Package main

Class Musial

java.lang.Object
main.Musial
public final class Musial extends Object
Main class of MUSIAL (MUlti Sample varIant AnaLysis), a tool to calculate SNV, gene, and whole genome alignments, together with other relevant statistics based on .vcf files.

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    static enum 
    Musial.Task
    Enum specifying tasks of MUSIAL to choose from.
    static class 
    Musial.Update
    Provides functionality to update (build or expand) a MUSIAL storage.
    static class 
    Musial.View
    Provides functionality to generate and display various types of tables based on the data stored in the `Storage` object.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static File
    outputDirectory
    Specifies the output directory for the program.
    static final String
    runId
    Unique run ID of this program instance; generated from the current date and time.
    static String
    softwareContact
    Author contact of the software; parsed from `/src/main/resources/info.properties`.
    static String
    softwareLicense
    License information of the software; parsed from `/src/main/resources/info.properties`.
    static String
    softwareName
    Name of the software; parsed from `/src/main/resources/info.properties`.
    static String
    softwareVersion
    Version of the software; parsed from `/src/main/resources/info.properties`.
    static long
    startTime
    Start time of the program.
    static final String
    storageExtension
    File extension used for MUSIAL storage files.
    static Musial.Task
    task
    Specifies the task to execute.

  • Constructor Summary

    Constructors
    Constructor
    Description
    Musial()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    main(String[] args)
    The main entry point of the MUSIAL application.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • runId

      public static final String runId
      Unique run ID of this program instance; generated from the current date and time.

    • softwareName

      public static String softwareName
      Name of the software; parsed from `/src/main/resources/info.properties`.

    • softwareVersion

      public static String softwareVersion
      Version of the software; parsed from `/src/main/resources/info.properties`.

    • softwareContact

      public static String softwareContact
      Author contact of the software; parsed from `/src/main/resources/info.properties`.

    • softwareLicense

      public static String softwareLicense
      License information of the software; parsed from `/src/main/resources/info.properties`.

    • task

      public static Musial.Task task
      Specifies the task to execute.

    • outputDirectory

      public static File outputDirectory
      Specifies the output directory for the program.

    • startTime

      public static long startTime
      Start time of the program.

    • storageExtension

      public static final String storageExtension
      File extension used for MUSIAL storage files.

      This constant specifies the default file extension for storage files created or used by the MUSIAL application. It is marked as `transient` to indicate that it should not be serialized as part of the class state.

      The extension should either be `.json` or `.json.gz` depending on the compression method used. For production, use `.json.gz` for compressed files.

      See Also:

  • Constructor Details

    • Musial

      public Musial()

  • Method Details

    • main

      public static void main(String[] args)
      The main entry point of the MUSIAL application.

      This method initializes the program, determines the task to execute based on the provided arguments, and executes the corresponding functionality. It handles errors gracefully and logs relevant information.

      Parameters:
      args - Command-line arguments specifying the task and its parameters.
      • args[0]: The task to execute (e.g., BUILD, UPDATE, VIEW, SEQUENCE).
      • Additional arguments are parsed by the CLI class.