Class: HTS::Bam::Pileup

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/hts/bam/pileup.rb

Instance Method Summary collapse

Constructor Details

#initialize(bam) ⇒ Pileup

Returns a new instance of Pileup.



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# File 'lib/hts/bam/pileup.rb', line 6

def initialize(bam)
  @bam = bam
  # typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);
  f = FFI::Function.new(:int, %i[pointer pointer], blocking: true) do |_data, _b|
    0
  end
  pt = FFI::MemoryPointer.new(:pointer)
  @iterator = LibHTS.bam_plp_init(f, pt)
  raise "Failed to initialize pileup" if @iterator.null?
end

Instance Method Details

#each(&block) ⇒ Object 



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# File 'lib/hts/bam/pileup.rb', line 17

def each(&block)
  return enum_for(:each) unless block_given?

  @bam.each do |record|
    raise "Failed to push BAM record" if LibHTS.bam_plp_push(@iterator, record.struct) < 0

    while (entries = fetch_next_pileup)
      entries.each(&block)
    end
  end
  # Signal the end of the BAM stream by pushing a NULL record
  LibHTS.bam_plp_push(@iterator, nil)
end