comparison pileup_to_vcf.py @ 1:bb0ac51f1b02

Handle delection char: *

0:3890f8ba0e4d

  parser = optparse.OptionParser()
  # files
  parser.add_option( '-i', '--input', dest='input', help='The input pileup file (else read from stdin)' )
  parser.add_option( '-o', '--output', dest='output', help='The output vcf file (else write to stdout)' )
  # filters
  parser.add_option( '-c', '--min_coverage', type='int', default='0', dest='min_coverage', help='The minimum read coverage depth to report a variant [default 0]' )
  parser.add_option( '-r', '--report_depth', type='choice', choices=['all','ref','qual'], default='ref', dest='report_depth', help='Coverage depth as: ref - reads covercovering base, all - reads spanning base, qual - reads with base call above min_base_quality' )
  parser.add_option( '-b', '--min_base_quality', type='int', default='0', dest='min_base_quality', help='The minimum base quality for a base call to be counted' )
  parser.add_option( '-f', '--min_allele_freq', type='float', default='.5', dest='min_allele_freq', help='The minimum frequency of an allele for it to be reported (default .5)' )
  parser.add_option( '-m', '--allow_multiples', action="store_true", dest='allow_multiples', default=False, help='Allow multiple alleles to be reported' )
  parser.add_option( '-s', '--snps_only', action="store_true", dest='snps_only', default=False, help='Only report SNPs, not indels' )

            max_deletion = max(indel_len,max_deletion)
            if indel in deletions: 
              deletions[indel] += 1
            else:
              deletions[indel] = 1
        elif base == '^' : #start of read (followed by read quality char)
          read_mapping_qual = ord(bases[bi]) - 33 
          bi += 1
        elif base == '$' : #end of read
          pass # no associated quality in either bases or quals
      dp = rdp if dp_as == 'ref' else qdp if dp_as == 'qual' else adp
      if debug: print >> sys.stderr, "snps: %s\tins: %s\tdel: %s" % (snps,insertions,deletions)
      # output any variants that meet the depth coverage requirement
      vcf_pos = pos
      vcf_ref = ref
      suffix = ''
      alts = []

1:bb0ac51f1b02

  parser = optparse.OptionParser()
  # files
  parser.add_option( '-i', '--input', dest='input', help='The input pileup file (else read from stdin)' )
  parser.add_option( '-o', '--output', dest='output', help='The output vcf file (else write to stdout)' )
  # filters
  parser.add_option( '-c', '--min_coverage', type='int', default='1', dest='min_coverage', help='The minimum read coverage depth to report a variant [default 1]' )
  parser.add_option( '-r', '--report_depth', type='choice', choices=['all','ref','qual'], default='ref', dest='report_depth', help='Coverage depth as: ref - reads covercovering base, all - reads spanning base, qual - reads with base call above min_base_quality' )
  parser.add_option( '-b', '--min_base_quality', type='int', default='0', dest='min_base_quality', help='The minimum base quality for a base call to be counted' )
  parser.add_option( '-f', '--min_allele_freq', type='float', default='.5', dest='min_allele_freq', help='The minimum frequency of an allele for it to be reported (default .5)' )
  parser.add_option( '-m', '--allow_multiples', action="store_true", dest='allow_multiples', default=False, help='Allow multiple alleles to be reported' )
  parser.add_option( '-s', '--snps_only', action="store_true", dest='snps_only', default=False, help='Only report SNPs, not indels' )

            max_deletion = max(indel_len,max_deletion)
            if indel in deletions: 
              deletions[indel] += 1
            else:
              deletions[indel] = 1
        elif base == '*' : # a deletion from a prior base
          qi += 1
        elif base == '^' : #start of read (followed by read quality char)
          read_mapping_qual = ord(bases[bi]) - 33 
          bi += 1
        elif base == '$' : #end of read
          pass # no associated quality in either bases or quals
      dp = rdp if dp_as == 'ref' else qdp if dp_as == 'qual' else adp
      if debug: print >> sys.stderr, "snps: %s\tins: %s\tdel: %s" % (snps,insertions,deletions)
      if dp < max(1,min_coverage) :
        continue
      # output any variants that meet the depth coverage requirement
      vcf_pos = pos
      vcf_ref = ref
      suffix = ''
      alts = []