Package org.snpeff.snpEffect.testCases.unity

Class TestCasesFileIndexChrPos

java.lang.Object

org.snpeff.snpEffect.testCases.unity.TestCasesBase

org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos

public class TestCasesFileIndexChrPos
extends TestCasesBase

Test cases for file index (chr:pos index on files)

Author:

pcingola

Field Summary

Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase

addUtrs, BASE_DIR, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, prefixes, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, testType, transcript, verbose

Constructor Summary

Constructors

Constructor	Description
TestCasesFileIndexChrPos()

Method Summary

Modifier and Type	Method	Description
void	test_00_long_file()	Test getting random lines from a file
void	test_00_short_file()	Test getting random lines from a file
void	test_01()	Test : Find beginning of a chromosome
void	test_02()	Test : Find a line
void	test_03()	Test : Find a chr:pos
void	test_04()	Test : Find a chr:pos
void	test_05()	Test : Find a chr:pos that does not exists
void	test_06()	Test : Find a chr:pos that does not exists
void	test_07()	Test : Find a chr:pos that does not exists
void	test_10()
void	test_11()	Test : Find a chr:pos that does not exists
void	test_20()	Test : Find a chr:pos that does not exists
void	test_21()	Test : Find a chr:pos that does not exists
void	test_22()	Test : Find a chr:pos that does not exists
void	test_23()	Test : Dump small portions of a file
void	test_24()	Test : Dump large portions of a file

Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase

after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, init, initRand, initSnpEffPredictor, initSnpEffPredictor, path, pathClassName, prependSequenceToFirstExon

Methods inherited from class java.lang.Object

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

Constructor Detail

TestCasesFileIndexChrPos

public TestCasesFileIndexChrPos()

Method Detail

test_00_long_file

@Test
public void test_00_long_file()

Test getting random lines from a file

test_00_short_file

@Test
public void test_00_short_file()

Test getting random lines from a file

test_01

@Test
public void test_01()
             throws java.io.IOException

Test : Find beginning of a chromosome

Throws:

java.io.IOException

test_02

@Test
public void test_02()
             throws java.io.IOException

Test : Find a line

Throws:

java.io.IOException

test_03

@Test
public void test_03()
             throws java.io.IOException

Test : Find a chr:pos

Throws:

java.io.IOException

test_04

@Test
public void test_04()
             throws java.io.IOException

Test : Find a chr:pos

Throws:

java.io.IOException

test_05

@Test
public void test_05()
             throws java.io.IOException

Test : Find a chr:pos that does not exists

Throws:

java.io.IOException

test_06

@Test
public void test_06()

Test : Find a chr:pos that does not exists

test_07

@Test
public void test_07()

Test : Find a chr:pos that does not exists

test_10

@Test
public void test_10()

test_11

@Test
public void test_11()

Test : Find a chr:pos that does not exists

test_20

@Test
public void test_20()

Test : Find a chr:pos that does not exists

test_21

@Test
public void test_21()

Test : Find a chr:pos that does not exists

test_22

@Test
public void test_22()

Test : Find a chr:pos that does not exists

test_23

@Test
public void test_23()

Test : Dump small portions of a file

test_24

@Test
public void test_24()

Test : Dump large portions of a file