Class: Bio::AssemblyGraphAlgorithms::BamProbeReadSelector

Inherits:
Object
  • Object
show all
Includes:
FinishM::Logging
Defined in:
lib/assembly/bam_probe_read_selector.rb

Instance Method Summary collapse

Methods included from FinishM::Logging

#log

Instance Method Details

#find_probe_read_alignment_from_contig_end(indexed_bam_file, contig_name, direction, position, kmer) ⇒ Object

Given a contig name and a side, together with a path to an indexed bam file, pick out a read that can be used to ‘locate’ the contig end in the assembly, and return a Bio::DB::Alignment object of it



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# File 'lib/assembly/bam_probe_read_selector.rb', line 23

def find_probe_read_alignment_from_contig_end(indexed_bam_file, contig_name, direction, position, kmer)
  # Search for all reads that overlap the overhang base, and are in the correct direction
  sam = Bio::DB::Sam.new(:bam => indexed_bam_file)
  position_hash = {:chr => contig_name}

  # The probes must overlap the position, to one back from
  # the contig end
  if direction
    position_hash[:start] = position-1
    position_hash[:stop] = position
  else
    position_hash[:start] = position
    position_hash[:stop] = position+1
  end
  sam.each_alignment(position_hash) do |alignment|
    # Reject reads that do not have matching stretches of DNA that are at least kmer length long
    # as these will not be included in the assembly.
    # If it passes, then return the alignment

  end

  # Return the 'best' read's name and sequence.
end

#find_probes(indexed_bam_file, contig_names_positions_directions, kmer, path_to_cny_unified_seq_names_file) ⇒ Object

Given an indexed bam file of reads mapped onto contigs, an array of one or more [contig_name, position, direction] entries (i.e. places in the contigs to locate reads for), a kmer (the match has to be at least one perfect kmer overlapping the position) and a path to a CnyUnifiedSeq.names file, return an Array of read_IDs of reads that can be used to locate the contig ends in the velvet graph.

This assumes that velvet hasn’t done anything to clean up the graph as cleaning might remove reads of interest



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# File 'lib/assembly/bam_probe_read_selector.rb', line 16

def find_probes(indexed_bam_file, contig_names_positions_directions, kmer, path_to_cny_unified_seq_names_file)
  # need to check the sequence of the aligned read is the same as what is in the cny_unified_seq_names_file
end