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.

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 11

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

  yield self if block_given?
end

Instance Method Details

#add_sample(sample, sync: true) ⇒ Object 



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

def add_sample(sample, sync: true)
  LibHTS.bcf_hdr_add_sample(@bcf_hdr, sample)
  self.sync if sync
end

#append(line) ⇒ Object 



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

def append(line)
  LibHTS.bcf_hdr_append(@bcf_hdr, line)
end

#delete(bcf_hl_type, key) ⇒ Object

FIXME



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

def delete(bcf_hl_type, key) # FIXME
  type = bcf_hl_type_to_int(bcf_hl_type)
  LibHTS.bcf_hdr_remove(@bcf_hdr, type, key)
end

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



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

def get_hrec(bcf_hl_type, key, value, str_class = nil)
  type = bcf_hl_type_to_int(bcf_hl_type)
  hrec = LibHTS.bcf_hdr_get_hrec(@bcf_hdr, type, key, value, str_class)
  HeaderRecord.new(hrec)
end

#get_version ⇒ Object 



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

def get_version
  LibHTS.bcf_hdr_get_version(@bcf_hdr)
end

#id2name(id) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 103

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

#merge(hdr) ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 58

def merge(hdr)
  LibHTS.bcf_hdr_merge(@bcf_hdr, hdr.struct)
end

#name2id(name) ⇒ Object 



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

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

#nsamples ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 42

def nsamples
  LibHTS.bcf_hdr_nsamples(@bcf_hdr)
end

#read_bcf(fname) ⇒ Object 



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

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

#samples ⇒ Object 



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

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

#seqnames ⇒ Object 



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

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

#set_version(version) ⇒ Object 



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

def set_version(version)
  LibHTS.bcf_hdr_set_version(@bcf_hdr, version)
end

#struct ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 26

def struct
  @bcf_hdr
end

#sync ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 62

def sync
  LibHTS.bcf_hdr_sync(@bcf_hdr)
end

#to_ptr ⇒ Object 



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

def to_ptr
  @bcf_hdr.to_ptr
end

#to_s ⇒ Object 



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# File 'lib/hts/bcf/header.rb', line 92

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

  kstr[:s]
end