original_docstring: 
          Worker function for splitting the FASTQ file into smaller chunks
  
          Parameters
          ----------
          genome_fa : str
              Location of the FASTA file of the genome to align the reads to
          genome_idx : str
              Location of the index files in .tar.gz file prepared by the BWA
              indexer
          fastq_file : str
              Location of the FASTQ file
          output_bam : str
              Location of the aligned reads in bam format
          
docstring: Worker function for splitting the FASTQ file into smaller chunks
  Parameters
  
  genome_fa : str
  Location of the FASTA file of the genome to align the reads to
  genome_idx : str
  Location of the index files in .tar.gz file prepared by the BWA
  indexer
  fastq_file : str
  Location of the FASTQ file
  output_bam : str
  Location of the aligned reads in bam format
docstring_tokens: Worker function for splitting the FASTQ file into smaller chunks Parameters genome_fa : str Location of the FASTA file of the genome to align the reads to genome_idx : str Location of the index files in . tar . gz file prepared by the BWA indexer fastq_file : str Location of the FASTQ file output_bam : str Location of the aligned reads in bam format
code: def work(self):
          """
          Worker function for splitting the FASTQ file into smaller chunks
  
          Parameters
          ----------
          genome_fa : str
              Location of the FASTA file of the genome to align the reads to
          genome_idx : str
              Location of the index files in .tar.gz file prepared by the BWA
              indexer
          fastq_file : str
              Location of the FASTQ file
          output_bam : str
              Location of the aligned reads in bam format
          """
          bwa_handle = bwaAlignerMEMTool({"no-untar" : True})
          bwa_handle.bwa_aligner_single(
              self.genome_fa,
              self.fastq_file,
              self.output_bam,
              self.genome_idx,
              {}
          )
  
          bam_handle = bamUtilsTask()
          bam_handle.bam_sort(self.output_bam)
code_tokens: def work ( self ) : bwa_handle = bwaAlignerMEMTool ( { "no-untar" : True } ) bwa_handle . bwa_aligner_single ( self . genome_fa , self . fastq_file , self . output_bam , self . genome_idx , { } ) bam_handle = bamUtilsTask ( ) bam_handle . bam_sort ( self . output_bam )
short_docstring: Worker function for splitting the FASTQ file into smaller chunks
  Parameters
short_docstring_tokens: Worker function for splitting the FASTQ file into smaller chunks Parameters
comment: """
          Worker function for splitting the FASTQ file into smaller chunks
  
          Parameters
          ----------
          genome_fa : str
              Location of the FASTA file of the genome to align the reads to
          genome_idx : str
              Location of the index files in .tar.gz file prepared by the BWA
              indexer
          fastq_file : str
              Location of the FASTQ file
          output_bam : str
              Location of the aligned reads in bam format
          """