docs: def computeCovarianceMatrixPlink(plink_path,out_dir,bfile,cfile,sim_type='RRM'):
      """
      computing the covariance matrix via plink
      """
  
      print("Using plink to create covariance matrix")
      cmd = '%s --bfile %s '%(plink_path,bfile)
  
      if sim_type=='RRM':
          # using variance standardization
          cmd += '--make-rel square '
      else:
          raise Exception('sim_type %s is not known'%sim_type)
  
      cmd+= '--out %s'%(os.path.join(out_dir,'plink'))
  
      subprocess.call(cmd,shell=True)
  
      # move file to specified file
      if sim_type=='RRM':
          old_fn = os.path.join(out_dir, 'plink.rel')
          os.rename(old_fn,cfile+'.cov')
  
          old_fn = os.path.join(out_dir, 'plink.rel.id')
          os.rename(old_fn,cfile+'.cov.id')
  
      if sim_type=='IBS':
          old_fn = os.path.join(out_dir, 'plink.mibs')
          os.rename(old_fn,cfile+'.cov')
  
          old_fn = os.path.join(out_dir, 'plink.mibs.id')
          os.rename(old_fn,cfile+'.cov.id')