Class TestCasesAnnotate

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.util.List<org.snpeff.vcf.VcfEntry> annotate​(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
      Annotate
      java.lang.String annotateOut​(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
      Annotate and return STDOUT as a string
      void annotateTest​(java.lang.String dbFileName, java.lang.String fileName)  
      void annotateTest​(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)
      Annotate a file and check that the new annotation matches the expected one
      protected java.lang.String[] argsList​(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)  
      void test_01()  
      void test_02()  
      void test_03()  
      void test_04()  
      void test_05()
      Chromosomes in VCF file are called 'chr22' instead of '22'.
      void test_06()
      Annotate info fields
      void test_07()
      Annotate only some info fields
      void test_08()
      Do not annotate ID column
      void test_09()
      Annotate only some info fields
      void test_11()
      Annotate only some info fields
      void test_12()
      Annotate without REF/ALT fields
      void test_13()
      Annotate using "reserved" VCF fields (e.g.
      void test_14()  
      void test_15()  
      void test_16()  
      void test_17()  
      void test_18()  
      void test_19()  
      void test_20()
      Annotate info fields
      void test_21()
      Annotate two consecutive variants in the same position
      void test_22()
      Annotate first base in a chromosome
      void test_23_allele_specific_annotation_missing_R()
      Database has one entry and VCF has multiple ALTs
      void test_24()
      Annotate using "-name" to prepend a name to VCF fields (e.g.
      void test_25()
      Annotate using "-name" to prepend a name to VCF fields (e.g.
      void test_26_repeat_db_entry()
      Annotate ID using entries that are duplicated in db.vcf
      void test_27_repeat_db_entry()
      Annotate INFO fields using entries that are duplicated in db.vcf
      void test_28_exists()
      Annotate if a VCF entry exists in the database file
      void test_29_repeated_IDs()
      Annotate if a VCF entry's ID might have multiple repeated entries
      void test_31_annotate_minimal_representation_db()
      Issue when database has REF several variants which have to be converted into minimal representation
      void test_32_annotate_minimal_representation_input()
      Issue when query has REF several variants which have to be converted into minimal representation
      void test_33_empty_db()
      Empty database
      void test_34_dbStartsOnDifferentChromo()
      Database has one entry and VCF has multiple ALTs
      void test_35()
      Annotate flags without '=true'
      void test_36()
      Annotate multi-allelic
      void test_38()
      Input VCf triggers a seek to a position after chromosome sections ends in database.
      void test_39()
      Annotate issues with discovered info fields (when annotating ALL info fields)
      void test_40()
      Problems when tabix database file has 'chr' in chromosome names and VCF file does not
      void test_41()  
      void test_42()
      Test multiple CAF annotations
      void test_43()
      Annotate empty
      void test_44()
      Annotate GnomAd with multiple entries
      void test_45()
      Annotate GnomAd with multiple entries
      • Methods inherited from class java.lang.Object

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

      • debug

        public static boolean debug
      • verbose

        public static boolean verbose
      • defaultExtraArgs

        protected java.lang.String[] defaultExtraArgs
      • deleteIndexFile

        protected boolean deleteIndexFile
    • Constructor Detail

      • TestCasesAnnotate

        public TestCasesAnnotate()
    • Method Detail

      • annotate

        public java.util.List<org.snpeff.vcf.VcfEntry> annotate​(java.lang.String dbFileName,
                                                                java.lang.String fileName,
                                                                java.lang.String[] extraArgs)
        Annotate
      • annotateOut

        public java.lang.String annotateOut​(java.lang.String dbFileName,
                                            java.lang.String fileName,
                                            java.lang.String[] extraArgs)
        Annotate and return STDOUT as a string
      • annotateTest

        public void annotateTest​(java.lang.String dbFileName,
                                 java.lang.String fileName)
      • annotateTest

        public void annotateTest​(java.lang.String dbFileName,
                                 java.lang.String fileName,
                                 java.lang.String[] extraArgs)
        Annotate a file and check that the new annotation matches the expected one
      • argsList

        protected java.lang.String[] argsList​(java.lang.String dbFileName,
                                              java.lang.String fileName,
                                              java.lang.String[] extraArgs)
      • test_01

        public void test_01()
      • test_02

        public void test_02()
      • test_03

        public void test_03()
      • test_04

        public void test_04()
      • test_05

        public void test_05()
        Chromosomes in VCF file are called 'chr22' instead of '22'. This should work OK as well.
      • test_06

        public void test_06()
        Annotate info fields
      • test_07

        public void test_07()
        Annotate only some info fields
      • test_08

        public void test_08()
        Do not annotate ID column
      • test_09

        public void test_09()
        Annotate only some info fields
      • test_11

        public void test_11()
        Annotate only some info fields
        Throws:
        java.io.IOException
      • test_12

        public void test_12()
        Annotate without REF/ALT fields
      • test_13

        public void test_13()
        Annotate using "reserved" VCF fields (e.g. "AA" ) Header should be added if it doesn't exits.
        Throws:
        java.io.IOException
      • test_14

        public void test_14()
      • test_15

        public void test_15()
      • test_16

        public void test_16()
      • test_17

        public void test_17()
      • test_18

        public void test_18()
      • test_19

        public void test_19()
      • test_20

        public void test_20()
        Annotate info fields
      • test_21

        public void test_21()
        Annotate two consecutive variants in the same position
      • test_22

        public void test_22()
        Annotate first base in a chromosome
      • test_23_allele_specific_annotation_missing_R

        public void test_23_allele_specific_annotation_missing_R()
        Database has one entry and VCF has multiple ALTs
      • test_24

        public void test_24()
        Annotate using "-name" to prepend a name to VCF fields (e.g. "AA" -> "PREPEND_AA") Header should be added changing the ID accordingly
      • test_25

        public void test_25()
        Annotate using "-name" to prepend a name to VCF fields (e.g. "AA" -> "PREPEND_AA") Header should be added changing the ID accordingly
      • test_26_repeat_db_entry

        public void test_26_repeat_db_entry()
        Annotate ID using entries that are duplicated in db.vcf
      • test_27_repeat_db_entry

        public void test_27_repeat_db_entry()
        Annotate INFO fields using entries that are duplicated in db.vcf
      • test_28_exists

        public void test_28_exists()
        Annotate if a VCF entry exists in the database file
      • test_29_repeated_IDs

        public void test_29_repeated_IDs()
        Annotate if a VCF entry's ID might have multiple repeated entries
      • test_31_annotate_minimal_representation_db

        public void test_31_annotate_minimal_representation_db()
        Issue when database has REF several variants which have to be converted into minimal representation
      • test_32_annotate_minimal_representation_input

        public void test_32_annotate_minimal_representation_input()
        Issue when query has REF several variants which have to be converted into minimal representation
      • test_33_empty_db

        public void test_33_empty_db()
        Empty database
      • test_34_dbStartsOnDifferentChromo

        public void test_34_dbStartsOnDifferentChromo()
        Database has one entry and VCF has multiple ALTs
      • test_35

        public void test_35()
        Annotate flags without '=true'
      • test_36

        public void test_36()
        Annotate multi-allelic
      • test_38

        public void test_38()
        Input VCf triggers a seek to a position after chromosome sections ends in database. Previously a bug it forced an infinite loop
      • test_39

        public void test_39()
        Annotate issues with discovered info fields (when annotating ALL info fields)
      • test_40

        public void test_40()
        Problems when tabix database file has 'chr' in chromosome names and VCF file does not
      • test_41

        public void test_41()
      • test_42

        public void test_42()
        Test multiple CAF annotations
      • test_43

        public void test_43()
        Annotate empty
      • test_44

        public void test_44()
        Annotate GnomAd with multiple entries
      • test_45

        public void test_45()
        Annotate GnomAd with multiple entries