Class TestCasesFilter

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

public class TestCasesFilter extends Object
Filter test cases
Author:
pcingola
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
     
    static boolean
     
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    void
    Filter by quality
    void
    Filter by chromosome
    void
    Filter by position
    void
    Filter by position
    void
    Filter by position
    void
    Filter by position
    void
    Filter by position (AND test)
    void
    Filter by position (OR test)
    void
    Regexp test
    void
    REF and ALT values
    void
    Filter by coverage
    void
    Filter by INDEL info tag
    void
    Filter by INDEL info tag
    void
    Filter by PL genottype tag
    void
    Filter by GT genottype tag
    void
    Filter by GT genottype functions
    void
    Filter by GT genottype functions
    void
    Filter by GT genottype functions
    void
    Filter by GT genottype functions
    void
    Filter by GT genottype functions
    void
    Filter by GT genottype functions
    void
    Filter by GT genottype functions
    void
    Filter by GT genottype functions
    void
    Filter by GT[*] (any genottype)
    void
    Filter by GT[0].VV[*] (any sub field in a genottype)
    void
    Filter by GT[*].VV[*] (any sub field in any genottype)
    void
    Filter by EFF[0].EFFECT (effect)
    void
    Filter by ANN[0].EFFECT (effect)
    void
    Filter by EFF[*].EFFECT (any effect)
    void
    Filter by ANN[*].EFFECT (any effect)
    void
    Filter by ANN[*].EFFECT (any effect)
    void
    Test countHom function
    void
    Test countHet function
    void
    Test countRef function
    void
    Test countVariant function
    void
    Filter by EFF[*].CODING
    void
    Filter by ANN[*].CODING
    void
    Filter by EFF[*].CODING
    void
    Filter by ANN[*].CODING
    void
    Filter by EFF[ALL].EFFECT
    void
    Filter by ANN[ALL].EFFECT
    void
    Filter by EFF[*].GENE
    void
    Filter by EFF[*].GENE
    void
    Inverse of a filter
    void
    Use filter field (add 'PASS' if expression is true)
    void
    Add a string to FILTER if expression is true)
    void
    Remove FILTER strings
    void
    Inverse FILTER strings
    void
    Remove filter option '-rmFilter' Bug reported by Jim Johnson
    void
    Test compare to missing field
    void
    Test compare to missing field
    void
    Test compare to missing field
    void
    LOF[*].PERC > 0.1
    void
     
    void
     
    void
     
    void
     
    void
    Filter by EFF[*] (whole field comparison)
    void
    LOF[*] : Whole field
    void
    Filter by "(Cases[0] = 3) invalid input: '&' (Controls[0] = 0)" Bug in Field.getReturnType() was causing some trouble.
    void
    Filter using 'has' operator
    void
    Filter: Operator precedence issue
    void
    Test compare a field having 'Number=A' INFO header
    void
    Test compare a field having 'Number=A' INFO header
    void
    Test compare a field having 'Number=A' INFO header
    void
    If header is shown when input file is empty
    void
    In AND operators, second expression should not be evaluated if first one is FALSE
    void
    Remove filter option '-rmFilter'.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Field Details

    • STDOUT_BUFFER_SIZE

      public static final int STDOUT_BUFFER_SIZE
      See Also:
    • verbose

      public static boolean verbose
  • Constructor Details

    • TestCasesFilter

      public TestCasesFilter()
  • Method Details

    • 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) invalid input: '&' (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