Class 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) & (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