Package org.snpsift.testCases.unit
Class TestCasesDbNsfp
- java.lang.Object
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- org.snpsift.testCases.unit.TestCasesDbNsfp
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- Direct Known Subclasses:
TestCasesDbNsfpDeleteCache
public class TestCasesDbNsfp extends java.lang.Object
Test cases for dbNSFP database annotations Note: This class tries to use 'data type cache' files- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
protected java.lang.String[]
defaultExtraArgs
protected boolean
removeDataTypesCache
static boolean
verbose
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Constructor Summary
Constructors Constructor Description TestCasesDbNsfp()
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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)
java.util.Map<java.lang.String,java.lang.String>
annotateGetFiledTypes(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
protected java.lang.String[]
argsList(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
void
test_01()
void
test_02()
Test dbnsfp having multiple lines per variantvoid
test_03()
Test dbnsfp having multiple lines per variant, without collapsingvoid
test_04()
void
test_05()
void
test_06()
void
test_07()
Check header values are correctly inferred.void
test_08()
Missing annotationsvoid
test_09()
Invalid INFO keysvoid
test_10()
Missing database entriesvoid
test_11()
Missing database entries + non-missing entry
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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)
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annotateGetFiledTypes
public java.util.Map<java.lang.String,java.lang.String> annotateGetFiledTypes(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
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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()
Test dbnsfp having multiple lines per variant
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test_03
public void test_03()
Test dbnsfp having multiple lines per variant, without collapsing
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test_04
public void test_04()
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test_05
public void test_05()
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test_06
public void test_06()
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test_07
public void test_07()
Check header values are correctly inferred.E.g. If the first value in the table is '0', we may infer that data type is INT, but if another value '0.5' appears, we change it to FLOAT
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test_08
public void test_08()
Missing annotations
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test_09
public void test_09()
Invalid INFO keys
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test_10
public void test_10()
Missing database entries
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test_11
public void test_11()
Missing database entries + non-missing entry
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