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, 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
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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, prependSequenceToFirstExon, showTranscripts
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Method Detail
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init
protected void init()
- Overrides:
init
in classTestCasesBase
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test_01
public void test_01()
Shift by one position
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test_02
public void test_02()
No shift
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test_03
public void test_03()
Shift by one position
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test_04_Intron
public void test_04_Intron()
Shift by one position in an intron
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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)
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test_05_savant_opposite
public void test_05_savant_opposite()
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test_06_savant
public void test_06_savant()
Same as test Savant's test case, but using variant and GenomicSequences
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test_07_savant
public void test_07_savant()
Another test case fmor Savant's poster
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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.
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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.
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