Class TestCasesFileIndexChrPos
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestCasesBase
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- org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
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public class TestCasesFileIndexChrPos extends TestCasesBase
Test cases for file index (chr:pos index on files)- Author:
- pcingola
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Field Summary
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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
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Constructor Summary
Constructors Constructor Description TestCasesFileIndexChrPos()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_00_long_file()
Test getting random lines from a filevoid
test_00_short_file()
Test getting random lines from a filevoid
test_01()
Test : Find beginning of a chromosomevoid
test_02()
Test : Find a linevoid
test_03()
Test : Find a chr:posvoid
test_04()
Test : Find a chr:posvoid
test_05()
Test : Find a chr:pos that does not existsvoid
test_06()
Test : Find a chr:pos that does not existsvoid
test_07()
Test : Find a chr:pos that does not existsvoid
test_10()
void
test_11()
Test : Find a chr:pos that does not existsvoid
test_20()
Test : Find a chr:pos that does not existsvoid
test_21()
Test : Find a chr:pos that does not existsvoid
test_22()
Test : Find a chr:pos that does not existsvoid
test_23()
Test : Dump small portions of a filevoid
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
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Method Detail
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test_00_long_file
@Test public void test_00_long_file()
Test getting random lines from a file
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test_00_short_file
@Test public void test_00_short_file()
Test getting random lines from a file
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test_01
@Test public void test_01() throws java.io.IOException
Test : Find beginning of a chromosome- Throws:
java.io.IOException
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test_02
@Test public void test_02() throws java.io.IOException
Test : Find a line- Throws:
java.io.IOException
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test_03
@Test public void test_03() throws java.io.IOException
Test : Find a chr:pos- Throws:
java.io.IOException
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test_04
@Test public void test_04() throws java.io.IOException
Test : Find a chr:pos- Throws:
java.io.IOException
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test_05
@Test public void test_05() throws java.io.IOException
Test : Find a chr:pos that does not exists- Throws:
java.io.IOException
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test_06
@Test public void test_06()
Test : Find a chr:pos that does not exists
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test_07
@Test public void test_07()
Test : Find a chr:pos that does not exists
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test_10
@Test public void test_10()
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test_11
@Test public void test_11()
Test : Find a chr:pos that does not exists
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test_20
@Test public void test_20()
Test : Find a chr:pos that does not exists
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test_21
@Test public void test_21()
Test : Find a chr:pos that does not exists
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test_22
@Test public void test_22()
Test : Find a chr:pos that does not exists
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test_23
@Test public void test_23()
Test : Dump small portions of a file
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test_24
@Test public void test_24()
Test : Dump large portions of a file
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