Class: HTS::Hts

Inherits:
Object
  • Object
show all
Defined in:
lib/hts/hts.rb

Direct Known Subclasses

Bam, Bcf, Tbx

Instance Method Summary collapse

Instance Method Details

#close ⇒ Object 



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# File 'lib/hts/hts.rb', line 30

def close
  return if closed?

  LibHTS.hts_close(@hts_file)
  @hts_file = nil
end

#closed? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/hts.rb', line 37

def closed?
  @hts_file.nil? || @hts_file.null?
end

#format ⇒ Object 



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# File 'lib/hts/hts.rb', line 15

def format
  LibHTS.hts_get_format(@hts_file)[:format].to_s
end

#format_version ⇒ Object 



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# File 'lib/hts/hts.rb', line 19

def format_version
  v = LibHTS.hts_get_format(@hts_file)[:version]
  major = v[:major]
  minor = v[:minor]
  if minor == -1
    major.to_s
  else
    "#{major}.#{minor}"
  end
end

#rewind ⇒ Object 



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# File 'lib/hts/hts.rb', line 63

def rewind
  if @start_position
    r = seek(@start_position)
    raise "Failed to rewind: #{r}" if r < 0

    tell
  else
    raise "Cannot rewind: no start position"
  end
end

#seek(offset) ⇒ Object 



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# File 'lib/hts/hts.rb', line 41

def seek(offset)
  if @hts_file[:is_cram] == 1
    LibHTS.cram_seek(@hts_file[:fp][:cram], offset, IO::SEEK_SET)
  elsif @hts_file[:is_bgzf] == 1
    LibHTS.bgzf_seek(@hts_file[:fp][:bgzf], offset, IO::SEEK_SET)
  else
    LibHTS.hseek(@hts_file[:fp][:hfile], offset, IO::SEEK_SET)
  end
end

#struct ⇒ Object 



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# File 'lib/hts/hts.rb', line 7

def struct
  @hts_file
end

#tell ⇒ Object 



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# File 'lib/hts/hts.rb', line 51

def tell
  if @hts_file[:is_cram] == 1
    # LibHTS.cram_tell(@hts_file[:fp][:cram])
    # warn 'cram_tell is not implemented in c htslib'
    nil
  elsif @hts_file[:is_bgzf] == 1
    LibHTS.bgzf_tell(@hts_file[:fp][:bgzf])
  else
    LibHTS.htell(@hts_file[:fp][:hfile])
  end
end

#to_ptr ⇒ Object 



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

def to_ptr
  @hts_file.to_ptr
end