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:



24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
 
# File 'lib/hts/bcf/header.rb', line 24

def initialize(arg = nil)
  case arg
  when LibHTS::HtsFile
    @bcf_hdr = LibHTS.bcf_hdr_read(arg)
  when LibHTS::BcfHdr
    @bcf_hdr = arg
  when nil
    @bcf_hdr = LibHTS.bcf_hdr_init("w")
  else
    raise TypeError, "Invalid argument"
  end

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

  yield self if block_given?
end

Instance Attribute Details

#subset_imap_pointer ⇒ Object (readonly)

Returns the value of attribute subset_imap_pointer.



93
94
95
 
# File 'lib/hts/bcf/header.rb', line 93

def subset_imap_pointer
  @subset_imap_pointer
end

#subset_samples ⇒ Object (readonly)

Returns the value of attribute subset_samples.



93
94
95
 
# File 'lib/hts/bcf/header.rb', line 93

def subset_samples
  @subset_samples
end

Instance Method Details

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



190
191
192
193
194
195
 
# File 'lib/hts/bcf/header.rb', line 190

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 



201
202
203
204
205
 
# File 'lib/hts/bcf/header.rb', line 201

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 



227
228
229
230
231
232
 
# File 'lib/hts/bcf/header.rb', line 227

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 



211
212
213
214
215
216
 
# File 'lib/hts/bcf/header.rb', line 211

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 



243
244
245
246
247
248
249
250
251
 
# File 'lib/hts/bcf/header.rb', line 243

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 



126
127
128
129
130
131
132
133
 
# File 'lib/hts/bcf/header.rb', line 126

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

  mark_sync_needed!
  sync_if_needed! if sync
  self
end

#append(line) ⇒ Object 



157
158
159
160
161
162
163
 
# File 'lib/hts/bcf/header.rb', line 157

def append(line)
  rc = LibHTS.bcf_hdr_append(@bcf_hdr, line)
  raise "Failed to append VCF header line" if rc.negative?

  mark_sync_needed!
  self
end

#delete(bcf_hl_type, key = nil) ⇒ Object

FIXME



165
166
167
168
169
170
171
 
# File 'lib/hts/bcf/header.rb', line 165

def delete(bcf_hl_type, key = nil) # FIXME
  existed = hrec_exists?(bcf_hl_type, key)
  type = bcf_hl_type_to_int(bcf_hl_type)
  LibHTS.bcf_hdr_remove(@bcf_hdr, type, key)
  mark_sync_needed! if existed
  existed
end

#edit ⇒ Object 



181
182
183
184
185
186
187
188
 
# File 'lib/hts/bcf/header.rb', line 181

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 



173
174
175
176
177
178
179
 
# File 'lib/hts/bcf/header.rb', line 173

def get_hrec(bcf_hl_type, key, value, str_class = nil)
  type = bcf_hl_type_to_int(bcf_hl_type)
  hrec = borrowed_hrec(type, key, value, str_class)
  return nil if hrec.to_ptr.null?

  HeaderRecord.new(owned_hrec(hrec))
end

#get_tid(name) ⇒ Object 



74
75
76
 
# File 'lib/hts/bcf/header.rb', line 74

def get_tid(name)
  name2id(name)
end

#get_version ⇒ Object 



53
54
55
 
# File 'lib/hts/bcf/header.rb', line 53

def get_version
  LibHTS.bcf_hdr_get_version(@bcf_hdr)
end

#id2name(id) ⇒ Object 



279
280
281
 
# File 'lib/hts/bcf/header.rb', line 279

def id2name(id)
  LibHTS.bcf_hdr_id2name(@bcf_hdr, id)
end

#merge(hdr) ⇒ Object 



135
136
137
138
139
140
141
142
143
 
# File 'lib/hts/bcf/header.rb', line 135

def merge(hdr)
  merged = LibHTS.bcf_hdr_merge(@bcf_hdr, hdr.struct)
  raise "Failed to merge BCF headers" if merged.to_ptr.null?

  @bcf_hdr = merged
  mark_sync_needed!
  sync_if_needed!
  self
end

#name2id(name) ⇒ Object 



275
276
277
 
# File 'lib/hts/bcf/header.rb', line 275

def name2id(name)
  LibHTS.bcf_hdr_name2id(@bcf_hdr, name)
end

#nsamples ⇒ Object 



66
67
68
 
# File 'lib/hts/bcf/header.rb', line 66

def nsamples
  LibHTS.bcf_hdr_nsamples(@bcf_hdr)
end

#read_bcf(fname) ⇒ Object 



153
154
155
 
# File 'lib/hts/bcf/header.rb', line 153

def read_bcf(fname)
  LibHTS.bcf_hdr_set(@bcf_hdr, fname)
end

#remove_contig(id) ⇒ Object 



197
198
199
 
# File 'lib/hts/bcf/header.rb', line 197

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

#remove_filter(id) ⇒ Object 



207
208
209
 
# File 'lib/hts/bcf/header.rb', line 207

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

#remove_format(id) ⇒ Object 



239
240
241
 
# File 'lib/hts/bcf/header.rb', line 239

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

#remove_info(id) ⇒ Object 



223
224
225
 
# File 'lib/hts/bcf/header.rb', line 223

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

#samples ⇒ Object 



86
87
88
89
90
91
 
# File 'lib/hts/bcf/header.rb', line 86

def samples
  # bcf_hdr_id2name is macro function
  @bcf_hdr[:samples]
    .read_array_of_pointer(nsamples)
    .map(&:read_string)
end

#seqnames ⇒ Object 



253
254
255
256
257
258
259
260
261
262
 
# File 'lib/hts/bcf/header.rb', line 253

def seqnames
  n = FFI::MemoryPointer.new(:int)
  names = LibHTS.bcf_hdr_seqnames(@bcf_hdr, n)
  begin
    names.read_array_of_pointer(n.read_int)
         .map(&:read_string)
  ensure
    LibHTS.hts_free(names) unless names.null?
  end
end

#set_version(version) ⇒ Object 



57
58
59
60
61
62
63
64
 
# File 'lib/hts/bcf/header.rb', line 57

def set_version(version)
  rc = LibHTS.bcf_hdr_set_version(@bcf_hdr, version)
  raise "Failed to set VCF header version" if rc.negative?

  mark_sync_needed!
  sync_if_needed!
  self
end

#struct ⇒ Object 



45
46
47
 
# File 'lib/hts/bcf/header.rb', line 45

def struct
  @bcf_hdr
end

#subset(samples) ⇒ Object

Raises:



103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
 
# File 'lib/hts/bcf/header.rb', line 103

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

  imap_pointer = nil
  if subset_samples.empty?
    subset_hdr = LibHTS.bcf_hdr_subset(@bcf_hdr, 0, ::FFI::Pointer::NULL, ::FFI::Pointer::NULL)
  else
    encoded_samples = subset_samples.map { |name| FFI::MemoryPointer.from_string(name) }
    sample_pointers = FFI::MemoryPointer.new(:pointer, subset_samples.length)
    sample_pointers.write_array_of_pointer(encoded_samples)
    imap_pointer = FFI::MemoryPointer.new(:int, subset_samples.length)
    subset_hdr = LibHTS.bcf_hdr_subset(@bcf_hdr, subset_samples.length, sample_pointers, imap_pointer)
  end

  raise SubsetError, "Failed to subset BCF header samples #{subset_samples.inspect}" if subset_hdr.to_ptr.null?

  composed_imap = compose_subset_imap(read_subset_imap(imap_pointer, subset_samples.length))
  self.class.new(subset_hdr).tap do |header|
    header.send(:set_subset_state, subset_samples, composed_imap)
  end
end

#subset? ⇒ Boolean

Returns:

  • (Boolean) 


95
96
97
 
# File 'lib/hts/bcf/header.rb', line 95

def subset?
  !@subset_imap.nil?
end

#subset_sample_count ⇒ Object 



99
100
101
 
# File 'lib/hts/bcf/header.rb', line 99

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

#sync ⇒ Object 



145
146
147
148
149
150
151
 
# File 'lib/hts/bcf/header.rb', line 145

def sync
  rc = LibHTS.bcf_hdr_sync(@bcf_hdr)
  raise "Failed to sync BCF header" if rc.negative?

  @sync_needed = false
  self
end

#target_count ⇒ Object 



70
71
72
 
# File 'lib/hts/bcf/header.rb', line 70

def target_count
  target_names.size
end

#target_name(rid) ⇒ Object 



78
79
80
 
# File 'lib/hts/bcf/header.rb', line 78

def target_name(rid)
  id2name(rid)
end

#target_names ⇒ Object 



82
83
84
 
# File 'lib/hts/bcf/header.rb', line 82

def target_names
  seqnames
end

#to_ptr ⇒ Object 



49
50
51
 
# File 'lib/hts/bcf/header.rb', line 49

def to_ptr
  @bcf_hdr.to_ptr
end

#to_s ⇒ Object 



264
265
266
267
268
269
270
271
272
273
 
# File 'lib/hts/bcf/header.rb', line 264

def to_s
  kstr = LibHTS::KString.new
  begin
    raise "Failed to get header string" if LibHTS.bcf_hdr_format(@bcf_hdr, 0, kstr).negative?

    kstr.read_string_copy
  ensure
    kstr.free_buffer
  end
end

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



234
235
236
237
 
# File 'lib/hts/bcf/header.rb', line 234

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 



218
219
220
221
 
# File 'lib/hts/bcf/header.rb', line 218

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