Module: Bgzf

Defined in:
lib/rbbt/util/misc/bgzf.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#block_cache_size ⇒ Object

Returns the value of attribute block_cache_size.



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# File 'lib/rbbt/util/misc/bgzf.rb', line 6

def block_cache_size
  @block_cache_size
end

#compressed_stream ⇒ Object

Returns the value of attribute compressed_stream.



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# File 'lib/rbbt/util/misc/bgzf.rb', line 6

def compressed_stream
  @compressed_stream
end

#data_offset ⇒ Object

Returns the value of attribute data_offset.



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# File 'lib/rbbt/util/misc/bgzf.rb', line 6

def data_offset
  @data_offset
end

Class Method Details

.bgzip_cmd ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 8

def self.bgzip_cmd
  @@bgzip_cmd ||= begin
                    path = `bash -c "type -p bgzip"`.strip
                    if path.empty?
                      Rbbt.claim Rbbt.software.opt.htslib, :install, Rbbt.share.install.software.HTSLIB.find(:lib)
                      Rbbt.software.opt.htslib.produce
                      Rbbt.software.opt.htslib.bin.bgzip.find
                    else
                      path
                    end
                  end
end

.setup(compressed_stream) ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 21

def self.setup(compressed_stream)
  require 'bio-bgzf'
  reader = Bio::BGZF::Reader.new(compressed_stream)
  reader.extend Bgzf
  reader.compressed_stream = compressed_stream
  reader.data_offset = 0
  reader
end

Instance Method Details

#_get_block(vo) ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 135

def _get_block(vo)
  @blocks ||= {}
  @access ||= []
  @access << vo
  if @blocks.include? vo
    @blocks[vo]
  else
    _purge_cache
    @blocks[vo] ||= read_block_at vo
  end
end

#_index ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 50

def _index
  @_index ||= begin
                index = Persist.persist("BGZF index" + (filename || "").sub(/.bgz$/,''), :marshal, :dir => Rbbt.var.bgzf_index) do
                  index = []
                  pos = 0
                  while true do
                    blockdata_offset = tell
                    block = begin
                              read_block
                            rescue Exception
                              raise "BGZF seems to be buggy so some compressed files will not decompress right. Try uncompressing #{filename}" if $!.message =~ /BGFZ.*expected/
                              raise $!
                            end
                    break unless block
                    index << [pos, blockdata_offset]
                    pos += block.length
                  end
                  index
                end
                @block_cache_size = Math.log(index.length).to_i + 1
                index
             end
end

#_purge_cache ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 127

def _purge_cache
  if @blocks.length > @block_cache_size
    @access.uniq!
    oldest = @access.last
    @blocks.delete oldest
  end
end

#block_offset ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 119

def block_offset
  pos = data_offset
  i = closest_page(data_offset)
  page = _index[i][1]
  offset = pos - _index[i][0]
  [page, offset]
end

#close ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 40

def close
  @compressed_stream.close unless @compressed_stream.closed?
  @access.clear if @access
  @blocks.clear if @blocks
end

#closed? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/util/misc/bgzf.rb', line 36

def closed?
  @compressed_stream.closed?
end

#closest_page(pos) ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 88

def closest_page(pos)
  upper = _index.size - 1
  lower = 0
  @_index_pos ||= _index.collect{|v| v.first }

  return -1 if upper < lower

  while(upper >= lower) do
    idx = (idx.nil? and @last_idx) ? @last_idx : (lower + (upper - lower) / 2)
    pos_idx = @_index_pos[idx]

    case pos <=> pos_idx
    when 0
      break
    when -1
      upper = idx - 1
    when 1
      lower = idx + 1
    end
  end

  @last_idx = idx

  if pos_idx > pos
    idx = idx - 1
  end


  idx.to_i
end

#filename ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 30

def filename
  @filename ||= begin
                compressed_stream.respond_to?(:filename) ? compressed_stream.filename : nil
              end
end

#get_block ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 147

def get_block
  block_vo, offset = block_offset
  block = _get_block block_vo
  block[offset..-1]
end

#getc ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 170

def getc
  read(1)
end

#gets ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 174

def gets
  str = nil
  current = @data_offset
  while true
    block = read(Misc::BLOCK_SIZE)
    break if block.empty?
    str = "" if str.nil?
    if i = block.index("\n")
      str << block[0..i]
      break
    else
      str << block
    end
  end
  return nil if str.nil?

  @data_offset = current + str.length

  str
end

#init ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 84

def init
  _index
end

#read(size = nil) ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 153

def read(size=nil)
  return read_all if size.nil?

  block = get_block 
  return "" if block.nil? or block.empty?
  len = block.length
  if len >= size
    @data_offset += size
    return block[0..size-1]
  else
    @data_offset += len
    str = block
    str << read(size - len)
    str
  end
end

#read_all ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 74

def read_all
  str = ""
  while true
    block = read_block
    break if block.nil?
    str << block
  end
  str
end

#seek(off) ⇒ Object 



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# File 'lib/rbbt/util/misc/bgzf.rb', line 46

def seek(off)
  @data_offset = off
end