TestCasesIntegrationEff (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
- - org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff

public class TestCasesIntegrationEff
extends TestCasesIntegrationBase

Test cases for other 'effect' issues

Author:: pcingola

Field Summary
- Fields inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
  BASE_DIR, debug, ignoreErrors, prefixes, shiftHgvs, SHOW_EVERY, testsDir, testType, verbose

Constructor Summary

Constructors
Constructor Description

TestCasesIntegrationEff()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`test_01()`	Test output order
`void`	`test_01_canonical()`	Test output order: Canonical first
`void`	`test_02()`	Test GATK option: At most one effect per VCF entry
`void`	`test_03_EmptyVcf()`	Make sure that empty VCF does not trigger an exception when creating the summary
`void`	`test_04()`	Test that CSV summary does not throw any error
`void`	`test_05()`	GATK mode should not have SPLICE_REGION (it is currently not supported)
`void`	`test_06()`	Test an MNP at the end of the transcript: We should be able to annotate without throwing any error
`void`	`test_07()`	Test an MNP at the end of the transcript: We should be able to annotate without throwing any error
`void`	`test_08_gatk_missing_annotations()`	Fixing bug: GATK does not annotate all VCF entries

Methods inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
applyTranscript, before, build, buildAndCompare, buildEmbl, buildGeneBank, buildGeneBank, buildGetBuildCmd, buildGff3AndCompare, buildGtfAndCompare, checkHgvs, checkNoChange, checkTranscriptError, compareHgvs, compareHgvs, compareVep, compareVepSO, init, loadSnpEffectPredictor, path, pathClassName, pathMigrate, showTranscripts, showTranscripts, snpEffect, snpEffect, snpEffectCancer

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

- Constructor Detail
  - TestCasesIntegrationEff
```
public TestCasesIntegrationEff()
```
- Method Detail
  - test_01
```
@Test
public void test_01()
```
    Test output order
  - test_01_canonical
```
@Test
public void test_01_canonical()
```
    Test output order: Canonical first
  - test_02
```
@Test
public void test_02()
```
    Test GATK option: At most one effect per VCF entry
  - test_03_EmptyVcf
```
@Test
public void test_03_EmptyVcf()
```
    Make sure that empty VCF does not trigger an exception when creating the summary
  - test_04
```
@Test
public void test_04()
```
    Test that CSV summary does not throw any error
  - test_05
```
@Test
public void test_05()
```
    GATK mode should not have SPLICE_REGION (it is currently not supported)
  - test_06
```
@Test
public void test_06()
```
    Test an MNP at the end of the transcript: We should be able to annotate without throwing any error
  - test_07
```
@Test
public void test_07()
```
    Test an MNP at the end of the transcript: We should be able to annotate without throwing any error
  - test_08_gatk_missing_annotations
```
@Test
public void test_08_gatk_missing_annotations()
```
    Fixing bug: GATK does not annotate all VCF entries