Class: HTS::Bcf::Header

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

Overview

A class for working with VCF records. NOTE: This class has a lot of methods that are not stable. The method names and the number of arguments may change in the future.

Constant Summary collapse

BCF_TYPE_MAP = 
{
  int: "Integer",
  integer: "Integer",
  int32: "Integer",
  float: "Float",
  real: "Float",
  string: "String",
  str: "String",
  character: "Character",
  char: "Character",
  flag: "Flag"
}.freeze

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(arg = nil) {|_self| ... } ⇒ Header

Returns a new instance of Header.

Yields:

  • (_self)

Yield Parameters:



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# File 'lib/hts/bcf/header.rb', line 24

def initialize(arg = nil)
  case arg
  when Native::BcfHeaderHandle
    @native = arg
  when nil
    @native = Native::BcfHeaderHandle.create
  else
    raise TypeError, "Invalid argument"
  end

  @sync_depth = 0
  @sync_needed = false
  @schema_version = 0
  @subset_samples = nil
  @subset_imap = nil
  @subset_imap_pointer = nil

  yield self if block_given?
end

Instance Attribute Details

#schema_version ⇒ Object (readonly)

Returns the value of attribute schema_version.



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# File 'lib/hts/bcf/header.rb', line 83

def schema_version
  @schema_version
end

#subset_imap_pointer ⇒ Object (readonly)

Returns the value of attribute subset_imap_pointer.



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# File 'lib/hts/bcf/header.rb', line 83

def subset_imap_pointer
  @subset_imap_pointer
end

#subset_samples ⇒ Object (readonly)

Returns the value of attribute subset_samples.



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# File 'lib/hts/bcf/header.rb', line 83

def subset_samples
  @subset_samples
end

Instance Method Details

#add_contig(id, length: nil, **attributes) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 166

def add_contig(id, length: nil, **attributes)
  fields = [["ID", id.to_s]]
  fields << ["length", length.to_s] unless length.nil?
  fields.concat normalize_meta_attributes(attributes)
  append_structured_meta("contig", fields)
end

#add_filter(id, description:, **attributes) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 177

def add_filter(id, description:, **attributes)
  fields = [["ID", id.to_s], ["Description", description.to_s]]
  fields.concat normalize_meta_attributes(attributes)
  append_structured_meta("FILTER", fields)
end

#add_format(id, number:, type:, description:, **attributes) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 203

def add_format(id, number:, type:, description:, **attributes)
  fields = [["ID", id.to_s], ["Number", normalize_bcf_number(number)], ["Type", normalize_bcf_type(type)],
            ["Description", description.to_s]]
  fields.concat normalize_meta_attributes(attributes)
  append_structured_meta("FORMAT", fields)
end

#add_info(id, number:, type:, description:, **attributes) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 187

def add_info(id, number:, type:, description:, **attributes)
  fields = [["ID", id.to_s], ["Number", normalize_bcf_number(number)], ["Type", normalize_bcf_type(type)],
            ["Description", description.to_s]]
  fields.concat normalize_meta_attributes(attributes)
  append_structured_meta("INFO", fields)
end

#add_meta(key, value = nil, **attributes) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 219

def add_meta(key, value = nil, **attributes)
  if attributes.empty?
    append("###{key}=#{value}")
    sync_if_needed!
    self
  else
    append_structured_meta(key.to_s, normalize_meta_attributes(attributes))
  end
end

#add_sample(sample, sync: true) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 107

def add_sample(sample, sync: true)
  rc = @native.add_sample(sample)
  raise "Failed to add sample #{sample}" if rc.negative?

  mark_sync_needed!
  sync_if_needed! if sync
  self
end

#append(line) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 137

def append(line)
  rc = @native.append(line)
  raise "Failed to append VCF header line" if rc.negative?

  mark_sync_needed!
  self
end

#delete(bcf_hl_type, key = nil) ⇒ Object

FIXME



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# File 'lib/hts/bcf/header.rb', line 145

def delete(bcf_hl_type, key = nil) # FIXME
  existed = hrec_exists?(bcf_hl_type, key)
  @native.remove(bcf_hl_type.to_s, key)
  mark_sync_needed! if existed
  existed
end

#edit ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 157

def edit
  @sync_depth += 1
  yield self
  self
ensure
  @sync_depth -= 1
  sync_if_needed!
end

#get_hrec(bcf_hl_type, key, value, str_class = nil) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 152

def get_hrec(bcf_hl_type, key, value, str_class = nil)
  hrec = @native.get_hrec(bcf_hl_type.to_s, key, value, str_class)
  hrec ? HeaderRecord.new(hrec) : nil
end

#get_tid(name) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 67

def get_tid(name)
  name2id(name)
end

#get_version ⇒ Object Also known as: version 



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# File 'lib/hts/bcf/header.rb', line 44

def get_version
  @native.version
end

#id2name(id) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 241

def id2name(id)
  @native.id2name(id)
end

#merge(hdr) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 116

def merge(hdr)
  @native.merge(hdr.__send__(:native_handle))
  mark_sync_needed!
  sync_if_needed!
  self
end

#name2id(name) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 237

def name2id(name)
  @native.name2id(name)
end

#nsamples ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 59

def nsamples
  @native.nsamples
end

#read_bcf(fname) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 131

def read_bcf(fname)
  result = @native.read_file(fname)
  @schema_version += 1 unless result.negative?
  result
end

#remove_contig(id) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 173

def remove_contig(id)
  delete("CONTIG", id.to_s).tap { sync_if_needed! }
end

#remove_filter(id) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 183

def remove_filter(id)
  delete("FILTER", id.to_s).tap { sync_if_needed! }
end

#remove_format(id) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 215

def remove_format(id)
  delete("FORMAT", id.to_s).tap { sync_if_needed! }
end

#remove_info(id) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 199

def remove_info(id)
  delete("INFO", id.to_s).tap { sync_if_needed! }
end

#samples ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 79

def samples
  @native.samples
end

#seqnames ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 229

def seqnames
  @native.seqnames
end

#set_version(version) ⇒ Object Also known as: version= 



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# File 'lib/hts/bcf/header.rb', line 49

def set_version(version)
  rc = @native.set_version(version)
  raise "Failed to set VCF header version" if rc.negative?

  mark_sync_needed!
  sync_if_needed!
  self
end

#subset(samples) ⇒ Object

Raises:



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# File 'lib/hts/bcf/header.rb', line 93

def subset(samples)
  subset_samples = normalize_subset_samples(samples)
  validate_subset_samples!(subset_samples)

  result = @native.subset(subset_samples)
  raise SubsetError, "Failed to subset BCF header samples #{subset_samples.inspect}" unless result

  subset_header, imap = result
  composed_imap = compose_subset_imap(imap)
  self.class.new(subset_header).tap do |header|
    header.send(:set_subset_state, subset_samples, composed_imap)
  end
end

#subset? ⇒ Boolean

Returns:

  • (Boolean) 


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

def subset?
  !@subset_imap.nil?
end

#subset_sample_count ⇒ Object 



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

def subset_sample_count
  subset? ? @subset_samples.length : 0
end

#sync ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 123

def sync
  rc = @native.sync
  raise "Failed to sync BCF header" if rc.negative?

  @sync_needed = false
  self
end

#target_count ⇒ Object 



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

def target_count
  target_names.size
end

#target_name(rid) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 71

def target_name(rid)
  id2name(rid)
end

#target_names ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 75

def target_names
  seqnames
end

#to_s ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 233

def to_s
  @native.to_s
end

#update_format(id, number:, type:, description:, **attributes) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 210

def update_format(id, number:, type:, description:, **attributes)
  delete("FORMAT", id.to_s)
  add_format(id, number:, type:, description:, **attributes)
end

#update_info(id, number:, type:, description:, **attributes) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 194

def update_info(id, number:, type:, description:, **attributes)
  delete("INFO", id.to_s)
  add_info(id, number:, type:, description:, **attributes)
end