Class: HTS::Bam::Pileup

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

Defined Under Namespace

Classes: BorrowedColumnView, BorrowedEntryView, PileupColumn, PileupRecord

Constant Summary collapse

BASE_COUNT_FIELDS = 
%i[depth a c g t n forward reverse deletion insertion].freeze

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(bam, region: nil, beg: nil, end_: nil, maxcnt: nil) ⇒ Pileup

Returns a new instance of Pileup.

Raises:

  • (ArgumentError) 


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# File 'lib/hts/bam/pileup.rb', line 82

def initialize(bam, region: nil, beg: nil, end_: nil, maxcnt: nil)
  raise ArgumentError, "beg and end_ must be specified together" if beg.nil? != end_.nil?
  raise ArgumentError, "region is required when beg/end_ are specified" if !beg.nil? && region.nil?

  @bam = bam
  @header = bam.header
  if region && !bam.__send__(:ensure_index_loaded)
    raise "Index file is required to use region pileup."
  end
  @native = Native::PileupHandle.open(
    bam.__send__(:native_handle), @header.__send__(:native_handle), region, beg, end_, maxcnt
  )
end

Class Method Details

.open(*args, **keywords) ⇒ Object 



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# File 'lib/hts/bam/pileup.rb', line 11

def self.open(*args, **keywords)
  pileup = new(*args, **keywords)
  return pileup unless block_given?

  begin
    yield pileup
  ensure
    pileup.close
  end
  pileup
end

Instance Method Details

#close ⇒ Object 



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# File 'lib/hts/bam/pileup.rb', line 163

def close = @native&.close

#each ⇒ Object 



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# File 'lib/hts/bam/pileup.rb', line 96

def each
  return to_enum(__method__) unless block_given?

  each_raw_column do |tid, pos, rows|
    alignments = rows.map { |row| PileupRecord.new(row, @header) }
    yield PileupColumn.new(tid:, pos:, alignments:)
  end
  self
end

#each_base_counts(min_base_quality: 0, min_mapping_quality: 0) ⇒ Object 



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# File 'lib/hts/bam/pileup.rb', line 130

def each_base_counts(min_base_quality: 0, min_mapping_quality: 0)
  return to_enum(__method__, min_base_quality:, min_mapping_quality:) unless block_given?

  min_base_quality = Integer(min_base_quality)
  min_mapping_quality = Integer(min_mapping_quality)
  if min_base_quality.negative? || min_mapping_quality.negative?
    raise ArgumentError,
          "quality thresholds must be non-negative"
  end

  counts = Array.new(BASE_COUNT_FIELDS.length, 0)
  each_raw_column do |tid, pos, rows|
    counts.fill(0)
    rows.each do |row|
      next if row[6] || row[10] < min_mapping_quality

      if row[3] || row[1].negative?
        counts[8] += 1
      else
        next if row[9] < min_base_quality

        counts[{ 1 => 1, 2 => 2, 4 => 3, 8 => 4 }.fetch(row[8], 5)] += 1
      end
      counts[0] += 1
      counts[(row[7] & 16).zero? ? 6 : 7] += 1
      counts[9] += 1 if row[2].positive?
    end
    yield tid, pos, counts
  end
  self
end

#each_depth ⇒ Object 



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# File 'lib/hts/bam/pileup.rb', line 106

def each_depth
  return to_enum(__method__) unless block_given?

  each_raw_column { |tid, pos, rows| yield tid, pos, rows.length }
  self
end

#each_entry_raw ⇒ Object 



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# File 'lib/hts/bam/pileup.rb', line 121

def each_entry_raw
  return to_enum(__method__) unless block_given?

  each_raw_column do |tid, pos, rows|
    rows.each { |row| yield tid, pos, row[1], row[7], row[8], row[9] }
  end
  self
end

#each_view ⇒ Object 



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# File 'lib/hts/bam/pileup.rb', line 113

def each_view
  return to_enum(__method__) unless block_given?

  view = BorrowedColumnView.new
  each_raw_column { |tid, pos, rows| yield view.reset(rows, tid, pos) }
  self
end

#reset ⇒ Object 



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# File 'lib/hts/bam/pileup.rb', line 162

def reset = @native.reset