Class TestCasesZzz


  • public class TestCasesZzz
    extends java.lang.Object
    Try test cases in this class before adding them to long test cases
    Author:
    pcingola
    • Constructor Summary

      Constructors 
      Constructor Description
      TestCasesZzz()  
    • 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_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

      • TestCasesZzz

        public TestCasesZzz()
    • 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_45

        public void test_45()
        Annotate GnomAd with multiple entries