Class: HTS::Bcf

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/hts/bcf.rb,
lib/hts/bcf/info.rb,
lib/hts/bcf/format.rb,
lib/hts/bcf/header.rb,
lib/hts/bcf/record.rb

Defined Under Namespace

Classes: Format, Header, Info, Record

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(filename, mode = "r", threads: nil) ⇒ Bcf

Returns a new instance of Bcf.



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# File 'lib/hts/bcf.rb', line 29

def initialize(filename, mode = "r", threads: nil)
  raise "HTS::Bcf.new() dose not take block; Please use HTS::Bcf.open() instead" if block_given?

  @file_path = filename == "-" ? "-" : File.expand_path(filename)

  if mode[0] == "r" && !File.exist?(file_path)
    message = "No such VCF/BCF file - #{file_path}"
    raise message
  end

  @mode      = mode
  @hts_file  = LibHTS.hts_open(file_path, mode)

  if threads&.> 0
    r = LibHTS.hts_set_threads(@hts_file, threads)
    raise "Failed to set number of threads: #{threads}" if r < 0
  end

  return if mode[0] == "w"

  @header = Bcf::Header.new(@hts_file)
end

Instance Attribute Details

#file_path ⇒ Object (readonly)

Returns the value of attribute file_path.



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

def file_path
  @file_path
end

#header ⇒ Object (readonly)

Returns the value of attribute header.



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

def header
  @header
end

#mode ⇒ Object (readonly)

Returns the value of attribute mode.



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

def mode
  @mode
end

Class Method Details

.open ⇒ Object 



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# File 'lib/hts/bcf.rb', line 17

def self.open(...)
  file = new(...)
  return file unless block_given?

  begin
    yield file
  ensure
    file.close
  end
  file
end

Instance Method Details

#close ⇒ Object

Close the current file.



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# File 'lib/hts/bcf.rb', line 72

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

#closed? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bcf.rb', line 77

def closed?
  @hts_file.nil?
end

#each ⇒ Object 



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# File 'lib/hts/bcf.rb', line 89

def each
  return to_enum(__method__) unless block_given?

  while LibHTS.bcf_read(@hts_file, header, bcf1 = LibHTS.bcf_init) != -1
    record = Record.new(bcf1, header)
    yield record
  end
  self
end

#sample_count ⇒ Object 



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# File 'lib/hts/bcf.rb', line 81

def sample_count
  header.sample_count
end

#sample_names ⇒ Object 



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# File 'lib/hts/bcf.rb', line 85

def sample_names
  header.sample_names
end

#struct ⇒ Object 



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# File 'lib/hts/bcf.rb', line 52

def struct
  @hts_file
end

#to_ptr ⇒ Object 



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# File 'lib/hts/bcf.rb', line 56

def to_ptr
  @hts_file.to_ptr
end

#write(var) ⇒ Object 



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# File 'lib/hts/bcf.rb', line 66

def write(var)
  var_dup = var.dup = var.dup
  LibHTS.bcf_write(@hts_file, header, var_dup) > 0 || raise
end

#write_header ⇒ Object 



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# File 'lib/hts/bcf.rb', line 60

def write_header
  @header = header.dup
  LibHTS.hts_set_fai_filename(header, @file_path)
  LibHTS.bcf_hdr_write(@hts_file, header.struct)
end