Class: Bio::BGZF::Writer

Inherits:
Object
  • Object
show all
Includes:
Bio::BGZF
Defined in:
lib/bio-bgzf/writer.rb

Constant Summary

Constants included from Bio::BGZF

CM, FLG, ID1, ID2, MAX_BYTES, MTIME, OS, SI1, SI2, SLEN, XFL, XLEN

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Bio::BGZF

decompress_block, pack, read_bgzf_block, unpack, vo_block_offset, vo_data_offset

Constructor Details

#initialize(f, level = 2) ⇒ Writer

Returns a new instance of Writer.



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# File 'lib/bio-bgzf/writer.rb', line 14

def initialize(f, level=2)
  @f = f
  @level = level
  @buf = ''
  @buf_write_pos = 0
  if block_given?
    begin
      yield self
    ensure
      self.close
    end
  end
end

Instance Attribute Details

#buf ⇒ Object (readonly)

Returns the value of attribute buf.



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# File 'lib/bio-bgzf/writer.rb', line 8

def buf
  @buf
end

#f ⇒ Object (readonly)

Returns the value of attribute f.



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# File 'lib/bio-bgzf/writer.rb', line 8

def f
  @f
end

#last_write_pos ⇒ Object (readonly)

Return the virtual offset of the last #write call. This is a hook for e.g. building an index on the fly.



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# File 'lib/bio-bgzf/writer.rb', line 12

def last_write_pos
  @last_write_pos
end

#level ⇒ Object (readonly)

Returns the value of attribute level.



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# File 'lib/bio-bgzf/writer.rb', line 8

def level
  @level
end

Instance Method Details

#_cur_write_pos ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



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# File 'lib/bio-bgzf/writer.rb', line 43

def _cur_write_pos
  @buf_write_pos + buf.bytesize
end

#_each_slice(s) ⇒ Object 



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# File 'lib/bio-bgzf/writer.rb', line 63

def _each_slice(s)
  n = 0
  size = s.bytesize
  while true
    offset = n * MAX_BYTES
    break if offset >= size
    yield s.slice(offset, MAX_BYTES)
    n += 1
  end
end

#close ⇒ Object 



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# File 'lib/bio-bgzf/writer.rb', line 74

def close
  write_buf
  f.close
end

#tell ⇒ Object 



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# File 'lib/bio-bgzf/writer.rb', line 28

def tell
  f.tell << 16
end

#write(s) ⇒ Object 



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# File 'lib/bio-bgzf/writer.rb', line 47

def write(s)
  if s.bytesize > MAX_BYTES
    write_buf
    @last_write_pos = _cur_write_pos
    _each_slice(s) do |slice|
      write(slice)
    end
  else
    if (s.bytesize + buf.bytesize) > MAX_BYTES
      write_buf
    end
    @last_write_pos = _cur_write_pos
    buf << s
  end
end

#write_buf ⇒ Object 



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# File 'lib/bio-bgzf/writer.rb', line 32

def write_buf
  if buf.size > 0
    raise "Buffer too large: #{buf.bytesize}" if buf.bytesize > MAX_BYTES
    block = pack(buf, level)
    f.write(block)
    @buf = ''
    @buf_write_pos = tell
  end
end