Class TestCasesVariantRealignment
java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
Test cases for variant realignment
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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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
init()
void
test_01()
Shift by one positionvoid
test_02()
No shiftvoid
test_03()
Shift by one positionvoid
Shift by one position in an intronvoid
Test case from Savant's poster http://www.well.ox.ac.uk/savant (Marton Munz, Elise Ruark, Nazneen Rahman, Gerton Lunter)void
void
Same as test Savant's test case, but using variant and GenomicSequencesvoid
Another test case fmor Savant's postervoid
This test should trigger progressive realignment.void
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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Constructor Details
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TestCasesVariantRealignment
public TestCasesVariantRealignment()
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Method Details
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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 -
test_02
@Test public void test_02()No shift -
test_03
@Test public void test_03()Shift by one position -
test_04_Intron
@Test public void test_04_Intron()Shift by one position in an intron -
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) -
test_05_savant_opposite
@Test public void test_05_savant_opposite() -
test_06_savant
@Test public void test_06_savant()Same as test Savant's test case, but using variant and GenomicSequences -
test_07_savant
@Test public void test_07_savant()Another test case fmor Savant's poster -
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. -
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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