htslib 0.0.2 → 0.0.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/README.md +25 -16
- data/lib/hts/bam.rb +38 -32
- data/lib/hts/bam/cigar.rb +3 -3
- data/lib/hts/bam/flag.rb +91 -0
- data/lib/hts/bam/header.rb +2 -2
- data/lib/hts/bam/{alignment.rb → record.rb} +49 -43
- data/lib/hts/fai.rb +8 -8
- data/lib/hts/libhts.rb +141 -0
- data/lib/hts/{ffi → libhts}/bgzf.rb +1 -1
- data/lib/hts/{ffi → libhts}/constants.rb +114 -43
- data/lib/hts/{ffi → libhts}/faidx.rb +1 -1
- data/lib/hts/{ffi → libhts}/hfile.rb +1 -1
- data/lib/hts/{ffi → libhts}/hts.rb +7 -1
- data/lib/hts/{ffi → libhts}/kfunc.rb +1 -1
- data/lib/hts/{ffi → libhts}/sam.rb +25 -25
- data/lib/hts/{ffi → libhts}/tbx.rb +1 -1
- data/lib/hts/{ffi → libhts}/vcf.rb +1 -1
- data/lib/hts/vcf.rb +17 -17
- data/lib/hts/vcf/format.rb +24 -0
- data/lib/hts/vcf/header.rb +2 -2
- data/lib/hts/vcf/info.rb +24 -0
- data/lib/hts/vcf/{variant.rb → record.rb} +2 -2
- data/lib/hts/version.rb +1 -1
- data/lib/htslib.rb +16 -19
- metadata +20 -17
- data/lib/hts/ffi.rb +0 -85
data/lib/hts/ffi.rb
DELETED
|
@@ -1,85 +0,0 @@
|
|
|
1
|
-
# frozen_string_literal: true
|
|
2
|
-
|
|
3
|
-
module HTS
|
|
4
|
-
module FFI
|
|
5
|
-
extend ::FFI::Library
|
|
6
|
-
|
|
7
|
-
begin
|
|
8
|
-
ffi_lib HTS.ffi_lib
|
|
9
|
-
rescue LoadError => e
|
|
10
|
-
raise LoadError, "#{e}\nCould not find #{HTS.ffi_lib}"
|
|
11
|
-
end
|
|
12
|
-
|
|
13
|
-
def self.attach_function(*)
|
|
14
|
-
super
|
|
15
|
-
rescue ::FFI::NotFoundError => e
|
|
16
|
-
warn e.message
|
|
17
|
-
end
|
|
18
|
-
end
|
|
19
|
-
end
|
|
20
|
-
|
|
21
|
-
module FFI
|
|
22
|
-
class Struct
|
|
23
|
-
class << self
|
|
24
|
-
def union_layout(*args)
|
|
25
|
-
Class.new(FFI::Union) { layout(*args) }
|
|
26
|
-
end
|
|
27
|
-
|
|
28
|
-
def struct_layout(*args)
|
|
29
|
-
Class.new(FFI::Struct) { layout(*args) }
|
|
30
|
-
end
|
|
31
|
-
end
|
|
32
|
-
end
|
|
33
|
-
|
|
34
|
-
class BitStruct < Struct
|
|
35
|
-
class << self
|
|
36
|
-
module BitFieldsModule
|
|
37
|
-
def [](name)
|
|
38
|
-
bit_fields = self.class.bit_fields_hash_table
|
|
39
|
-
parent, start, width = bit_fields[name]
|
|
40
|
-
if parent
|
|
41
|
-
(super(parent) >> start) & ((1 << width) - 1)
|
|
42
|
-
else
|
|
43
|
-
super(name)
|
|
44
|
-
end
|
|
45
|
-
end
|
|
46
|
-
end
|
|
47
|
-
private_constant :BitFieldsModule
|
|
48
|
-
|
|
49
|
-
attr_reader :bit_fields_hash_table
|
|
50
|
-
|
|
51
|
-
def bitfields(*args)
|
|
52
|
-
unless instance_variable_defined?(:@bit_fields_hash_table)
|
|
53
|
-
@bit_fields_hash_table = {}
|
|
54
|
-
prepend BitFieldsModule
|
|
55
|
-
end
|
|
56
|
-
|
|
57
|
-
parent = args.shift
|
|
58
|
-
labels = []
|
|
59
|
-
widths = []
|
|
60
|
-
args.each_slice(2) do |l, w|
|
|
61
|
-
labels << l
|
|
62
|
-
widths << w
|
|
63
|
-
end
|
|
64
|
-
starts = widths.inject([0]) do |result, w|
|
|
65
|
-
result << (result.last + w)
|
|
66
|
-
end
|
|
67
|
-
labels.zip(starts, widths).each do |l, s, w|
|
|
68
|
-
@bit_fields_hash_table[l] = [parent, s, w]
|
|
69
|
-
end
|
|
70
|
-
end
|
|
71
|
-
end
|
|
72
|
-
end
|
|
73
|
-
end
|
|
74
|
-
|
|
75
|
-
require_relative 'ffi/constants'
|
|
76
|
-
|
|
77
|
-
# alphabetical order
|
|
78
|
-
require_relative 'ffi/bgzf'
|
|
79
|
-
require_relative 'ffi/faidx'
|
|
80
|
-
require_relative 'ffi/hfile'
|
|
81
|
-
require_relative 'ffi/hts'
|
|
82
|
-
require_relative 'ffi/sam'
|
|
83
|
-
require_relative 'ffi/kfunc'
|
|
84
|
-
require_relative 'ffi/tbx'
|
|
85
|
-
require_relative 'ffi/vcf'
|