Class TestCasesAnnotate

java.lang.Object
org.snpsift.testCases.unit.TestCasesAnnotate
Direct Known Subclasses:
TestCasesAnnotateCreateIndex, TestCasesAnnotateMem, TestCasesAnnotateTabix, TestCasesAnnotateUseIndex

public class TestCasesAnnotate extends Object
Annotate test case
Author:
pcingola
  • Field Details

    • debug

      public static boolean debug
    • verbose

      public static boolean verbose
    • defaultExtraArgs

      protected String[] defaultExtraArgs
    • deleteIndexFile

      protected boolean deleteIndexFile
  • Constructor Details

    • TestCasesAnnotate

      public TestCasesAnnotate()
  • Method Details

    • annotate

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

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

      public void annotateTest(String dbFileName, String fileName)
    • annotateTest

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

      protected String[] argsList(String dbFileName, String fileName, 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:
      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:
      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