Package org.snpsift.testCases.unit

Class TestCasesDbNsfp

  • Direct Known Subclasses:
    TestCasesDbNsfpDeleteCache
    public class TestCasesDbNsfp
extends java.lang.Object
    Test cases for dbNSFP database annotations Note: This class tries to use 'data type cache' files
    Author:
    pcingola

    • Constructor Summary

      Constructors 
      Constructor Description
      TestCasesDbNsfp()  

    • 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)  
      java.util.Map<java.lang.String,​java.lang.String> annotateGetFiledTypes​(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)  
      protected java.lang.String[] argsList​(java.lang.String dbFileName, java.lang.String fileName, java.lang.String[] extraArgs)  
      void test_01()  
      void test_02()
      Test dbnsfp having multiple lines per variant
      void test_03()
      Test dbnsfp having multiple lines per variant, without collapsing
      void test_04()  
      void test_05()  
      void test_06()  
      void test_07()
      Check header values are correctly inferred.
      void test_08()
      Missing annotations
      void test_09()
      Invalid INFO keys
      void test_10()
      Missing database entries
      void test_11()
      Missing database entries + non-missing entry

      • 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

      • debug

        public static boolean debug

      • defaultExtraArgs

        protected java.lang.String[] defaultExtraArgs

      • removeDataTypesCache

        protected boolean removeDataTypesCache

    • Constructor Detail

      • TestCasesDbNsfp

        public TestCasesDbNsfp()

    • Method Detail

      • annotate

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

      • annotateGetFiledTypes

        public java.util.Map<java.lang.String,​java.lang.String> annotateGetFiledTypes​(java.lang.String dbFileName,
                                                                                    java.lang.String fileName,
                                                                                    java.lang.String[] extraArgs)

      • 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 dbnsfp having multiple lines per variant

      • test_03

        public void test_03()
        Test dbnsfp having multiple lines per variant, without collapsing

      • test_04

        public void test_04()

      • test_05

        public void test_05()

      • test_06

        public void test_06()

      • test_07

        public void test_07()
        Check header values are correctly inferred.

        E.g. If the first value in the table is '0', we may infer that data type is INT, but if another value '0.5' appears, we change it to FLOAT

      • test_08

        public void test_08()
        Missing annotations

      • test_09

        public void test_09()
        Invalid INFO keys

      • test_10

        public void test_10()
        Missing database entries

      • test_11

        public void test_11()
        Missing database entries + non-missing entry