original_docstring:  Wrap toil-vg run as a shell command.  Expects reads to be in single fastq
          inputs can be None if toil-vg supports not having them (ie don't need to 
          include gcsa_path if want to reindex)
          
docstring: Wrap toil-vg run as a shell command.  Expects reads to be in single fastq
  inputs can be None if toil-vg supports not having them
docstring_tokens: Wrap toil - vg run as a shell command . Expects reads to be in single fastq inputs can be None if toil - vg supports not having them
code: def _toil_vg_run(self, sample_name, chrom, graph_path, xg_path, gcsa_path, fq_path,
                       true_vcf_path, fasta_path, interleaved, mapper, misc_opts, genotype, tag):
          """ Wrap toil-vg run as a shell command.  Expects reads to be in single fastq
          inputs can be None if toil-vg supports not having them (ie don't need to 
          include gcsa_path if want to reindex)
          """
  
          job_store = self._jobstore(tag)
          out_store = self._outstore(tag)
          opts = ' '.join(self._toil_vg_io_opts()) + ' '
          if self.vg_docker:
              opts += '--vg_docker {} '.format(self.vg_docker)
          if self.container:
              opts += '--container {} '.format(self.container)
          if chrom:
              opts += '--chroms {} '.format(chrom)
          if graph_path:
              opts += '--graphs {} '.format(graph_path)
          if xg_path:
              opts += '--xg_index {} '.format(xg_path)
          if gcsa_path:
              opts += '--gcsa_index {} '.format(gcsa_path)
          if fq_path:
              opts += '--fastq {} '.format(fq_path)
          if true_vcf_path:
              opts += '--vcfeval_baseline {} '.format(true_vcf_path)
              opts += '--vcfeval_fasta {} '.format(fasta_path)
              opts += '--vcfeval_opts \' --ref-overlap --vcf-score-field GQ\'  '
          if interleaved:
              opts += '--interleaved '
          opts += '--mapper {} '.format(mapper)
          if misc_opts:
              opts += ' {} '.format(misc_opts)
          opts += '--gcsa_index_cores {} \
          --alignment_cores {} --calling_cores {} --calling_cores {} --vcfeval_cores {} '.format(
              self.cores, self.cores, self.cores, int(max(1, self.cores / 4)),
              int(max(1, self.cores / 2)), self.cores)
          
          cmd = 'toil-vg run {} {} {} {}'.format(job_store, sample_name, out_store, opts)
          print(("Run toil-vg with {}".format(cmd)))
          
          subprocess.check_call(cmd, shell=True)
code_tokens: def _toil_vg_run ( self , sample_name , chrom , graph_path , xg_path , gcsa_path , fq_path , true_vcf_path , fasta_path , interleaved , mapper , misc_opts , genotype , tag ) : job_store = self . _jobstore ( tag ) out_store = self . _outstore ( tag ) opts = ' ' . join ( self . _toil_vg_io_opts ( ) ) + ' ' if self . vg_docker : opts += '--vg_docker {} ' . format ( self . vg_docker ) if self . container : opts += '--container {} ' . format ( self . container ) if chrom : opts += '--chroms {} ' . format ( chrom ) if graph_path : opts += '--graphs {} ' . format ( graph_path ) if xg_path : opts += '--xg_index {} ' . format ( xg_path ) if gcsa_path : opts += '--gcsa_index {} ' . format ( gcsa_path ) if fq_path : opts += '--fastq {} ' . format ( fq_path ) if true_vcf_path : opts += '--vcfeval_baseline {} ' . format ( true_vcf_path ) opts += '--vcfeval_fasta {} ' . format ( fasta_path ) opts += '--vcfeval_opts \' --ref-overlap --vcf-score-field GQ\'  ' if interleaved : opts += '--interleaved ' opts += '--mapper {} ' . format ( mapper ) if misc_opts : opts += ' {} ' . format ( misc_opts ) opts += '--gcsa_index_cores {} \
          --alignment_cores {} --calling_cores {} --calling_cores {} --vcfeval_cores {} ' . format ( self . cores , self . cores , self . cores , int ( max ( 1 , self . cores / 4 ) ) , int ( max ( 1 , self . cores / 2 ) ) , self . cores ) cmd = 'toil-vg run {} {} {} {}' . format ( job_store , sample_name , out_store , opts ) print ( ( "Run toil-vg with {}" . format ( cmd ) ) ) subprocess . check_call ( cmd , shell = True )
short_docstring: Wrap toil-vg run as a shell command.
short_docstring_tokens: Wrap toil - vg run as a shell command .
comment: """ Wrap toil-vg run as a shell command.  Expects reads to be in single fastq
          inputs can be None if toil-vg supports not having them (ie don't need to 
          include gcsa_path if want to reindex)
          """