Class TestCasesVcf
java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
org.snpeff.snpEffect.testCases.unity.TestCasesVcf
VCF parsing test cases
- Author:
- pcingola
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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 TypeMethodDescriptionvoid
test_00()
Check that the size is correct (at least for SNPs)void
test_01()
Basic parsingvoid
Deletionsvoid
Problems parsingvoid
Problems creating variantsvoid
Extremely weird long lines in a VCF file (thousands of bases long)void
Test for "" in ALT fieldvoid
Empty ALT: Not a variantvoid
Empty Quality: Not a variantvoid
Empty fields should show '.' when printedvoid
void
Header should NOT have a trailing '\n'void
void
void
void
void
void
void
void
void
Parsing effect that created an exception (going from SO -> Classic)void
Parsing Genomic VCFs http://www.broadinstitute.org/gatk/guide/article?id=4017void
Add a new INFO and the respective headervoid
Add and replace an INFO headervoid
Add and replace an INFO headervoid
test_29()
Test old effect separator '+' instead of '&'void
Non-variant gVCF entries (i.e.void
void
void
void
void
void
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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Constructor Details
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TestCasesVcf
public TestCasesVcf()
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Method Details
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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 -
test_04_del
@Test public void test_04_del()Deletions -
test_05_choking_on_dot_slash_dot
@Test public void test_05_choking_on_dot_slash_dot()Problems parsing -
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) -
test_08_alt_del
@Test public void test_08_alt_del()Test for "" in ALT field -
test_09_empty_ALT
@Test public void test_09_empty_ALT()Empty ALT: Not a variant -
test_10_empty_QUAL
@Test public void test_10_empty_QUAL()Empty Quality: Not a variant -
test_11_empty
@Test public void test_11_empty()Empty fields should show '.' when printed -
test_12_readHeader
@Test public void test_12_readHeader() -
test_12_readHeader_NL
@Test public void test_12_readHeader_NL()Header should NOT have a trailing '\n' -
test_13_chrOri
@Test public void test_13_chrOri() -
test_14_VcfInfoKey
@Test public void test_14_VcfInfoKey() -
test_14_VcfInfoValue
@Test public void test_14_VcfInfoValue() -
test_15_Eff_format_version_guess
@Test public void test_15_Eff_format_version_guess() -
test_16_indels
@Test public void test_16_indels() -
test_18_vcf_tabix
@Test public void test_18_vcf_tabix() -
test_22_huge_headers
@Test public void test_22_huge_headers() -
test_23_VcfUnsorted
@Test public void test_23_VcfUnsorted() -
test_24_VcfEffect_parse_SO
@Test public void test_24_VcfEffect_parse_SO()Parsing effect that created an exception (going from SO -> Classic) -
test_25_Genomic_VCF
@Test public void test_25_Genomic_VCF()Parsing Genomic VCFs http://www.broadinstitute.org/gatk/guide/article?id=4017 -
test_26_vcfInfoHeaderAdd
@Test public void test_26_vcfInfoHeaderAdd()Add a new INFO and the respective header -
test_27_vcfInfoHeaderReplace
@Test public void test_27_vcfInfoHeaderReplace()Add and replace an INFO header -
test_28_vcfInfoReplace
@Test public void test_28_vcfInfoReplace()Add and replace an INFO header -
test_29
@Test public void test_29()Test old effect separator '+' instead of '&' -
test_30_gVCF_NON_REF
@Test public void test_30_gVCF_NON_REF()Non-variant gVCF entries (i.e. ALT=) -
test_31_MISSING_REF
@Test public void test_31_MISSING_REF() -
test_32_VcfInfoKeyNames
@Test public void test_32_VcfInfoKeyNames() -
test_33_translocations
@Test public void test_33_translocations() -
test_34_vcfInfoEncoding
@Test public void test_34_vcfInfoEncoding() -
test_35_translocations_parsing
@Test public void test_35_translocations_parsing() -
test_36_cleanupUnderscores
@Test public void test_36_cleanupUnderscores()
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