Class TestCasesVariantRealignment
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestCasesBase
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- org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
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public class TestCasesVariantRealignment extends TestCasesBase
Test cases for variant realignment
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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 TestCasesVariantRealignment()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
init()
void
test_01()
Shift by one positionvoid
test_02()
No shiftvoid
test_03()
Shift by one positionvoid
test_04_Intron()
Shift by one position in an intronvoid
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 GenomicSequencesvoid
test_07_savant()
Another test case fmor Savant's postervoid
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, path, pathClassName, prependSequenceToFirstExon
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Method Detail
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init
protected void init()
- Overrides:
init
in classTestCasesBase
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test_01
@Test public void test_01()
Shift by one position
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test_02
@Test public void test_02()
No shift
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test_03
@Test public void test_03()
Shift by one position
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test_04_Intron
@Test public void test_04_Intron()
Shift by one position in an intron
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test_05_savant
@Test 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)
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test_05_savant_opposite
@Test public void test_05_savant_opposite()
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test_06_savant
@Test public void test_06_savant()
Same as test Savant's test case, but using variant and GenomicSequences
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test_07_savant
@Test public void test_07_savant()
Another test case fmor Savant's poster
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test_08_reallyLongRealign
@Test 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.
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test_09_reallyLongRealign
@Test 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.
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