Class TestCasesFilter


  • public class TestCasesFilter
    extends java.lang.Object
    Filter test cases
    Author:
    pcingola
    • 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

      • 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