Package org.snpsift.testCases.unit

Class TestCasesDbNsfp

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

  • Field Details

    • verbose

      public static boolean verbose

    • debug

      public static boolean debug

    • defaultExtraArgs

      protected String[] defaultExtraArgs

    • removeDataTypesCache

      protected boolean removeDataTypesCache

  • Constructor Details

    • TestCasesDbNsfp

      public TestCasesDbNsfp()

  • Method Details

    • annotate

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

    • annotateGetFiledTypes

      public Map<String,String> annotateGetFiledTypes(String dbFileName, String fileName, String[] extraArgs)

    • argsList

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