Package main

Class Par

  • public final class Par
extends java.lang.Object

    Class Parameters represents the parameters for a Beagle analysis.

    Instances of class Parameters are immutable.

    • Constructor Summary

      Constructors 
      Constructor Description
      Par​(java.lang.String[] args)
      Constructs a new Parameters instance from the specified command line arguments.

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean ap()
      Returns the ap parameter.
      java.lang.String[] args()
      Returns the command line arguments.
      float buffer()
      Return the buffer parameter.
      int burnin()
      Returns the burnin parameter.
      ChromInterval chromInt()
      Returns the chromosome interval or null if no chrom parameter was specified.
      float cluster()
      Returns the cluster parameter.
      float err​(int nHaps)
      Returns the allele mismatch parameter for the specified number of samples.
      java.io.File excludemarkers()
      Returns the excludemarkers parameter or null if no excludemarkers parameter was specified.
      java.io.File excludesamples()
      Returns the excludesamples parameter or null if no excludesamples parameter was specified.
      boolean gp()
      Returns the gp parameter.
      java.io.File gt()
      Returns the gt parameter or null if no gt parameter was specified.
      int imp_nsteps()
      Returns the imp-nsteps parameter.
      float imp_segment()
      Returns the imp-segment parameter.
      int imp_states()
      Returns the imp-states parameter.
      float imp_step()
      Returns the imp-step parameter.
      boolean impute()
      Returns the impute parameter.
      int iterations()
      Returns the iterations parameter.
      java.io.File map()
      Returns the map parameter.
      float ne()
      Returns the ne parameter
      int nthreads()
      Returns the nthreads parameter.
      java.lang.String out()
      Returns the out parameter.
      float overlap()
      Return the overlap parameter.
      java.io.File ped()
      Returns the ped parameter or null if no ped parameter was specified.
      int phase_states()
      Returns the phase-states parameter.
      float phase_step()
      Returns the phase-step parameter.
      float rare()
      Returns the rare parameter
      java.io.File ref()
      Returns the ref parameter or null if no ref parameter was specified.
      float scaleFactor()
      Return the ratio of the phase-states parameter and the default phase-states parameter
      long seed()
      Returns the seed parameter.
      java.io.File truth()
      Returns the truth parameter
      static java.lang.String usage()
      Returns a description of the Beagle command line arguments.
      float window()
      Returns the window parameter.

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • Par

        public Par​(java.lang.String[] args)
        Constructs a new Parameters instance from the specified command line arguments.
        Parameters:
        args - the command line arguments
        Throws:
        java.lang.IllegalArgumentException - if a command line argument is incorrectly specified
        java.lang.NumberFormatException - if a numeric value for a parameter is incorrectly specified
        java.lang.NullPointerException - if args == null

    • Method Detail

      • args

        public java.lang.String[] args()
        Returns the command line arguments.
        Returns:
        the command line arguments

      • usage

        public static java.lang.String usage()
        Returns a description of the Beagle command line arguments.
        Returns:
        a description of the Beagle command line arguments

      • gt

        public java.io.File gt()
        Returns the gt parameter or null if no gt parameter was specified.
        Returns:
        the gt parameter or null if no gt parameter was specified

      • ref

        public java.io.File ref()
        Returns the ref parameter or null if no ref parameter was specified.
        Returns:
        the ref parameter or null if no ref parameter was specified

      • out

        public java.lang.String out()
        Returns the out parameter.
        Returns:
        the out parameter

      • ped

        public java.io.File ped()
        Returns the ped parameter or null if no ped parameter was specified.
        Returns:
        the ped parameter or null if no ped parameter was specified

      • map

        public java.io.File map()
        Returns the map parameter.
        Returns:
        the map parameter

      • chromInt

        public ChromInterval chromInt()
        Returns the chromosome interval or null if no chrom parameter was specified.
        Returns:
        the chromosome interval or null if no chrom parameter was specified.

      • excludesamples

        public java.io.File excludesamples()
        Returns the excludesamples parameter or null if no excludesamples parameter was specified.
        Returns:
        the excludesamples parameter or null if no excludesamples parameter was specified

      • excludemarkers

        public java.io.File excludemarkers()
        Returns the excludemarkers parameter or null if no excludemarkers parameter was specified.
        Returns:
        the excludemarkers parameter or null if no excludemarkers parameter was specified

      • burnin

        public int burnin()
        Returns the burnin parameter.
        Returns:
        the burnin parameter

      • iterations

        public int iterations()
        Returns the iterations parameter.
        Returns:
        the iterations parameter

      • phase_states

        public int phase_states()
        Returns the phase-states parameter.
        Returns:
        the phase-states parameter

      • scaleFactor

        public float scaleFactor()
        Return the ratio of the phase-states parameter and the default phase-states parameter
        Returns:
        the ratio of the phase-states parameter and the default phase-states parameter

      • phase_step

        public float phase_step()
        Returns the phase-step parameter.
        Returns:
        the phase-step parameter

      • rare

        public float rare()
        Returns the rare parameter
        Returns:
        the rare parameter

      • impute

        public boolean impute()
        Returns the impute parameter.
        Returns:
        the impute parameter

      • imp_states

        public int imp_states()
        Returns the imp-states parameter.
        Returns:
        the imp-states parameter

      • imp_segment

        public float imp_segment()
        Returns the imp-segment parameter.
        Returns:
        the imp-segment parameter

      • imp_step

        public float imp_step()
        Returns the imp-step parameter.
        Returns:
        the imp-step parameter

      • imp_nsteps

        public int imp_nsteps()
        Returns the imp-nsteps parameter.
        Returns:
        the imp-nsteps parameter

      • cluster

        public float cluster()
        Returns the cluster parameter.
        Returns:
        the cluster parameter

      • ap

        public boolean ap()
        Returns the ap parameter.
        Returns:
        the ap parameter

      • gp

        public boolean gp()
        Returns the gp parameter.
        Returns:
        the gp parameter

      • ne

        public float ne()
        Returns the ne parameter
        Returns:
        the ne parameter

      • err

        public float err​(int nHaps)
        Returns the allele mismatch parameter for the specified number of samples.
        Parameters:
        nHaps - the number of reference and target haplotypes
        Returns:
        the allele mismatch parameter for the specified number of samples

      • window

        public float window()
        Returns the window parameter.
        Returns:
        the window parameter

      • overlap

        public float overlap()
        Return the overlap parameter.
        Returns:
        the overlap parameter.

      • buffer

        public float buffer()
        Return the buffer parameter.
        Returns:
        the buffer parameter.

      • seed

        public long seed()
        Returns the seed parameter.
        Returns:
        the seed parameter

      • nthreads

        public int nthreads()
        Returns the nthreads parameter.
        Returns:
        the nthreads parameter

      • truth

        public java.io.File truth()
        Returns the truth parameter
        Returns:
        the truth