Package org.snpsift.testCases.unit
Class TestCasesAnnotate
- java.lang.Object
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- org.snpsift.testCases.unit.TestCasesAnnotate
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- Direct Known Subclasses:
TestCasesAnnotateCreateIndex
,TestCasesAnnotateMem
,TestCasesAnnotateTabix
,TestCasesAnnotateUseIndex
public class TestCasesAnnotate extends java.lang.Object
Annotate test case- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
protected java.lang.String[]
defaultExtraArgs
protected boolean
deleteIndexFile
static boolean
verbose
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Constructor Summary
Constructors Constructor Description TestCasesAnnotate()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.List<org.snpeff.vcf.VcfEntry>
annotate(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
Annotatejava.lang.String
annotateOut(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
Annotate and return STDOUT as a stringvoid
annotateTest(java.lang.String dbFileName, java.lang.String fileName)
void
annotateTest(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
Annotate a file and check that the new annotation matches the expected oneprotected java.lang.String[]
argsList(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
void
test_01()
void
test_02()
void
test_03()
void
test_04()
void
test_05()
Chromosomes in VCF file are called 'chr22' instead of '22'.void
test_06()
Annotate info fieldsvoid
test_07()
Annotate only some info fieldsvoid
test_08()
Do not annotate ID columnvoid
test_09()
Annotate only some info fieldsvoid
test_11()
Annotate only some info fieldsvoid
test_12()
Annotate without REF/ALT fieldsvoid
test_13()
Annotate using "reserved" VCF fields (e.g.void
test_14()
void
test_15()
void
test_16()
void
test_17()
void
test_18()
void
test_19()
void
test_20()
Annotate info fieldsvoid
test_21()
Annotate two consecutive variants in the same positionvoid
test_22()
Annotate first base in a chromosomevoid
test_23_allele_specific_annotation_missing_R()
Database has one entry and VCF has multiple ALTsvoid
test_24()
Annotate using "-name" to prepend a name to VCF fields (e.g.void
test_25()
Annotate using "-name" to prepend a name to VCF fields (e.g.void
test_26_repeat_db_entry()
Annotate ID using entries that are duplicated in db.vcfvoid
test_27_repeat_db_entry()
Annotate INFO fields using entries that are duplicated in db.vcfvoid
test_28_exists()
Annotate if a VCF entry exists in the database filevoid
test_29_repeated_IDs()
Annotate if a VCF entry's ID might have multiple repeated entriesvoid
test_31_annotate_minimal_representation_db()
Issue when database has REF several variants which have to be converted into minimal representationvoid
test_32_annotate_minimal_representation_input()
Issue when query has REF several variants which have to be converted into minimal representationvoid
test_33_empty_db()
Empty databasevoid
test_34_dbStartsOnDifferentChromo()
Database has one entry and VCF has multiple ALTsvoid
test_35()
Annotate flags without '=true'void
test_36()
Annotate multi-allelicvoid
test_38()
Input VCf triggers a seek to a position after chromosome sections ends in database.void
test_39()
Annotate issues with discovered info fields (when annotating ALL info fields)void
test_40()
Problems when tabix database file has 'chr' in chromosome names and VCF file does notvoid
test_41()
void
test_42()
Test multiple CAF annotationsvoid
test_43()
Annotate emptyvoid
test_44()
Annotate GnomAd with multiple entriesvoid
test_45()
Annotate GnomAd with multiple entries
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Method Detail
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annotate
public java.util.List<org.snpeff.vcf.VcfEntry> annotate(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
Annotate
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annotateOut
public java.lang.String annotateOut(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
Annotate and return STDOUT as a string
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annotateTest
public void annotateTest(java.lang.String dbFileName, java.lang.String fileName)
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annotateTest
public void annotateTest(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
Annotate a file and check that the new annotation matches the expected one
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argsList
protected java.lang.String[] argsList(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
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test_01
public void test_01()
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test_02
public void test_02()
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test_03
public void test_03()
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test_04
public void test_04()
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test_05
public void test_05()
Chromosomes in VCF file are called 'chr22' instead of '22'. This should work OK as well.
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test_06
public void test_06()
Annotate info fields
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test_07
public void test_07()
Annotate only some info fields
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test_08
public void test_08()
Do not annotate ID column
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test_09
public void test_09()
Annotate only some info fields
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test_11
public void test_11()
Annotate only some info fields- Throws:
java.io.IOException
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test_12
public void test_12()
Annotate without REF/ALT fields
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test_13
public void test_13()
Annotate using "reserved" VCF fields (e.g. "AA" ) Header should be added if it doesn't exits.- Throws:
java.io.IOException
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test_14
public void test_14()
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test_15
public void test_15()
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test_16
public void test_16()
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test_17
public void test_17()
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test_18
public void test_18()
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test_19
public void test_19()
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test_20
public void test_20()
Annotate info fields
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test_21
public void test_21()
Annotate two consecutive variants in the same position
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test_22
public void test_22()
Annotate first base in a chromosome
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test_23_allele_specific_annotation_missing_R
public void test_23_allele_specific_annotation_missing_R()
Database has one entry and VCF has multiple ALTs
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test_24
public void test_24()
Annotate using "-name" to prepend a name to VCF fields (e.g. "AA" -> "PREPEND_AA") Header should be added changing the ID accordingly
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test_25
public void test_25()
Annotate using "-name" to prepend a name to VCF fields (e.g. "AA" -> "PREPEND_AA") Header should be added changing the ID accordingly
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test_26_repeat_db_entry
public void test_26_repeat_db_entry()
Annotate ID using entries that are duplicated in db.vcf
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test_27_repeat_db_entry
public void test_27_repeat_db_entry()
Annotate INFO fields using entries that are duplicated in db.vcf
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test_28_exists
public void test_28_exists()
Annotate if a VCF entry exists in the database file
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test_29_repeated_IDs
public void test_29_repeated_IDs()
Annotate if a VCF entry's ID might have multiple repeated entries
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test_31_annotate_minimal_representation_db
public void test_31_annotate_minimal_representation_db()
Issue when database has REF several variants which have to be converted into minimal representation
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test_32_annotate_minimal_representation_input
public void test_32_annotate_minimal_representation_input()
Issue when query has REF several variants which have to be converted into minimal representation
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test_33_empty_db
public void test_33_empty_db()
Empty database
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test_34_dbStartsOnDifferentChromo
public void test_34_dbStartsOnDifferentChromo()
Database has one entry and VCF has multiple ALTs
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test_35
public void test_35()
Annotate flags without '=true'
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test_36
public void test_36()
Annotate multi-allelic
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test_38
public void test_38()
Input VCf triggers a seek to a position after chromosome sections ends in database. Previously a bug it forced an infinite loop
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test_39
public void test_39()
Annotate issues with discovered info fields (when annotating ALL info fields)
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test_40
public void test_40()
Problems when tabix database file has 'chr' in chromosome names and VCF file does not
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test_41
public void test_41()
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test_42
public void test_42()
Test multiple CAF annotations
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test_43
public void test_43()
Annotate empty
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test_44
public void test_44()
Annotate GnomAd with multiple entries
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test_45
public void test_45()
Annotate GnomAd with multiple entries
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