java.lang.Object
- org.snpsift.testCases.unit.TestCasesFilter

public class TestCasesFilter
extends java.lang.Object

Filter test cases

Author:: pcingola

Field Summary

Fields
Modifier and Type Field Description

static int STDOUT_BUFFER_SIZE

static boolean verbose

Constructor Summary

Constructors
Constructor Description

TestCasesFilter()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`test_01()`	Filter by quality
`void`	`test_02()`	Filter by chromosome
`void`	`test_03()`	Filter by position
`void`	`test_04()`	Filter by position
`void`	`test_05()`	Filter by position
`void`	`test_06()`	Filter by position
`void`	`test_07()`	Filter by position (AND test)
`void`	`test_08()`	Filter by position (OR test)
`void`	`test_09()`	Regexp test
`void`	`test_10()`	REF and ALT values
`void`	`test_11()`	Filter by coverage
`void`	`test_12()`	Filter by INDEL info tag
`void`	`test_13()`	Filter by INDEL info tag
`void`	`test_14()`	Filter by PL genottype tag
`void`	`test_15()`	Filter by GT genottype tag
`void`	`test_16()`	Filter by GT genottype functions
`void`	`test_17()`	Filter by GT genottype functions
`void`	`test_18()`	Filter by GT genottype functions
`void`	`test_19()`	Filter by GT genottype functions
`void`	`test_20()`	Filter by GT genottype functions
`void`	`test_21()`	Filter by GT genottype functions
`void`	`test_22()`	Filter by GT genottype functions
`void`	`test_22_3()`	Filter by GT genottype functions
`void`	`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 function
`void`	`test_29()`	Test countHet function
`void`	`test_30()`	Test countRef function
`void`	`test_31()`	Test countVariant function
`void`	`test_32()`	Filter by EFF[*].CODING
`void`	`test_32_ann()`	Filter by ANN[*].CODING
`void`	`test_33()`	Filter by EFF[*].CODING
`void`	`test_33_ann()`	Filter by ANN[*].CODING
`void`	`test_34()`	Filter by EFF[ALL].EFFECT
`void`	`test_34_ann()`	Filter by ANN[ALL].EFFECT
`void`	`test_35()`	Filter by EFF[*].GENE
`void`	`test_35_ann()`	Filter by EFF[*].GENE
`void`	`test_36()`	Inverse of a filter
`void`	`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 strings
`void`	`test_40()`	Inverse FILTER strings
`void`	`test_41()`	Remove filter option '-rmFilter' Bug reported by Jim Johnson
`void`	`test_42()`	Test compare to missing field
`void`	`test_43()`	Test compare to missing field
`void`	`test_44()`	Test compare to missing field
`void`	`test_45()`	LOF[*].PERC > 0.1
`void`	`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 field
`void`	`test_52()`	Filter by "(Cases[0] = 3) & (Controls[0] = 0)" Bug in Field.getReturnType() was causing some trouble.
`void`	`test_53()`	Filter using 'has' operator
`void`	`test_54()`	Filter: Operator precedence issue
`void`	`test_55()`	Test compare a field having 'Number=A' INFO header
`void`	`test_55_2()`	Test compare a field having 'Number=A' INFO header
`void`	`test_55_3()`	Test compare a field having 'Number=A' INFO header
`void`	`test_56_empty_vcf()`	If header is shown when input file is empty
`void`	`test_57_short_circuit_AND_OR_operators()`	In AND operators, second expression should not be evaluated if first one is FALSE
`void`	`test_58_rmFilter_info_field()`	Remove filter option '-rmFilter'.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - STDOUT_BUFFER_SIZE
```
public static final int STDOUT_BUFFER_SIZE
```
    See Also:
    
    Constant Field Values
  - verbose
```
public static boolean verbose
```
- Constructor Detail
  - TestCasesFilter
```
public TestCasesFilter()
```
- Method Detail
  - test_01
```
public void test_01()
```
    Filter by quality
  - test_02
```
public void test_02()
```
    Filter by chromosome
  - test_03
```
public void test_03()
```
    Filter by position
  - test_04
```
public void test_04()
```
    Filter by position
  - test_05
```
public void test_05()
```
    Filter by position
  - test_06
```
public void test_06()
```
    Filter by position
  - test_07
```
public void test_07()
```
    Filter by position (AND test)
  - test_08
```
public void test_08()
```
    Filter by position (OR test)
  - test_09
```
public void test_09()
```
    Regexp test
  - test_10
```
public void test_10()
```
    REF and ALT values
  - test_11
```
public void test_11()
```
    Filter by coverage
  - test_12
```
public void test_12()
```
    Filter by INDEL info tag
  - test_13
```
public void test_13()
```
    Filter by INDEL info tag
  - test_14
```
public void test_14()
```
    Filter by PL genottype tag
  - test_15
```
public void test_15()
```
    Filter by GT genottype tag
  - test_16
```
public void test_16()
```
    Filter by GT genottype functions
  - test_17
```
public void test_17()
```
    Filter by GT genottype functions
  - test_18
```
public void test_18()
```
    Filter by GT genottype functions
  - test_19
```
public void test_19()
```
    Filter by GT genottype functions
  - test_20
```
public void test_20()
```
    Filter by GT genottype functions
  - test_21
```
public void test_21()
```
    Filter by GT genottype functions
  - test_22
```
public void test_22()
```
    Filter by GT genottype functions
  - test_22_3
```
public void test_22_3()
```
    Filter by GT genottype functions
  - test_23
```
public void test_23()
```
    Filter by GT[*] (any genottype)
  - test_24
```
public void test_24()
```
    Filter by GT[0].VV[*] (any sub field in a genottype)
  - test_25
```
public void test_25()
```
    Filter by GT[*].VV[*] (any sub field in any genottype)
  - test_26
```
public void test_26()
```
    Filter by EFF[0].EFFECT (effect)
  - test_26_ann
```
public void test_26_ann()
```
    Filter by ANN[0].EFFECT (effect)
  - test_27
```
public void test_27()
```
    Filter by EFF[*].EFFECT (any effect)
  - test_27_ann
```
public void test_27_ann()
```
    Filter by ANN[*].EFFECT (any effect)
  - test_27_ann2
```
public void test_27_ann2()
```
    Filter by ANN[*].EFFECT (any effect)
  - test_28
```
public void test_28()
```
    Test countHom function
  - test_29
```
public void test_29()
```
    Test countHet function
  - test_30
```
public void test_30()
```
    Test countRef function
  - test_31
```
public void test_31()
```
    Test countVariant function
  - test_32
```
public void test_32()
```
    Filter by EFF[*].CODING
  - test_32_ann
```
public void test_32_ann()
```
    Filter by ANN[*].CODING
  - test_33
```
public void test_33()
```
    Filter by EFF[*].CODING
  - test_33_ann
```
public void test_33_ann()
```
    Filter by ANN[*].CODING
  - test_34
```
public void test_34()
```
    Filter by EFF[ALL].EFFECT
  - test_34_ann
```
public void test_34_ann()
```
    Filter by ANN[ALL].EFFECT
  - test_35
```
public void test_35()
```
    Filter by EFF[*].GENE
  - test_35_ann
```
public void test_35_ann()
```
    Filter by EFF[*].GENE
  - test_36
```
public void test_36()
```
    Inverse of a filter
  - test_37
```
public void test_37()
```
    Use filter field (add 'PASS' if expression is true)
  - test_38
```
public void test_38()
```
    Add a string to FILTER if expression is true)
  - test_39
```
public void test_39()
```
    Remove FILTER strings
  - test_40
```
public void test_40()
```
    Inverse FILTER strings
  - test_41
```
public void test_41()
```
    Remove filter option '-rmFilter' Bug reported by Jim Johnson
  - test_42
```
public void test_42()
```
    Test compare to missing field
  - test_43
```
public void test_43()
```
    Test compare to missing field
  - test_44
```
public void test_44()
```
    Test compare to missing field
  - test_45
```
public void test_45()
```
    LOF[*].PERC > 0.1
  - test_46
```
public void test_46()
```
  - test_47
```
public void test_47()
```
  - test_48
```
public void test_48()
```
  - test_49
```
public void test_49()
```
  - test_50
```
public void test_50()
```
    Filter by EFF[*] (whole field comparison)
  - test_51
```
public void test_51()
```
    LOF[*] : Whole field
  - test_52
```
public void test_52()
```
    Filter by "(Cases[0] = 3) & (Controls[0] = 0)" Bug in Field.getReturnType() was causing some trouble.
  - test_53
```
public void test_53()
```
    Filter using 'has' operator
  - test_54
```
public void test_54()
```
    Filter: Operator precedence issue
  - test_55
```
public void test_55()
```
    Test compare a field having 'Number=A' INFO header
  - test_55_2
```
public void test_55_2()
```
    Test compare a field having 'Number=A' INFO header
  - test_55_3
```
public void test_55_3()
```
    Test compare a field having 'Number=A' INFO header
  - test_56_empty_vcf
```
public void test_56_empty_vcf()
```
    If header is shown when input file is empty
  - 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
  - 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

Fields
Modifier and Type	Field	Description
`static int`	`STDOUT_BUFFER_SIZE`
`static boolean`	`verbose`

Class TestCasesFilter

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

STDOUT_BUFFER_SIZE

verbose

Constructor Detail

TestCasesFilter

Method Detail

test_01

test_02

test_03

test_04

test_05

test_06

test_07

test_08

test_09

test_10

test_11

test_12

test_13

test_14

test_15

test_16

test_17

test_18

test_19

test_20

test_21

test_22

test_22_3

test_23

test_24

test_25

test_26

test_26_ann

test_27

test_27_ann

test_27_ann2

test_28

test_29

test_30

test_31

test_32

test_32_ann

test_33

test_33_ann

test_34

test_34_ann

test_35

test_35_ann

test_36

test_37

test_38

test_39

test_40

test_41

test_42

test_43

test_44

test_45

test_46

test_47

test_48

test_49

test_50

test_51

test_52

test_53

test_54

test_55

test_55_2

test_55_3

test_56_empty_vcf

test_57_short_circuit_AND_OR_operators

test_58_rmFilter_info_field