Class: Bio::BGZF::Reader

Inherits:
Object
  • Object
show all
Includes:
Bio::BGZF
Defined in:
lib/bio-bgzf/reader.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) ⇒ Reader

Returns a new instance of Reader.



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

def initialize(f)
  @f = f
  @cur_block = nil
end

Instance Attribute Details

#f ⇒ Object (readonly)

Returns the value of attribute f.



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# File 'lib/bio-bgzf/reader.rb', line 6

def f
  @f
end

Instance Method Details

#each_block ⇒ Object

Iterates over the blocks in a BGZF file, yielding [block, vo] pairs where



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# File 'lib/bio-bgzf/reader.rb', line 52

def each_block
  if block_given?
    while true
      pos = tell
      b = read_block
      break unless b
      yield b, pos
    end
  else
    enum_for(:each_block)
  end
end

#read_block ⇒ String

Reads the BGZF block at the current position. Returns its decompressed data.

Returns:

  • (String) —

    decompressed block data



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# File 'lib/bio-bgzf/reader.rb', line 27

def read_block
  decompress_block(f)
end

#read_block_at(vo) ⇒ String

Reads a portion of a BGZF block, starting from the given virtual offset. If the offset is the start of a block (low 16 bits are zero) the entire block’s data will be returned. Otherwise, the subset of the data starting at the given offset will be returned.

Parameters:

  • vo (Integer) —

    virtual offset to start from

Returns:

  • (String) —

    decompressed block data



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# File 'lib/bio-bgzf/reader.rb', line 39

def read_block_at(vo)
  block_offset = vo_block_offset(vo)
  data_offset = vo_data_offset(vo)
  f.seek(block_offset)
  block_data = decompress_block(f)
  if data_offset == 0
    return block_data
  else
    return block_data.slice(data_offset...block_data.size)
  end
end

#tell ⇒ Integer

Returns the reader’s current virtual offset. Between #read_block calls, the file position will always be at the start of a block or at EOF, so the low 16 bits of the virtual offset will always be zero.

Returns:

  • (Integer) —

    virtual offset for current position



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# File 'lib/bio-bgzf/reader.rb', line 19

def tell
  f.tell << 16
end