1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
|
require_relative "error.rb"
# Array of {RGFA::CIGAR::Operation CIGAR operations}.
# Represents the contents of a CIGAR string.
class RGFA::CIGAR < Array
# Compute the CIGAR for the segments when these are switched.
#
# @example Computing the complement CIGAR
#
# RGFA::CIGAR.from_string("2M1D3M").complement.to_s
# # => "3M1I2M"
#
# # S1 + S2 + 2M1D3M
# #
# # S1+ ACGACTGTGA
# # S2+ CT-TGACGG
# #
# # S2- CCGTCA-AG
# # S1- TCACAGTCGT
# #
# # S2 - S1 - 3M1I2M
#
# @return [RGFA::CIGAR] (empty if CIGAR string is *)
def complement
reverse.map do |op|
if op.code == :I
op.code = :D
elsif op.code == :D
op.code = :I
end
op
end
end
# Parse a CIGAR string into an array of CIGAR operations.
#
# Each operation is represented by a {RGFA::CIGAR::Operation},
# i.e. a tuple of operation length and operation
# symbol (one of MIDNSHPX=).
#
# @return [RGFA::CIGAR] (empty if string is *)
# @raise [RGFA::CIGAR::ValueError] if the string is not a valid CIGAR string
def self.from_string(str)
a = RGFA::CIGAR.new
if str != "*"
raise RGFA::CIGAR::ValueError if str !~ /^([0-9]+[MIDNSHPX=])+$/
str.scan(/[0-9]+[MIDNSHPX=]/).each do |op|
len = op[0..-2].to_i
code = op[-1..-1].to_sym
a << RGFA::CIGAR::Operation.new(len, code)
end
end
return a
end
# String representation of the CIGAR
# @return [String] CIGAR string
def to_s
if empty?
return "*"
else
map(&:to_s).join
end
end
# Validate the instance
# @raise if any component of the CIGAR array is invalid.
# @return [void]
def validate!
any? do |op|
op.to_cigar_operation.validate!
end
end
# @return [RGFA::CIGAR] self
def to_cigar
self
end
# Create a copy
# @return [RGFA::CIGAR]
def clone
map{|x|x.clone}
end
end
# Exception raised by invalid CIGAR string content
class RGFA::CIGAR::ValueError < RGFA::Error; end
# An operation in a CIGAR string
class RGFA::CIGAR::Operation
attr_accessor :len
attr_accessor :code
# CIGAR operation code
CODE = [:M, :I, :D, :N, :S, :H, :P, :X, :"="]
# @param len [Integer] length of the operation
# @param code [RGFA::CIGAR::Operation::CODE] code of the operation
def initialize(len, code)
@len = len
@code = code
end
# The string representation of the operation
# @return [String]
def to_s
"#{len}#{code}"
end
# Compare two operations
# @return [Boolean]
def ==(other)
other.len == len and other.code == code
end
# Validate the operation
# @return [void]
# @raise [RGFA::CIGAR::ValueError] if the code is invalid or the length is not
# an integer larger than zero
def validate!
if Integer(len) <= 0 or
!RGFA::CIGAR::Operation::CODE.include?(code)
raise RGFA::CIGAR::ValueError
end
end
# @return [RGFA::CIGAR::Operation] self
def to_cigar_operation
self
end
end
class Array
# Create a {RGFA::CIGAR} instance from the content of the array.
# @return [RGFA::CIGAR]
def to_cigar
RGFA::CIGAR.new(self)
end
# Create a {RGFA::CIGAR::Operation} instance from the content of the array.
# @return [RGFA::CIGAR::Operation]
def to_cigar_operation
RGFA::CIGAR::Operation.new(Integer(self[0]), self[1].to_sym)
end
end
class String
# Parse CIGAR string and return an array of CIGAR operations
# @return [RGFA::CIGAR] CIGAR operations (empty if string is "*")
# @raise [RGFA::CIGAR::ValueError] if the string is not a valid CIGAR string
def to_cigar
RGFA::CIGAR.from_string(self)
end
end
|
