old_contents: """
  The executor of AsmVar2 and it just could be called by ``Asmvar.py``
  """
  import variantutil as vutil
  import haplotype
  
  class VariantCaller(object):
      """
      A class for variants' calling.
  
      Input required:
          (1) Long reads or genome VS genome alignment files, sam/bam format
              and must be sorted
          (2) Target genome(Reference) fasta, has been index (.fai)
          (3) Query genome fasta, has been index (.fai)
      """
      def __init__(self, alignfile, targetfile, queryfile, options):
          """
          Constructor.
  
          """
          self.align_input = alignfile
          self.target_fa   = targetfile
          self.query_fa    = queryfile
          self.opt         = options
      
  
  
  class VariantGenotype(object):
      """
      A class for variants' genotyping.
  
      Input required:
          (1) VCF files, bgzip format and has been index(.tbi) by tabix
          (2) Short reads' alignment files, sam/bam format and hash been
              sorted and index (.bai)
          (3) Reference fasta, has been index(.fai)
      
      """
      def __init__(self, vcffile, bamfile, referencefasta, options):
          """
          Constructor.
  
          """
          self.vcf_infile = vcffile
          self.bam_input  = bamfile
          self.ref_fasta  = referencefasta
          self.opt = options
          
  
  
new_contents: """
  The executor of AsmVar2 and it just could be called by ``Asmvar.py``
  """
  import pysam
  import vcf
  
  import variantutil as vutil
  import haplotype
  
  class VariantCaller(object):
      """
      A class for variants' calling.
  
      Input required:
          (1) Long reads or genome VS genome alignment files, sam/bam format
              and must be sorted
          (2) Target genome(Reference) fasta, has been index (.fai)
          (3) Query genome fasta, has been index (.fai)
      """
      def __init__(self, alignfile, targetfile, queryfile, options):
          """
          Constructor.
  
          """
          self.align_input = alignfile
          self.target_fa   = targetfile
          self.query_fa    = queryfile
          self.opt         = options
      
  
  
  class VariantGenotype(object):
      """
      A class for variants' genotyping.
  
      Input required:
          (1) VCF files [list], bgzip format and has been index(.tbi) by tabix
          (2) Short reads' alignment files[list], sam/bam format and hash been
              sorted and index (.bai)
          (3) Reference fasta, has been index(.fai)
      
      """
      def __init__(self, vcffiles, bamfiles, referencefasta, options = None):
          """
          Constructor.
  
          """
          # Perhaps I should check the files before I open them?!
          # Checking whether vcffiles been tabix or not
          # Checking whether bamfiles been index or not
          # Checking whether fastafile been tabix or not
          self.ref_fasta   = pysam.FastaFile(referencefasta)
          self.vcf_readers = vutil.VariantCandidateReader(vcffiles)
          self.bam_readers = [pysam.AlignmentFile(bf) for bf in bamfiles]
          self.opt         = options
          
  
  
  
  
  
subject: add parameters for VariantGenotype module