Package org.snpsift.testCases.unit
Class TestCasesFilter
- java.lang.Object
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- org.snpsift.testCases.unit.TestCasesFilter
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public class TestCasesFilter extends java.lang.Object
Filter test cases- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static int
STDOUT_BUFFER_SIZE
static boolean
verbose
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Constructor Summary
Constructors Constructor Description TestCasesFilter()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_01()
Filter by qualityvoid
test_02()
Filter by chromosomevoid
test_03()
Filter by positionvoid
test_04()
Filter by positionvoid
test_05()
Filter by positionvoid
test_06()
Filter by positionvoid
test_07()
Filter by position (AND test)void
test_08()
Filter by position (OR test)void
test_09()
Regexp testvoid
test_10()
REF and ALT valuesvoid
test_11()
Filter by coveragevoid
test_12()
Filter by INDEL info tagvoid
test_13()
Filter by INDEL info tagvoid
test_14()
Filter by PL genottype tagvoid
test_15()
Filter by GT genottype tagvoid
test_16()
Filter by GT genottype functionsvoid
test_17()
Filter by GT genottype functionsvoid
test_18()
Filter by GT genottype functionsvoid
test_19()
Filter by GT genottype functionsvoid
test_20()
Filter by GT genottype functionsvoid
test_21()
Filter by GT genottype functionsvoid
test_22()
Filter by GT genottype functionsvoid
test_22_3()
Filter by GT genottype functionsvoid
test_23()
Filter by GT[*] (any genottype)void
test_24()
Filter by GT[0].VV[*] (any sub field in a genottype)void
test_25()
Filter by GT[*].VV[*] (any sub field in any genottype)void
test_26()
Filter by EFF[0].EFFECT (effect)void
test_26_ann()
Filter by ANN[0].EFFECT (effect)void
test_27()
Filter by EFF[*].EFFECT (any effect)void
test_27_ann()
Filter by ANN[*].EFFECT (any effect)void
test_27_ann2()
Filter by ANN[*].EFFECT (any effect)void
test_28()
Test countHom functionvoid
test_29()
Test countHet functionvoid
test_30()
Test countRef functionvoid
test_31()
Test countVariant functionvoid
test_32()
Filter by EFF[*].CODINGvoid
test_32_ann()
Filter by ANN[*].CODINGvoid
test_33()
Filter by EFF[*].CODINGvoid
test_33_ann()
Filter by ANN[*].CODINGvoid
test_34()
Filter by EFF[ALL].EFFECTvoid
test_34_ann()
Filter by ANN[ALL].EFFECTvoid
test_35()
Filter by EFF[*].GENEvoid
test_35_ann()
Filter by EFF[*].GENEvoid
test_36()
Inverse of a filtervoid
test_37()
Use filter field (add 'PASS' if expression is true)void
test_38()
Add a string to FILTER if expression is true)void
test_39()
Remove FILTER stringsvoid
test_40()
Inverse FILTER stringsvoid
test_41()
Remove filter option '-rmFilter' Bug reported by Jim Johnsonvoid
test_42()
Test compare to missing fieldvoid
test_43()
Test compare to missing fieldvoid
test_44()
Test compare to missing fieldvoid
test_45()
LOF[*].PERC > 0.1void
test_46()
void
test_47()
void
test_48()
void
test_49()
void
test_50()
Filter by EFF[*] (whole field comparison)void
test_51()
LOF[*] : Whole fieldvoid
test_52()
Filter by "(Cases[0] = 3) & (Controls[0] = 0)" Bug in Field.getReturnType() was causing some trouble.void
test_53()
Filter using 'has' operatorvoid
test_54()
Filter: Operator precedence issuevoid
test_55()
Test compare a field having 'Number=A' INFO headervoid
test_55_2()
Test compare a field having 'Number=A' INFO headervoid
test_55_3()
Test compare a field having 'Number=A' INFO headervoid
test_56_empty_vcf()
If header is shown when input file is emptyvoid
test_57_short_circuit_AND_OR_operators()
In AND operators, second expression should not be evaluated if first one is FALSEvoid
test_58_rmFilter_info_field()
Remove filter option '-rmFilter'.
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Field Detail
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STDOUT_BUFFER_SIZE
public static final int STDOUT_BUFFER_SIZE
- See Also:
- Constant Field Values
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verbose
public static boolean verbose
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Method Detail
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test_01
public void test_01()
Filter by quality
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test_02
public void test_02()
Filter by chromosome
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test_03
public void test_03()
Filter by position
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test_04
public void test_04()
Filter by position
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test_05
public void test_05()
Filter by position
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test_06
public void test_06()
Filter by position
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test_07
public void test_07()
Filter by position (AND test)
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test_08
public void test_08()
Filter by position (OR test)
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test_09
public void test_09()
Regexp test
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test_10
public void test_10()
REF and ALT values
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test_11
public void test_11()
Filter by coverage
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test_12
public void test_12()
Filter by INDEL info tag
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test_13
public void test_13()
Filter by INDEL info tag
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test_14
public void test_14()
Filter by PL genottype tag
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test_15
public void test_15()
Filter by GT genottype tag
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test_16
public void test_16()
Filter by GT genottype functions
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test_17
public void test_17()
Filter by GT genottype functions
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test_18
public void test_18()
Filter by GT genottype functions
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test_19
public void test_19()
Filter by GT genottype functions
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test_20
public void test_20()
Filter by GT genottype functions
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test_21
public void test_21()
Filter by GT genottype functions
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test_22
public void test_22()
Filter by GT genottype functions
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test_22_3
public void test_22_3()
Filter by GT genottype functions
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test_23
public void test_23()
Filter by GT[*] (any genottype)
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test_24
public void test_24()
Filter by GT[0].VV[*] (any sub field in a genottype)
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test_25
public void test_25()
Filter by GT[*].VV[*] (any sub field in any genottype)
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test_26
public void test_26()
Filter by EFF[0].EFFECT (effect)
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test_26_ann
public void test_26_ann()
Filter by ANN[0].EFFECT (effect)
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test_27
public void test_27()
Filter by EFF[*].EFFECT (any effect)
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test_27_ann
public void test_27_ann()
Filter by ANN[*].EFFECT (any effect)
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test_27_ann2
public void test_27_ann2()
Filter by ANN[*].EFFECT (any effect)
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test_28
public void test_28()
Test countHom function
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test_29
public void test_29()
Test countHet function
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test_30
public void test_30()
Test countRef function
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test_31
public void test_31()
Test countVariant function
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test_32
public void test_32()
Filter by EFF[*].CODING
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test_32_ann
public void test_32_ann()
Filter by ANN[*].CODING
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test_33
public void test_33()
Filter by EFF[*].CODING
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test_33_ann
public void test_33_ann()
Filter by ANN[*].CODING
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test_34
public void test_34()
Filter by EFF[ALL].EFFECT
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test_34_ann
public void test_34_ann()
Filter by ANN[ALL].EFFECT
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test_35
public void test_35()
Filter by EFF[*].GENE
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test_35_ann
public void test_35_ann()
Filter by EFF[*].GENE
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test_36
public void test_36()
Inverse of a filter
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test_37
public void test_37()
Use filter field (add 'PASS' if expression is true)
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test_38
public void test_38()
Add a string to FILTER if expression is true)
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test_39
public void test_39()
Remove FILTER strings
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test_40
public void test_40()
Inverse FILTER strings
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test_41
public void test_41()
Remove filter option '-rmFilter' Bug reported by Jim Johnson
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test_42
public void test_42()
Test compare to missing field
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test_43
public void test_43()
Test compare to missing field
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test_44
public void test_44()
Test compare to missing field
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test_45
public void test_45()
LOF[*].PERC > 0.1
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test_46
public void test_46()
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test_47
public void test_47()
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test_48
public void test_48()
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test_49
public void test_49()
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test_50
public void test_50()
Filter by EFF[*] (whole field comparison)
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test_51
public void test_51()
LOF[*] : Whole field
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test_52
public void test_52()
Filter by "(Cases[0] = 3) & (Controls[0] = 0)" Bug in Field.getReturnType() was causing some trouble.
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test_53
public void test_53()
Filter using 'has' operator
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test_54
public void test_54()
Filter: Operator precedence issue
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test_55
public void test_55()
Test compare a field having 'Number=A' INFO header
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test_55_2
public void test_55_2()
Test compare a field having 'Number=A' INFO header
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test_55_3
public void test_55_3()
Test compare a field having 'Number=A' INFO header
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test_56_empty_vcf
public void test_56_empty_vcf()
If header is shown when input file is empty
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test_57_short_circuit_AND_OR_operators
public void test_57_short_circuit_AND_OR_operators()
In AND operators, second expression should not be evaluated if first one is FALSE
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test_58_rmFilter_info_field
public void test_58_rmFilter_info_field()
Remove filter option '-rmFilter'. Check that INFO field 'FILTER_DELETED' is properly added
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