class

HTS::Bam::Header

Inherits Reference < Object

Constants

HD_TAG_MAP = {:version => "VN", :sort_order => "SO", :group_order => "GO", :subsorting => "SS"}

RG_TAG_MAP = {:id => "ID", :sample => "SM", :library => "LB", :platform => "PL", :platform_unit => "PU", :center => "CN", :description => "DS", :date => "DT", :flow_order => "FO", :key_sequence => "KS", :program => "PG", :insert_size => "PI", :molecule_topology => "PM"}

SQ_TAG_MAP = {:name => "SN", :length => "LN", :assembly => "AS", :md5 => "M5", :species => "SP", :uri => "UR", :alt_names => "AN"}

Constructors

new(hts_file : Pointer(HTS::LibHTS::HtsFile))

new(sam_hdr : Pointer(HTS::LibHTS::SamHdrT))

for clone

new

Class methods

parse(text)

Instance methods

add_pg(name, *args)

add_rg(id : String, **tags)

add_sq(name : String, length : Int, **tags)

append(line : String)

clone

count_lines(type : String) : Int32

delete_line(type : String, id_key : String | Nil = nil, id_value : String | Nil = nil) : Bool

delete_tag(type : String, id_key : String | Nil, id_value : String | Nil, key : String) : Bool

finalize

find_line(type : String, id_key : String | Nil = nil, id_value : String | Nil = nil) : String | Nil

find_tag(type : String, id_key : String | Nil, id_value : String | Nil, key : String) : String | Nil

get_tid(name)

experimental

line_index(type : String, key : String) : Int32

line_name(type : String, pos : Int) : String | Nil

remove_rg(id : String) : Bool

remove_sq(name : String) : Bool

target_count

target_len

target_name(tid)

target_names

to_s(io : IO)

Appends a short String representation of this object which includes its class name and its object address.

class Person
  def initialize(@name : String, @age : Int32)
  end
end

Person.new("John", 32).to_s # => #<Person:0x10a199f20>

to_unsafe

update_hd

update_rg(id : String, **tags)

update_sq(name : String, **tags)