htslib 0.1.0 → 0.2.2
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- checksums.yaml +4 -4
- data/README.md +30 -11
- data/lib/hts/bam/aux.rb +1 -0
- data/lib/hts/bam/cigar.rb +5 -7
- data/lib/hts/bam/flag.rb +5 -0
- data/lib/hts/bam/header.rb +1 -0
- data/lib/hts/bam/record.rb +7 -4
- data/lib/hts/bam.rb +128 -35
- data/lib/hts/bcf/format.rb +4 -4
- data/lib/hts/bcf/header.rb +1 -0
- data/lib/hts/bcf/header_record.rb +11 -0
- data/lib/hts/bcf/info.rb +3 -2
- data/lib/hts/bcf/record.rb +31 -30
- data/lib/hts/bcf.rb +183 -30
- data/lib/hts/faidx.rb +62 -21
- data/lib/hts/hts.rb +54 -2
- data/lib/hts/libhts/bgzf.rb +5 -5
- data/lib/hts/libhts/constants.rb +42 -20
- data/lib/hts/libhts/cram.rb +312 -279
- data/lib/hts/libhts/hfile.rb +29 -11
- data/lib/hts/libhts/hts.rb +158 -25
- data/lib/hts/libhts/sam.rb +695 -94
- data/lib/hts/libhts/sam_funcs.rb +131 -588
- data/lib/hts/libhts/tbx.rb +1 -1
- data/lib/hts/libhts/tbx_funcs.rb +25 -0
- data/lib/hts/libhts/vcf.rb +460 -234
- data/lib/hts/libhts/vcf_funcs.rb +277 -424
- data/lib/hts/libhts.rb +1 -0
- data/lib/hts/tbx.rb +39 -8
- data/lib/hts/version.rb +1 -1
- metadata +5 -3
data/lib/hts/bcf.rb
CHANGED
@@ -9,10 +9,11 @@ require_relative "bcf/format"
|
|
9
9
|
require_relative "bcf/record"
|
10
10
|
|
11
11
|
module HTS
|
12
|
+
# A class for working with VCF, BCF files.
|
12
13
|
class Bcf < Hts
|
13
14
|
include Enumerable
|
14
15
|
|
15
|
-
attr_reader :file_name, :index_name, :mode, :header
|
16
|
+
attr_reader :file_name, :index_name, :mode, :header, :nthreads
|
16
17
|
|
17
18
|
def self.open(*args, **kw)
|
18
19
|
file = new(*args, **kw) # do not yield
|
@@ -26,8 +27,8 @@ module HTS
|
|
26
27
|
file
|
27
28
|
end
|
28
29
|
|
29
|
-
def initialize(file_name, mode = "r", index: nil,
|
30
|
-
|
30
|
+
def initialize(file_name, mode = "r", index: nil, threads: nil,
|
31
|
+
build_index: false)
|
31
32
|
if block_given?
|
32
33
|
message = "HTS::Bcf.new() dose not take block; Please use HTS::Bcf.open() instead"
|
33
34
|
raise message
|
@@ -38,36 +39,39 @@ module HTS
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|
38
39
|
@file_name = file_name
|
39
40
|
@index_name = index
|
40
41
|
@mode = mode
|
42
|
+
@nthreads = threads
|
41
43
|
@hts_file = LibHTS.hts_open(@file_name, mode)
|
42
44
|
|
43
45
|
raise Errno::ENOENT, "Failed to open #{@file_name}" if @hts_file.null?
|
44
46
|
|
45
|
-
if threads
|
46
|
-
r = LibHTS.hts_set_threads(@hts_file, threads)
|
47
|
-
raise "Failed to set number of threads: #{threads}" if r < 0
|
48
|
-
end
|
47
|
+
set_threads(threads) if threads
|
49
48
|
|
50
49
|
return if @mode[0] == "w"
|
51
50
|
|
52
51
|
@header = Bcf::Header.new(@hts_file)
|
53
|
-
|
54
|
-
create_index(index) if create_index
|
55
|
-
|
52
|
+
build_index(index) if build_index
|
56
53
|
@idx = load_index(index)
|
57
|
-
|
58
54
|
@start_position = tell
|
55
|
+
super # do nothing
|
59
56
|
end
|
60
57
|
|
61
|
-
def
|
62
|
-
|
63
|
-
|
64
|
-
|
58
|
+
def build_index(index_name = nil, min_shift: 14)
|
59
|
+
check_closed
|
60
|
+
|
61
|
+
if index_name
|
62
|
+
warn "Create index for #{@file_name} to #{index_name}"
|
65
63
|
else
|
66
|
-
|
64
|
+
warn "Create index for #{@file_name}"
|
67
65
|
end
|
66
|
+
r = LibHTS.bcf_index_build3(@file_name, index_name, min_shift, @nthreads)
|
67
|
+
raise "Failed to build index for #{@file_name}" if r < 0
|
68
|
+
|
69
|
+
self
|
68
70
|
end
|
69
71
|
|
70
72
|
def load_index(index_name = nil)
|
73
|
+
check_closed
|
74
|
+
|
71
75
|
if index_name
|
72
76
|
LibHTS.bcf_index_load2(@file_name, index_name)
|
73
77
|
else
|
@@ -76,39 +80,50 @@ module HTS
|
|
76
80
|
end
|
77
81
|
|
78
82
|
def index_loaded?
|
83
|
+
check_closed
|
84
|
+
|
79
85
|
!@idx.null?
|
80
86
|
end
|
81
87
|
|
82
88
|
def write_header
|
83
|
-
|
89
|
+
check_closed
|
84
90
|
|
85
91
|
@header = header.dup
|
86
92
|
LibHTS.hts_set_fai_filename(header, @file_name)
|
87
|
-
LibHTS.bcf_hdr_write(@hts_file, header
|
93
|
+
LibHTS.bcf_hdr_write(@hts_file, header)
|
88
94
|
end
|
89
95
|
|
90
96
|
def write(var)
|
91
|
-
|
97
|
+
check_closed
|
92
98
|
|
93
|
-
var_dup = var.dup
|
99
|
+
var_dup = var.dup
|
94
100
|
LibHTS.bcf_write(@hts_file, header, var_dup) > 0 || raise
|
95
101
|
end
|
96
102
|
|
97
103
|
# Close the current file.
|
98
104
|
|
99
105
|
def nsamples
|
106
|
+
check_closed
|
107
|
+
|
100
108
|
header.nsamples
|
101
109
|
end
|
102
110
|
|
103
111
|
def samples
|
112
|
+
check_closed
|
113
|
+
|
104
114
|
header.samples
|
105
115
|
end
|
106
116
|
|
107
|
-
|
108
|
-
|
109
|
-
|
110
|
-
|
111
|
-
|
117
|
+
def each(copy: false, &block)
|
118
|
+
if copy
|
119
|
+
each_record_copy(&block)
|
120
|
+
else
|
121
|
+
each_record_reuse(&block)
|
122
|
+
end
|
123
|
+
end
|
124
|
+
|
125
|
+
private def each_record_copy
|
126
|
+
check_closed
|
112
127
|
|
113
128
|
return to_enum(__method__) unless block_given?
|
114
129
|
|
@@ -119,11 +134,8 @@ module HTS
|
|
119
134
|
self
|
120
135
|
end
|
121
136
|
|
122
|
-
|
123
|
-
|
124
|
-
# Faster than each_copy.
|
125
|
-
def each
|
126
|
-
raise IOError, "closed stream" if closed?
|
137
|
+
private def each_record_reuse
|
138
|
+
check_closed
|
127
139
|
|
128
140
|
return to_enum(__method__) unless block_given?
|
129
141
|
|
@@ -132,5 +144,146 @@ module HTS
|
|
132
144
|
yield record while LibHTS.bcf_read(@hts_file, header, bcf1) != -1
|
133
145
|
self
|
134
146
|
end
|
147
|
+
|
148
|
+
def query(...)
|
149
|
+
querys(...) # Fixme
|
150
|
+
end
|
151
|
+
|
152
|
+
# def queryi
|
153
|
+
# end
|
154
|
+
|
155
|
+
def querys(region, copy: false, &block)
|
156
|
+
if copy
|
157
|
+
querys_copy(region, &block)
|
158
|
+
else
|
159
|
+
querys_reuse(region, &block)
|
160
|
+
end
|
161
|
+
end
|
162
|
+
|
163
|
+
# private def queryi_copy
|
164
|
+
# end
|
165
|
+
|
166
|
+
# private def queryi_reuse
|
167
|
+
# end
|
168
|
+
|
169
|
+
private def querys_copy(region)
|
170
|
+
check_closed
|
171
|
+
|
172
|
+
raise "query is only available for BCF files" unless file_format == "bcf"
|
173
|
+
raise "Index file is required to call the query method." unless index_loaded?
|
174
|
+
return to_enum(__method__, region) unless block_given?
|
175
|
+
|
176
|
+
qitr = LibHTS.bcf_itr_querys(@idx, header, region)
|
177
|
+
|
178
|
+
begin
|
179
|
+
loop do
|
180
|
+
bcf1 = LibHTS.bcf_init
|
181
|
+
slen = LibHTS.hts_itr_next(@hts_file[:fp][:bgzf], qitr, bcf1, ::FFI::Pointer::NULL)
|
182
|
+
break if slen == -1
|
183
|
+
raise if slen < -1
|
184
|
+
|
185
|
+
yield Record.new(bcf1, header)
|
186
|
+
end
|
187
|
+
ensure
|
188
|
+
LibHTS.bcf_itr_destroy(qitr)
|
189
|
+
end
|
190
|
+
self
|
191
|
+
end
|
192
|
+
|
193
|
+
private def querys_reuse(region)
|
194
|
+
check_closed
|
195
|
+
|
196
|
+
raise "query is only available for BCF files" unless file_format == "bcf"
|
197
|
+
raise "Index file is required to call the query method." unless index_loaded?
|
198
|
+
return to_enum(__method__, region) unless block_given?
|
199
|
+
|
200
|
+
qitr = LibHTS.bcf_itr_querys(@idx, header, region)
|
201
|
+
|
202
|
+
bcf1 = LibHTS.bcf_init
|
203
|
+
record = Record.new(bcf1, header)
|
204
|
+
begin
|
205
|
+
loop do
|
206
|
+
slen = LibHTS.hts_itr_next(@hts_file[:fp][:bgzf], qitr, bcf1, ::FFI::Pointer::NULL)
|
207
|
+
break if slen == -1
|
208
|
+
raise if slen < -1
|
209
|
+
|
210
|
+
yield record
|
211
|
+
end
|
212
|
+
ensure
|
213
|
+
LibHTS.bcf_itr_destroy(qitr)
|
214
|
+
end
|
215
|
+
self
|
216
|
+
end
|
217
|
+
|
218
|
+
# @!macro [attach] define_getter
|
219
|
+
# @method $1
|
220
|
+
# Get $1 array
|
221
|
+
# @return [Array] the $1 array
|
222
|
+
define_getter :chrom
|
223
|
+
define_getter :pos
|
224
|
+
define_getter :endpos
|
225
|
+
define_getter :id
|
226
|
+
define_getter :ref
|
227
|
+
define_getter :alt
|
228
|
+
define_getter :qual
|
229
|
+
define_getter :filter
|
230
|
+
|
231
|
+
def info(key = nil)
|
232
|
+
check_closed
|
233
|
+
position = tell
|
234
|
+
if key
|
235
|
+
ary = map { |r| r.info(key) }
|
236
|
+
else
|
237
|
+
raise NotImplementedError
|
238
|
+
# ary = each_copy.map { |r| r.info }
|
239
|
+
# ary = map { |r| r.info.clone }
|
240
|
+
end
|
241
|
+
seek(position)
|
242
|
+
ary
|
243
|
+
end
|
244
|
+
|
245
|
+
def format(key = nil)
|
246
|
+
check_closed
|
247
|
+
position = tell
|
248
|
+
if key
|
249
|
+
ary = map { |r| r.format(key) }
|
250
|
+
else
|
251
|
+
raise NotImplementedError
|
252
|
+
# ary = each_copy.map { |r| r.format }
|
253
|
+
# ary = map { |r| r.format.clone }
|
254
|
+
end
|
255
|
+
seek(position)
|
256
|
+
ary
|
257
|
+
end
|
258
|
+
|
259
|
+
# @!macro [attach] define_iterator
|
260
|
+
# @method each_$1
|
261
|
+
# Get $1 iterator
|
262
|
+
define_iterator :chrom
|
263
|
+
define_iterator :pos
|
264
|
+
define_iterator :endpos
|
265
|
+
define_iterator :id
|
266
|
+
define_iterator :ref
|
267
|
+
define_iterator :alt
|
268
|
+
define_iterator :qual
|
269
|
+
define_iterator :filter
|
270
|
+
|
271
|
+
def each_info(key)
|
272
|
+
check_closed
|
273
|
+
return to_enum(__method__, key) unless block
|
274
|
+
|
275
|
+
each do |r|
|
276
|
+
yield r.info(key)
|
277
|
+
end
|
278
|
+
end
|
279
|
+
|
280
|
+
def each_format(key)
|
281
|
+
check_closed
|
282
|
+
return to_enum(__method__, key) unless block
|
283
|
+
|
284
|
+
each do |r|
|
285
|
+
yield r.format(key)
|
286
|
+
end
|
287
|
+
end
|
135
288
|
end
|
136
289
|
end
|
data/lib/hts/faidx.rb
CHANGED
@@ -6,40 +6,52 @@ module HTS
|
|
6
6
|
class Faidx
|
7
7
|
attr_reader :file_name
|
8
8
|
|
9
|
-
|
10
|
-
|
9
|
+
def self.open(*args, **kw)
|
10
|
+
file = new(*args, **kw) # do not yield
|
11
|
+
return file unless block_given?
|
12
|
+
|
13
|
+
begin
|
14
|
+
yield file
|
15
|
+
ensure
|
16
|
+
file.close
|
17
|
+
end
|
18
|
+
file
|
11
19
|
end
|
12
20
|
|
13
21
|
def initialize(file_name)
|
22
|
+
if block_given?
|
23
|
+
message = "HTS::Faidx.new() dose not take block; Please use HTS::Faidx.open() instead"
|
24
|
+
raise message
|
25
|
+
end
|
26
|
+
|
14
27
|
@file_name = file_name
|
15
28
|
@fai = LibHTS.fai_load(@file_name)
|
16
29
|
|
17
|
-
#
|
18
|
-
|
19
|
-
|
20
|
-
|
21
|
-
|
22
|
-
close
|
23
|
-
end
|
24
|
-
end
|
30
|
+
raise Errno::ENOENT, "Failed to open #{@file_name}" if @fai.null?
|
31
|
+
end
|
32
|
+
|
33
|
+
def struct
|
34
|
+
@fai
|
25
35
|
end
|
26
36
|
|
27
37
|
def close
|
28
38
|
LibHTS.fai_destroy(@fai)
|
29
39
|
end
|
30
40
|
|
41
|
+
# FIXME: This doesn't seem to work as expected
|
42
|
+
# def closed?
|
43
|
+
# @fai.null?
|
44
|
+
# end
|
45
|
+
|
31
46
|
# the number of sequences in the index.
|
32
|
-
def
|
47
|
+
def length
|
33
48
|
LibHTS.faidx_nseq(@fai)
|
34
49
|
end
|
35
|
-
alias length
|
50
|
+
alias size length
|
36
51
|
|
37
52
|
# return the length of the requested chromosome.
|
38
53
|
def chrom_size(chrom)
|
39
|
-
unless chrom.is_a?(String) || chrom.is_a?(Symbol)
|
40
|
-
# FIXME
|
41
|
-
raise ArgumentError, "Expect chrom to be String or Symbol"
|
42
|
-
end
|
54
|
+
raise ArgumentError, "Expect chrom to be String or Symbol" unless chrom.is_a?(String) || chrom.is_a?(Symbol)
|
43
55
|
|
44
56
|
chrom = chrom.to_s
|
45
57
|
result = LibHTS.faidx_seq_len(@fai, chrom)
|
@@ -47,12 +59,41 @@ module HTS
|
|
47
59
|
end
|
48
60
|
alias chrom_length chrom_size
|
49
61
|
|
50
|
-
#
|
51
|
-
def
|
62
|
+
# return the length of the requested chromosome.
|
63
|
+
def chrom_names
|
64
|
+
Array.new(length) { |i| LibHTS.faidx_iseq(@fai, i) }
|
65
|
+
end
|
66
|
+
|
67
|
+
# @overload fetch(name)
|
68
|
+
# Fetch the sequence as a String.
|
69
|
+
# @param name [String] chr1:0-10
|
70
|
+
# @overload fetch(name, start, stop)
|
71
|
+
# Fetch the sequence as a String.
|
72
|
+
# @param name [String] the name of the chromosome
|
73
|
+
# @param start [Integer] the start position of the sequence (0-based)
|
74
|
+
# @param stop [Integer] the end position of the sequence (0-based)
|
75
|
+
# @return [String] the sequence
|
76
|
+
|
77
|
+
def seq(name, start = nil, stop = nil)
|
78
|
+
name = name.to_s
|
79
|
+
rlen = FFI::MemoryPointer.new(:int)
|
52
80
|
|
53
|
-
|
54
|
-
|
81
|
+
if start.nil? && stop.nil?
|
82
|
+
result = LibHTS.fai_fetch(@fai, name, rlen)
|
83
|
+
else
|
84
|
+
start < 0 && raise(ArgumentError, "Expect start to be >= 0")
|
85
|
+
stop < 0 && raise(ArgumentError, "Expect stop to be >= 0")
|
86
|
+
start > stop && raise(ArgumentError, "Expect start to be <= stop")
|
55
87
|
|
56
|
-
|
88
|
+
result = LibHTS.faidx_fetch_seq(@fai, name, start, stop, rlen)
|
89
|
+
end
|
90
|
+
|
91
|
+
case rlen.read_int
|
92
|
+
when -2 then raise "Invalid chromosome name: #{name}"
|
93
|
+
when -1 then raise "Error fetching sequence: #{name}:#{start}-#{stop}"
|
94
|
+
end
|
95
|
+
|
96
|
+
result
|
97
|
+
end
|
57
98
|
end
|
58
99
|
end
|
data/lib/hts/hts.rb
CHANGED
@@ -3,7 +3,38 @@
|
|
3
3
|
require_relative "../htslib"
|
4
4
|
|
5
5
|
module HTS
|
6
|
+
# A base class for hts files.
|
6
7
|
class Hts
|
8
|
+
class << self
|
9
|
+
private
|
10
|
+
|
11
|
+
def define_getter(name)
|
12
|
+
define_method(name) do
|
13
|
+
check_closed
|
14
|
+
position = tell
|
15
|
+
ary = map(&name)
|
16
|
+
seek(position)
|
17
|
+
ary
|
18
|
+
end
|
19
|
+
end
|
20
|
+
|
21
|
+
def define_iterator(name)
|
22
|
+
define_method("each_#{name}") do |&block|
|
23
|
+
check_closed
|
24
|
+
return to_enum(__method__) unless block
|
25
|
+
|
26
|
+
each do |record|
|
27
|
+
block.call(record.public_send(name))
|
28
|
+
end
|
29
|
+
self
|
30
|
+
end
|
31
|
+
end
|
32
|
+
end
|
33
|
+
|
34
|
+
def initialize(*args)
|
35
|
+
# do nothing
|
36
|
+
end
|
37
|
+
|
7
38
|
def struct
|
8
39
|
@hts_file
|
9
40
|
end
|
@@ -12,11 +43,11 @@ module HTS
|
|
12
43
|
@hts_file.to_ptr
|
13
44
|
end
|
14
45
|
|
15
|
-
def
|
46
|
+
def file_format
|
16
47
|
LibHTS.hts_get_format(@hts_file)[:format].to_s
|
17
48
|
end
|
18
49
|
|
19
|
-
def
|
50
|
+
def file_format_version
|
20
51
|
v = LibHTS.hts_get_format(@hts_file)[:version]
|
21
52
|
major = v[:major]
|
22
53
|
minor = v[:minor]
|
@@ -38,6 +69,21 @@ module HTS
|
|
38
69
|
@hts_file.nil? || @hts_file.null?
|
39
70
|
end
|
40
71
|
|
72
|
+
def set_threads(n = nil)
|
73
|
+
if n.nil?
|
74
|
+
require "etc"
|
75
|
+
n = [Etc.nprocessors - 1, 1].max
|
76
|
+
end
|
77
|
+
raise TypeError unless n.is_a?(Integer)
|
78
|
+
raise ArgumentError, "Number of threads must be positive" if n < 1
|
79
|
+
|
80
|
+
r = LibHTS.hts_set_threads(@hts_file, n)
|
81
|
+
raise "Failed to set number of threads: #{threads}" if r < 0
|
82
|
+
|
83
|
+
@nthreads = n
|
84
|
+
self
|
85
|
+
end
|
86
|
+
|
41
87
|
def seek(offset)
|
42
88
|
if @hts_file[:is_cram] == 1
|
43
89
|
LibHTS.cram_seek(@hts_file[:fp][:cram], offset, IO::SEEK_SET)
|
@@ -70,5 +116,11 @@ module HTS
|
|
70
116
|
raise "Cannot rewind: no start position"
|
71
117
|
end
|
72
118
|
end
|
119
|
+
|
120
|
+
private
|
121
|
+
|
122
|
+
def check_closed
|
123
|
+
raise IOError, "closed stream" if closed?
|
124
|
+
end
|
73
125
|
end
|
74
126
|
end
|
data/lib/hts/libhts/bgzf.rb
CHANGED
@@ -18,19 +18,19 @@ module HTS
|
|
18
18
|
# Open an existing hFILE stream for reading or writing.
|
19
19
|
attach_function \
|
20
20
|
:bgzf_hopen,
|
21
|
-
[
|
21
|
+
[HFile, :string],
|
22
22
|
BGZF.by_ref
|
23
23
|
|
24
24
|
# Close the BGZF and free all associated resources.
|
25
25
|
attach_function \
|
26
26
|
:bgzf_close,
|
27
|
-
[
|
27
|
+
[HFile],
|
28
28
|
:int
|
29
29
|
|
30
30
|
# Read up to _length_ bytes from the file storing into _data_.
|
31
31
|
attach_function \
|
32
32
|
:bgzf_read,
|
33
|
-
[
|
33
|
+
[HFile, :pointer, :size_t],
|
34
34
|
:ssize_t
|
35
35
|
|
36
36
|
# Write _length_ bytes from _data_ to the file. If no I/O errors occur,
|
@@ -181,7 +181,7 @@ module HTS
|
|
181
181
|
# Load BGZF index from an hFILE
|
182
182
|
attach_function \
|
183
183
|
:bgzf_index_load_hfile,
|
184
|
-
[BGZF,
|
184
|
+
[BGZF, HFile, :string],
|
185
185
|
:int
|
186
186
|
|
187
187
|
# Save BGZF index
|
@@ -193,7 +193,7 @@ module HTS
|
|
193
193
|
# Write a BGZF index to an hFILE
|
194
194
|
attach_function \
|
195
195
|
:bgzf_index_dump_hfile,
|
196
|
-
[BGZF,
|
196
|
+
[BGZF, HFile, :string],
|
197
197
|
:int
|
198
198
|
end
|
199
199
|
end
|
data/lib/hts/libhts/constants.rb
CHANGED
@@ -1,6 +1,7 @@
|
|
1
1
|
# frozen_string_literal: true
|
2
2
|
|
3
3
|
module HTS
|
4
|
+
# Module for working with C HTSlib.
|
4
5
|
module LibHTS
|
5
6
|
typedef :int64, :hts_pos_t
|
6
7
|
typedef :pointer, :bam_plp_auto_f
|
@@ -24,9 +25,9 @@ module HTS
|
|
24
25
|
:f, :pointer # kstream_t
|
25
26
|
end
|
26
27
|
|
27
|
-
#
|
28
|
+
# HFile
|
28
29
|
|
29
|
-
class
|
30
|
+
class HFile < FFI::BitStruct
|
30
31
|
layout \
|
31
32
|
:buffer, :string,
|
32
33
|
:begin, :string,
|
@@ -56,7 +57,7 @@ module HTS
|
|
56
57
|
:uncompressed_block, :pointer,
|
57
58
|
:compressed_block, :pointer,
|
58
59
|
:cache, :pointer,
|
59
|
-
:fp,
|
60
|
+
:fp, HFile.ptr,
|
60
61
|
:mt, :pointer,
|
61
62
|
:idx, :pointer,
|
62
63
|
:idx_build_otf, :int,
|
@@ -189,6 +190,16 @@ module HTS
|
|
189
190
|
)
|
190
191
|
end
|
191
192
|
|
193
|
+
class HtsReglist < FFI::Struct
|
194
|
+
layout \
|
195
|
+
:reg, :string,
|
196
|
+
:intervals, :pointer, # hts_pair_pos_t
|
197
|
+
:tid, :int,
|
198
|
+
:count, :uint32_t,
|
199
|
+
:min_beg, :hts_pos_t,
|
200
|
+
:max_end, :hts_pos_t
|
201
|
+
end
|
202
|
+
|
192
203
|
# HtsFile
|
193
204
|
class SamHdr < FFI::Struct
|
194
205
|
layout \
|
@@ -217,7 +228,7 @@ module HTS
|
|
217
228
|
union_layout(
|
218
229
|
:bgzf, BGZF.ptr,
|
219
230
|
:cram, :pointer, # cram_fd
|
220
|
-
:hfile,
|
231
|
+
:hfile, HFile.ptr
|
221
232
|
),
|
222
233
|
:state, :pointer,
|
223
234
|
:format, HtsFormat,
|
@@ -263,7 +274,7 @@ module HTS
|
|
263
274
|
:n_reg, :int,
|
264
275
|
:beg, :int64,
|
265
276
|
:end, :int64,
|
266
|
-
:reg_list, :pointer,
|
277
|
+
:reg_list, :pointer, # HtsReglist.ptr,
|
267
278
|
:curr_tid, :int,
|
268
279
|
:curr_reg, :int,
|
269
280
|
:curr_intv, :int,
|
@@ -392,6 +403,7 @@ module HTS
|
|
392
403
|
:n, :int
|
393
404
|
end
|
394
405
|
|
406
|
+
# Complete textual representation of a header line
|
395
407
|
class BcfHrec < FFI::Struct
|
396
408
|
layout \
|
397
409
|
:type, :int,
|
@@ -402,21 +414,6 @@ module HTS
|
|
402
414
|
:vals, :pointer
|
403
415
|
end
|
404
416
|
|
405
|
-
class BcfFmt < FFI::BitStruct
|
406
|
-
layout \
|
407
|
-
:id, :int,
|
408
|
-
:n, :int,
|
409
|
-
:size, :int,
|
410
|
-
:type, :int,
|
411
|
-
:p, :pointer, # uint8_t
|
412
|
-
:p_len, :uint32,
|
413
|
-
:_p_off_free, :uint32 # bit_fields
|
414
|
-
|
415
|
-
bit_fields :_p_off_free,
|
416
|
-
:p_off, 31,
|
417
|
-
:p_free, 1
|
418
|
-
end
|
419
|
-
|
420
417
|
class BcfInfo < FFI::BitStruct
|
421
418
|
layout \
|
422
419
|
:key, :int,
|
@@ -466,6 +463,21 @@ module HTS
|
|
466
463
|
:m, [:int, 3]
|
467
464
|
end
|
468
465
|
|
466
|
+
class BcfFmt < FFI::BitStruct
|
467
|
+
layout \
|
468
|
+
:id, :int,
|
469
|
+
:n, :int,
|
470
|
+
:size, :int,
|
471
|
+
:type, :int,
|
472
|
+
:p, :pointer, # uint8_t
|
473
|
+
:p_len, :uint32,
|
474
|
+
:_p_off_free, :uint32 # bit_fields
|
475
|
+
|
476
|
+
bit_fields :_p_off_free,
|
477
|
+
:p_off, 31,
|
478
|
+
:p_free, 1
|
479
|
+
end
|
480
|
+
|
469
481
|
class BcfDec < FFI::Struct
|
470
482
|
layout \
|
471
483
|
:m_fmt, :int,
|
@@ -516,5 +528,15 @@ module HTS
|
|
516
528
|
LibHTS.bcf_destroy(ptr) unless ptr.null?
|
517
529
|
end
|
518
530
|
end
|
531
|
+
|
532
|
+
CramContentType = enum(
|
533
|
+
:ct_error, -1,
|
534
|
+
:file_header, 0,
|
535
|
+
:compression_header, 1,
|
536
|
+
:mapped_slice, 2,
|
537
|
+
:unmapped_slice, 3, # cram v1.0 only
|
538
|
+
:external, 4,
|
539
|
+
:core, 5
|
540
|
+
)
|
519
541
|
end
|
520
542
|
end
|