Class: Bio::Bam::AlignmentIterator

Inherits:
Object
  • Object
show all
Includes:
SambambaStderrParser, Enumerable
Defined in:
lib/bio-sambamba/alignmentiterator.rb

Overview

Class for iterating through alignments

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(command, references) ⇒ AlignmentIterator

Creates a new AlignmentIterator object which will parse JSON outputted by a specified command. Names of reference sequences must be provided as well.



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 12

def initialize(command, references)
  @command = command
  @references = references
end

Instance Attribute Details

#chromosome ⇒ Object

Returns the value of attribute chromosome.



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 125

def chromosome
  @chromosome
end

#command ⇒ Object

Returns the value of attribute command.



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 127

def command
  @command
end

#region ⇒ Object

Returns the value of attribute region.



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 126

def region
  @region
end

Instance Method Details

#[](reg) ⇒ Object 



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 114

def [](reg)
  overlapping(reg)
end

#clone ⇒ Object 



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 118

def clone
  iter = AlignmentIterator.new @command, @references
  iter.chromosome = chromosome
  iter.region = region
  iter
end

#count ⇒ Object 



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 93

def count
  command = get_command
  command.push('-c')
  Bio::Command.call_command_open3(command) do |pin, pout, perr|
    raise_exception_if_stderr_is_not_empty(perr)
    pout.readline.to_i
  end
end

#each ⇒ Object

Iterate through all alignments skipping validation checks



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 56

def each
  return enum_for(:each) if not block_given?

  command = get_command

  Bio::Command.call_command_open3(command) do |pin, pout, perr|

    counter = 0 # for triggering garbage collection manually
    unpacker = MessagePack::Unpacker.new pout

    begin
      unpacker.each do |obj|
        counter += 1
        yield Bio::Bam::Alignment.new(obj, @references)
        if (counter & 0xFFF) == 0 then
          ObjectSpace.garbage_collect
        end
      end
    rescue EOFError
    end

    raise_exception_if_stderr_is_not_empty(perr)
  end
end

#each_valid ⇒ Object

Iterate only through valid alignments



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 18

def each_valid

  return enum_for(:each_valid) if not block_given?

  command = get_command
  if command.index('--valid').nil?
    command.push '--valid'
  end

  iter = self.clone
  iter.command = command
  iter.each do |read|
    yield read
  end
end

#overlapping(reg) ⇒ Object 



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 108

def overlapping(reg)
  iter = self.clone
  iter.region = reg
  iter
end

#referencing(chr) ⇒ Object 



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 102

def referencing(chr)
  iter = self.clone
  iter.chromosome = chr
  iter
end

#select(&block) ⇒ Object 



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 89

def select(&block)
  with_filter (Bio::Bam::filter &block)
end

#with_filter(filter) ⇒ Object

Set filter for alignments



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# File 'lib/bio-sambamba/alignmentiterator.rb', line 82

def with_filter(filter)
  iter = self.clone
  iter.command.push('-F')
  iter.command.push(filter.to_s)
  iter
end