Class TestCasesVcf
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestCasesBase
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- org.snpeff.snpEffect.testCases.unity.TestCasesVcf
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public class TestCasesVcf extends TestCasesBase
VCF parsing test cases- 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 TestCasesVcf()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_00()
Check that the size is correct (at least for SNPs)void
test_01()
Basic parsingvoid
test_04_del()
Deletionsvoid
test_05_choking_on_dot_slash_dot()
Problems parsingvoid
test_06_mixed_change()
Problems creating variantsvoid
test_07_long_lines()
Extremely weird long lines in a VCF file (thousands of bases long)void
test_08_alt_del()
Test for "" in ALT fieldvoid
test_09_empty_ALT()
Empty ALT: Not a variantvoid
test_10_empty_QUAL()
Empty Quality: Not a variantvoid
test_11_empty()
Empty fields should show '.' when printedvoid
test_12_readHeader()
void
test_12_readHeader_NL()
Header should NOT have a trailing '\n'void
test_13_chrOri()
void
test_14_VcfInfoKey()
void
test_14_VcfInfoValue()
void
test_15_Eff_format_version_guess()
void
test_16_indels()
void
test_18_vcf_tabix()
void
test_22_huge_headers()
void
test_23_VcfUnsorted()
void
test_24_VcfEffect_parse_SO()
Parsing effect that created an exception (going from SO -> Classic)void
test_25_Genomic_VCF()
Parsing Genomic VCFs http://www.broadinstitute.org/gatk/guide/article?id=4017void
test_26_vcfInfoHeaderAdd()
Add a new INFO and the respective headervoid
test_27_vcfInfoHeaderReplace()
Add and replace an INFO headervoid
test_28_vcfInfoReplace()
Add and replace an INFO headervoid
test_29()
Test old effect separator '+' instead of '&'void
test_30_gVCF_NON_REF()
Non-variant gVCF entries (i.e.void
test_31_MISSING_REF()
void
test_32_VcfInfoKeyNames()
void
test_33_translocations()
void
test_34_vcfInfoEncoding()
void
test_35_translocations_parsing()
void
test_36_cleanupUnderscores()
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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
@Test public void test_00()
Check that the size is correct (at least for SNPs)Louis Letourneau discovered this horrendous bug. This is my first attempt to fix it....
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test_01
@Test public void test_01()
Basic parsing
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test_04_del
@Test public void test_04_del()
Deletions
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test_05_choking_on_dot_slash_dot
@Test public void test_05_choking_on_dot_slash_dot()
Problems parsing
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test_06_mixed_change
@Test public void test_06_mixed_change()
Problems creating variantsThe problem is when creating a variant from this line: Chr1 223919 . CTCGACCACTGGAA CTCACATCCATACAT,CATGACCACTGGAA
There are two changes: CTCGACCACTGGAA CTCACATCCATACAT => GACCACTGGAA / ACATCCATACAT (Mixed change?)
CTCGACCACTGGAA CATGACCACTGGAA ^^ => CG / TG (MNP)
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test_07_long_lines
@Test public void test_07_long_lines()
Extremely weird long lines in a VCF file (thousands of bases long)
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test_08_alt_del
@Test public void test_08_alt_del()
Test for "" in ALT field
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test_09_empty_ALT
@Test public void test_09_empty_ALT()
Empty ALT: Not a variant
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test_10_empty_QUAL
@Test public void test_10_empty_QUAL()
Empty Quality: Not a variant
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test_11_empty
@Test public void test_11_empty()
Empty fields should show '.' when printed
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test_12_readHeader
@Test public void test_12_readHeader()
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test_12_readHeader_NL
@Test public void test_12_readHeader_NL()
Header should NOT have a trailing '\n'
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test_13_chrOri
@Test public void test_13_chrOri()
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test_14_VcfInfoKey
@Test public void test_14_VcfInfoKey()
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test_14_VcfInfoValue
@Test public void test_14_VcfInfoValue()
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test_15_Eff_format_version_guess
@Test public void test_15_Eff_format_version_guess()
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test_16_indels
@Test public void test_16_indels()
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test_18_vcf_tabix
@Test public void test_18_vcf_tabix()
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test_22_huge_headers
@Test public void test_22_huge_headers()
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test_23_VcfUnsorted
@Test public void test_23_VcfUnsorted()
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test_24_VcfEffect_parse_SO
@Test public void test_24_VcfEffect_parse_SO()
Parsing effect that created an exception (going from SO -> Classic)
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test_25_Genomic_VCF
@Test public void test_25_Genomic_VCF()
Parsing Genomic VCFs http://www.broadinstitute.org/gatk/guide/article?id=4017
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test_26_vcfInfoHeaderAdd
@Test public void test_26_vcfInfoHeaderAdd()
Add a new INFO and the respective header
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test_27_vcfInfoHeaderReplace
@Test public void test_27_vcfInfoHeaderReplace()
Add and replace an INFO header
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test_28_vcfInfoReplace
@Test public void test_28_vcfInfoReplace()
Add and replace an INFO header
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test_29
@Test public void test_29()
Test old effect separator '+' instead of '&'
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test_30_gVCF_NON_REF
@Test public void test_30_gVCF_NON_REF()
Non-variant gVCF entries (i.e. ALT=)
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test_31_MISSING_REF
@Test public void test_31_MISSING_REF()
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test_32_VcfInfoKeyNames
@Test public void test_32_VcfInfoKeyNames()
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test_33_translocations
@Test public void test_33_translocations()
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test_34_vcfInfoEncoding
@Test public void test_34_vcfInfoEncoding()
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test_35_translocations_parsing
@Test public void test_35_translocations_parsing()
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test_36_cleanupUnderscores
@Test public void test_36_cleanupUnderscores()
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