    Shift by one position in an intron
  - test_05_savant
```
public void test_05_savant()
```
    Test case from Savant's poster http://www.well.ox.ac.uk/savant (Marton Munz, Elise Ruark, Nazneen Rahman, Gerton Lunter)
  - test_05_savant_opposite
```
public void test_05_savant_opposite()
```
  - test_06_savant
```
public void test_06_savant()
```
    Same as test Savant's test case, but using variant and GenomicSequences
  - test_07_savant
```
public void test_07_savant()
```
    Another test case fmor Savant's poster
  - test_08_reallyLongRealign
```
public void test_08_reallyLongRealign()
```
    This test should trigger progressive realignment. I.e. requiring more bases to the right in order to make a good alignment.
  - test_09_reallyLongRealign
```
public void test_09_reallyLongRealign()
```
    This test should trigger (AND fail) to make a progressive realignment. I.e. requiring more bases to the right in order to make a good alignment, but there are no more bases available from GenomicSequences.