Class: HTS::Bcf::Info

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

Constant Summary collapse

TYPE_CODES = 
{
  flag: Native::BCF_HT_FLAG, bool: Native::BCF_HT_FLAG,
  int: Native::BCF_HT_INT, int32: Native::BCF_HT_INT,
  int64: Native::BCF_HT_LONG, long: Native::BCF_HT_LONG,
  float: Native::BCF_HT_REAL, real: Native::BCF_HT_REAL,
  string: Native::BCF_HT_STR, str: Native::BCF_HT_STR
}.freeze

Instance Method Summary collapse

Constructor Details

#initialize(record) ⇒ Info

Returns a new instance of Info.



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# File 'lib/hts/bcf/info.rb', line 14

def initialize(record) = @record = record

Instance Method Details

#[](key) ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 36

def [](key) = get(key)

#[]=(key, value) ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 38

def []=(key, value)
  case value
  when nil then delete(key)
  when true, false then update_flag(key, value)
  when Integer
    unless int32?(value)
      raise RangeError,
            "Integer out of int32 range for []=. Current htslib backend does not support int64 INFO update."
    end

    update_int(key, [value])
  when Float then update_float(key, [value])
  when String then update_string(key, value)
  when Array
    raise ArgumentError, "Cannot set INFO field to empty array. Use nil to delete." if value.empty?

    if value.all? { |item| item.is_a?(Integer) }
      unless value.all? do |item|
        int32?(item)
      end
        raise RangeError,
              "Integer array contains out-of-int32 values for []=. Current htslib backend does not support int64 INFO update."
      end

      update_int(key, value)
    elsif value.all? { |item| item.is_a?(Numeric) }
      update_float(key, value)
    else
      raise ArgumentError, "INFO array must contain only integers or floats, got: #{value.map(&:class).uniq}"
    end
  else raise ArgumentError, "Unsupported INFO value type: #{value.class}"
  end
end

#delete(key) ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 82

def delete(key)
  schema = header.schema("INFO", key.to_s)
  return false unless schema && key?(key)

  native.info_update(header_native, key.to_s, TYPE_CODES.fetch(schema.first), false)
  true
end

#fields ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 96

def fields = native.info_fields(header_native)

#get(key, type = nil) ⇒ Object

Raises:



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# File 'lib/hts/bcf/info.rb', line 16

def get(key, type = nil)
  schema = header.schema("INFO", key.to_s)
  raise InfoDefinitionError, "INFO tag #{key} not defined in header" unless schema

  actual_type = schema.first
  requested = type&.to_sym
  if requested && !type_compatible?(actual_type, requested)
    raise InfoTypeError, "Tag #{key} is not #{type_label(requested)} INFO field"
  end

  code = TYPE_CODES.fetch(requested || actual_type)
  value = native.info_get(header_native, key.to_s, code)
  code == Native::BCF_HT_FLAG && value.nil? ? false : value
end

#get_flag(key) ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 35

def get_flag(key) = get(key, :flag)

#get_float(key) ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 32

def get_float(key) = get(key, :float)

#get_int(key) ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 31

def get_int(key) = get(key, :int)

#get_int64(key) ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 33

def get_int64(key) = get(key, :int64)

#get_string(key) ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 34

def get_string(key) = get(key, :string)

#key?(key) ⇒ Boolean Also known as: include?

Returns:

  • (Boolean) 


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# File 'lib/hts/bcf/info.rb', line 90

def key?(key)
  schema = header.schema("INFO", key.to_s)
  schema ? native.info_present?(header_native, key.to_s, TYPE_CODES.fetch(schema.first)) : false
end

#keys ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 97

def keys = fields.map { |field| field[:key] }

#length ⇒ Object Also known as: size 



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# File 'lib/hts/bcf/info.rb', line 98

def length = fields.length

#to_h ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 100

def to_h = fields.to_h { |field| [field[:name], get(field[:name])] }

#update_flag(key, present = true) ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 80

def update_flag(key, present = true) = update(key, Native::BCF_HT_FLAG, !!present, "flag")

#update_float(key, values) ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 73

def update_float(key, values) = update(key, Native::BCF_HT_REAL, Array(values).map(&:to_f), "float")

#update_int(key, values) ⇒ Object 



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

def update_int(key, values) = update(key, Native::BCF_HT_INT, Array(values).map { |value| Integer(value) }, "int")

#update_int64(_key, _values) ⇒ Object

Raises:



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# File 'lib/hts/bcf/info.rb', line 76

def update_int64(_key,
                       _values) = raise(UnsupportedInfoOperationError,
"htslib backend does not implement int64 INFO update (BCF_HT_LONG)")

#update_string(key, value) ⇒ Object 



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# File 'lib/hts/bcf/info.rb', line 74

def update_string(key, value) = update(key, Native::BCF_HT_STR, value.to_s, "string")