htslib 0.0.5 → 0.0.10
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- checksums.yaml +4 -4
- data/README.md +71 -29
- data/lib/hts/bam/cigar.rb +7 -4
- data/lib/hts/bam/flag.rb +7 -3
- data/lib/hts/bam/header.rb +22 -7
- data/lib/hts/bam/record.rb +27 -21
- data/lib/hts/bam.rb +97 -52
- data/lib/hts/bcf/format.rb +28 -6
- data/lib/hts/bcf/header.rb +33 -5
- data/lib/hts/bcf/info.rb +28 -6
- data/lib/hts/bcf/record.rb +21 -13
- data/lib/hts/bcf.rb +69 -31
- data/lib/hts/faidx.rb +6 -4
- data/lib/hts/ffi_ext/struct.rb +1 -1
- data/lib/hts/hts.rb +56 -0
- data/lib/hts/libhts/bgzf.rb +10 -5
- data/lib/hts/libhts/constants.rb +23 -5
- data/lib/hts/libhts/cram.rb +297 -0
- data/lib/hts/libhts/hfile.rb +19 -11
- data/lib/hts/libhts/hts.rb +9 -3
- data/lib/hts/libhts/sam.rb +2 -590
- data/lib/hts/libhts/sam_funcs.rb +596 -0
- data/lib/hts/libhts/thread_pool.rb +139 -0
- data/lib/hts/libhts/vcf.rb +32 -439
- data/lib/hts/libhts/vcf_funcs.rb +430 -0
- data/lib/hts/libhts.rb +5 -3
- data/lib/hts/tabix.rb +42 -17
- data/lib/hts/version.rb +1 -1
- data/lib/htslib.rb +5 -5
- metadata +8 -3
data/lib/hts/bcf/header.rb
CHANGED
@@ -1,18 +1,46 @@
|
|
1
1
|
# frozen_string_literal: true
|
2
2
|
|
3
3
|
module HTS
|
4
|
-
class Bcf
|
4
|
+
class Bcf < Hts
|
5
5
|
class Header
|
6
|
-
def initialize(
|
7
|
-
@
|
6
|
+
def initialize(hts_file)
|
7
|
+
@bcf_hdr = LibHTS.bcf_hdr_read(hts_file)
|
8
8
|
end
|
9
9
|
|
10
10
|
def struct
|
11
|
-
@
|
11
|
+
@bcf_hdr
|
12
12
|
end
|
13
13
|
|
14
14
|
def to_ptr
|
15
|
-
@
|
15
|
+
@bcf_hdr.to_ptr
|
16
|
+
end
|
17
|
+
|
18
|
+
def get_version
|
19
|
+
LibHTS.bcf_hdr_get_version(@bcf_hdr)
|
20
|
+
end
|
21
|
+
|
22
|
+
def nsamples
|
23
|
+
LibHTS.bcf_hdr_nsamples(@bcf_hdr)
|
24
|
+
end
|
25
|
+
|
26
|
+
def samples
|
27
|
+
# bcf_hdr_id2name is macro function
|
28
|
+
@bcf_hdr[:samples]
|
29
|
+
.read_array_of_pointer(nsamples)
|
30
|
+
.map(&:read_string)
|
31
|
+
end
|
32
|
+
|
33
|
+
def to_s
|
34
|
+
kstr = LibHTS::KString.new
|
35
|
+
raise "Failed to get header string" unless LibHTS.bcf_hdr_format(@bcf_hdr, 0, kstr)
|
36
|
+
|
37
|
+
kstr[:s]
|
38
|
+
end
|
39
|
+
|
40
|
+
private
|
41
|
+
|
42
|
+
def initialize_copy(orig)
|
43
|
+
@bcf_hdr = LibHTS.bcf_hdr_dup(orig.struct)
|
16
44
|
end
|
17
45
|
end
|
18
46
|
end
|
data/lib/hts/bcf/info.rb
CHANGED
@@ -1,17 +1,38 @@
|
|
1
1
|
# frozen_string_literal: true
|
2
2
|
|
3
3
|
module HTS
|
4
|
-
class Bcf
|
4
|
+
class Bcf < Hts
|
5
5
|
class Info
|
6
6
|
def initialize(record)
|
7
7
|
@record = record
|
8
|
+
@p1 = FFI::MemoryPointer.new(:pointer) # FIXME: naming
|
9
|
+
end
|
10
|
+
|
11
|
+
# For compatibility with htslib.cr.
|
12
|
+
def get_int(key)
|
13
|
+
get(key, :int)
|
14
|
+
end
|
15
|
+
|
16
|
+
# For compatibility with htslib.cr.
|
17
|
+
def get_float(key)
|
18
|
+
get(key, :float)
|
19
|
+
end
|
20
|
+
|
21
|
+
# For compatibility with htslib.cr.
|
22
|
+
def get_string(key)
|
23
|
+
get(key, :string)
|
24
|
+
end
|
25
|
+
|
26
|
+
# For compatibility with htslib.cr.
|
27
|
+
def get_flag(key)
|
28
|
+
get(key, :flag)
|
8
29
|
end
|
9
30
|
|
10
31
|
# @note Specify the type. If you don't specify a type, it will still work, but it will be slower.
|
11
32
|
def get(key, type = nil)
|
12
33
|
n = FFI::MemoryPointer.new(:int)
|
13
|
-
p1 = @
|
14
|
-
h = @record.
|
34
|
+
p1 = @p1
|
35
|
+
h = @record.header.struct
|
15
36
|
r = @record.struct
|
16
37
|
|
17
38
|
info_values = proc do |type|
|
@@ -44,6 +65,7 @@ module HTS
|
|
44
65
|
end
|
45
66
|
end
|
46
67
|
|
68
|
+
# FIXME: naming? room for improvement.
|
47
69
|
def fields
|
48
70
|
n_info = @record.struct[:n_info]
|
49
71
|
Array.new(n_info) do |i|
|
@@ -53,10 +75,10 @@ module HTS
|
|
53
75
|
)
|
54
76
|
{
|
55
77
|
name: LibHTS.bcf_hdr_int2id(
|
56
|
-
@record.
|
78
|
+
@record.header.struct, LibHTS::BCF_DT_ID, fld[:key]
|
57
79
|
),
|
58
80
|
n: LibHTS.bcf_hdr_id2number(
|
59
|
-
@record.
|
81
|
+
@record.header.struct, LibHTS::BCF_HL_INFO, fld[:key]
|
60
82
|
),
|
61
83
|
vtype: fld[:type], i: fld[:key]
|
62
84
|
}
|
@@ -72,7 +94,7 @@ module HTS
|
|
72
94
|
i * LibHTS::BcfInfo.size
|
73
95
|
)
|
74
96
|
id = LibHTS.bcf_hdr_int2id(
|
75
|
-
@record.
|
97
|
+
@record.header.struct, LibHTS::BCF_DT_ID, fld[:key]
|
76
98
|
)
|
77
99
|
return fld[:type] if id == key
|
78
100
|
end
|
data/lib/hts/bcf/record.rb
CHANGED
@@ -1,22 +1,21 @@
|
|
1
1
|
# frozen_string_literal: true
|
2
2
|
|
3
3
|
module HTS
|
4
|
-
class Bcf
|
4
|
+
class Bcf < Hts
|
5
5
|
class Record
|
6
|
-
def initialize(bcf_t,
|
6
|
+
def initialize(bcf_t, header)
|
7
7
|
@bcf1 = bcf_t
|
8
|
-
@
|
9
|
-
@p1 = FFI::MemoryPointer.new(:pointer) # FIXME: naming
|
8
|
+
@header = header
|
10
9
|
end
|
11
10
|
|
12
|
-
attr_reader :
|
11
|
+
attr_reader :header
|
13
12
|
|
14
13
|
def struct
|
15
14
|
@bcf1
|
16
15
|
end
|
17
16
|
|
18
17
|
def to_ptr
|
19
|
-
@
|
18
|
+
@bcf1.to_ptr
|
20
19
|
end
|
21
20
|
|
22
21
|
# def inspect; end
|
@@ -26,10 +25,9 @@ module HTS
|
|
26
25
|
def genotypes; end
|
27
26
|
|
28
27
|
def chrom
|
29
|
-
hdr = @bcf.header.struct
|
30
28
|
rid = @bcf1[:rid]
|
31
29
|
|
32
|
-
LibHTS.bcf_hdr_id2name(
|
30
|
+
LibHTS.bcf_hdr_id2name(@header.struct, rid)
|
33
31
|
end
|
34
32
|
|
35
33
|
def pos
|
@@ -59,11 +57,13 @@ module HTS
|
|
59
57
|
"PASS"
|
60
58
|
when 1
|
61
59
|
i = d[:flt].read_int
|
62
|
-
LibHTS.bcf_hdr_int2id(@
|
60
|
+
LibHTS.bcf_hdr_int2id(@header.struct, LibHTS::BCF_DT_ID, i)
|
63
61
|
when 2
|
64
62
|
d[:flt].get_array_of_int(0, n_flt).map do |i|
|
65
|
-
LibHTS.bcf_hdr_int2id(@
|
63
|
+
LibHTS.bcf_hdr_int2id(@header.struct, LibHTS::BCF_DT_ID, i)
|
66
64
|
end
|
65
|
+
else
|
66
|
+
raise "Unexpected number of filters. n_flt: #{n_flt}"
|
67
67
|
end
|
68
68
|
end
|
69
69
|
|
@@ -80,13 +80,14 @@ module HTS
|
|
80
80
|
LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_STR)
|
81
81
|
@bcf1[:d][:allele].get_array_of_pointer(
|
82
82
|
FFI::TYPE_POINTER.size, @bcf1[:n_allele] - 1
|
83
|
-
).map
|
83
|
+
).map(&:read_string)
|
84
84
|
end
|
85
85
|
|
86
86
|
def alleles
|
87
|
+
LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_STR)
|
87
88
|
@bcf1[:d][:allele].get_array_of_pointer(
|
88
89
|
0, @bcf1[:n_allele]
|
89
|
-
).map
|
90
|
+
).map(&:read_string)
|
90
91
|
end
|
91
92
|
|
92
93
|
def info
|
@@ -101,10 +102,17 @@ module HTS
|
|
101
102
|
|
102
103
|
def to_s
|
103
104
|
ksr = LibHTS::KString.new
|
104
|
-
raise "Failed to format record" if LibHTS.vcf_format(@
|
105
|
+
raise "Failed to format record" if LibHTS.vcf_format(@header.struct, @bcf1, ksr) == -1
|
105
106
|
|
106
107
|
ksr[:s]
|
107
108
|
end
|
109
|
+
|
110
|
+
private
|
111
|
+
|
112
|
+
def initialize_copy(orig)\
|
113
|
+
@header = orig.header
|
114
|
+
@bcf1 = LibHTS.bcf_dup(orig.struct)
|
115
|
+
end
|
108
116
|
end
|
109
117
|
end
|
110
118
|
end
|
data/lib/hts/bcf.rb
CHANGED
@@ -3,71 +3,109 @@
|
|
3
3
|
# Based on hts-python
|
4
4
|
# https://github.com/quinlan-lab/hts-python
|
5
5
|
|
6
|
+
require_relative "../htslib"
|
7
|
+
|
8
|
+
require_relative "hts"
|
6
9
|
require_relative "bcf/header"
|
7
10
|
require_relative "bcf/info"
|
8
11
|
require_relative "bcf/format"
|
9
12
|
require_relative "bcf/record"
|
10
13
|
|
11
14
|
module HTS
|
12
|
-
class Bcf
|
15
|
+
class Bcf < Hts
|
13
16
|
include Enumerable
|
14
17
|
|
15
|
-
attr_reader :
|
16
|
-
# HtfFile is FFI::BitStruct
|
17
|
-
attr_reader :htf_file
|
18
|
+
attr_reader :file_name, :index_path, :mode, :header
|
18
19
|
|
19
|
-
|
20
|
-
|
21
|
-
|
20
|
+
def self.open(*args, **kw)
|
21
|
+
file = new(*args, **kw) # do not yield
|
22
|
+
return file unless block_given?
|
22
23
|
|
23
|
-
|
24
|
-
|
24
|
+
begin
|
25
|
+
yield file
|
26
|
+
ensure
|
27
|
+
file.close
|
28
|
+
end
|
29
|
+
file
|
30
|
+
end
|
25
31
|
|
26
|
-
|
27
|
-
|
32
|
+
def initialize(file_name, mode = "r", index: nil, fai: nil, threads: nil,
|
33
|
+
create_index: false)
|
34
|
+
if block_given?
|
35
|
+
message = "HTS::Bcf.new() dose not take block; Please use HTS::Bcf.open() instead"
|
28
36
|
raise message
|
29
37
|
end
|
30
38
|
|
31
|
-
|
39
|
+
# NOTE: Do not check for the existence of local files, since file_names may be remote URIs.
|
40
|
+
|
41
|
+
@file_name = file_name
|
32
42
|
@mode = mode
|
33
|
-
@
|
34
|
-
@header = Bcf::Header.new(LibHTS.bcf_hdr_read(htf_file))
|
43
|
+
@hts_file = LibHTS.hts_open(@file_name, mode)
|
35
44
|
|
36
|
-
#
|
37
|
-
|
38
|
-
|
39
|
-
|
40
|
-
|
41
|
-
close
|
42
|
-
end
|
45
|
+
raise Errno::ENOENT, "Failed to open #{@file_name}" if @hts_file.null?
|
46
|
+
|
47
|
+
if threads&.> 0
|
48
|
+
r = LibHTS.hts_set_threads(@hts_file, threads)
|
49
|
+
raise "Failed to set number of threads: #{threads}" if r < 0
|
43
50
|
end
|
51
|
+
|
52
|
+
return if @mode[0] == "w"
|
53
|
+
|
54
|
+
@header = Bcf::Header.new(@hts_file)
|
44
55
|
end
|
45
56
|
|
46
|
-
def
|
47
|
-
|
57
|
+
def write_header
|
58
|
+
@header = header.dup
|
59
|
+
LibHTS.hts_set_fai_filename(header, @file_name)
|
60
|
+
LibHTS.bcf_hdr_write(@hts_file, header.struct)
|
48
61
|
end
|
49
62
|
|
50
|
-
def
|
51
|
-
|
63
|
+
def write(var)
|
64
|
+
var_dup = var.dup = var.dup
|
65
|
+
LibHTS.bcf_write(@hts_file, header, var_dup) > 0 || raise
|
52
66
|
end
|
53
67
|
|
54
68
|
# Close the current file.
|
55
69
|
def close
|
56
|
-
LibHTS.hts_close(
|
70
|
+
LibHTS.hts_close(@hts_file)
|
71
|
+
@hts_file = nil
|
57
72
|
end
|
58
73
|
|
59
|
-
def
|
74
|
+
def closed?
|
75
|
+
@hts_file.nil?
|
76
|
+
end
|
77
|
+
|
78
|
+
def nsamples
|
79
|
+
header.nsamples
|
80
|
+
end
|
81
|
+
|
82
|
+
def samples
|
83
|
+
header.samples
|
84
|
+
end
|
85
|
+
|
86
|
+
# Iterate over each record.
|
87
|
+
# Generate a new Record object each time.
|
88
|
+
# Slower than each.
|
89
|
+
def each_copy
|
60
90
|
return to_enum(__method__) unless block_given?
|
61
91
|
|
62
|
-
while LibHTS.bcf_read(
|
63
|
-
record = Record.new(bcf1,
|
92
|
+
while LibHTS.bcf_read(@hts_file, header, bcf1 = LibHTS.bcf_init) != -1
|
93
|
+
record = Record.new(bcf1, header)
|
64
94
|
yield record
|
65
95
|
end
|
66
96
|
self
|
67
97
|
end
|
68
98
|
|
69
|
-
|
70
|
-
|
99
|
+
# Iterate over each record.
|
100
|
+
# Record object is reused.
|
101
|
+
# Faster than each_copy.
|
102
|
+
def each
|
103
|
+
return to_enum(__method__) unless block_given?
|
104
|
+
|
105
|
+
bcf1 = LibHTS.bcf_init
|
106
|
+
record = Record.new(bcf1, header)
|
107
|
+
yield record while LibHTS.bcf_read(@hts_file, header, bcf1) != -1
|
108
|
+
self
|
71
109
|
end
|
72
110
|
end
|
73
111
|
end
|
data/lib/hts/faidx.rb
CHANGED
@@ -3,17 +3,19 @@
|
|
3
3
|
# Based on hts-python
|
4
4
|
# https://github.com/quinlan-lab/hts-python
|
5
5
|
|
6
|
+
require_relative "../htslib"
|
7
|
+
|
6
8
|
module HTS
|
7
9
|
class Faidx
|
8
|
-
attr_reader :
|
10
|
+
attr_reader :file_name
|
9
11
|
|
10
12
|
class << self
|
11
13
|
alias open new
|
12
14
|
end
|
13
15
|
|
14
|
-
def initialize(
|
15
|
-
@
|
16
|
-
@fai = LibHTS.fai_load(
|
16
|
+
def initialize(file_name)
|
17
|
+
@file_name = file_name
|
18
|
+
@fai = LibHTS.fai_load(@file_name)
|
17
19
|
|
18
20
|
# IO like API
|
19
21
|
if block_given?
|
data/lib/hts/ffi_ext/struct.rb
CHANGED
data/lib/hts/hts.rb
ADDED
@@ -0,0 +1,56 @@
|
|
1
|
+
require_relative "../htslib"
|
2
|
+
|
3
|
+
module HTS
|
4
|
+
class Hts
|
5
|
+
def struct
|
6
|
+
@hts_file
|
7
|
+
end
|
8
|
+
|
9
|
+
def to_ptr
|
10
|
+
@hts_file.to_ptr
|
11
|
+
end
|
12
|
+
|
13
|
+
def format
|
14
|
+
LibHTS.hts_get_format(@hts_file)[:format].to_s
|
15
|
+
end
|
16
|
+
|
17
|
+
def format_version
|
18
|
+
v = LibHTS.hts_get_format(@hts_file)[:version]
|
19
|
+
major = v[:major]
|
20
|
+
minor = v[:minor]
|
21
|
+
if minor == -1
|
22
|
+
major.to_s
|
23
|
+
else
|
24
|
+
"#{major}.#{minor}"
|
25
|
+
end
|
26
|
+
end
|
27
|
+
|
28
|
+
def seek(offset)
|
29
|
+
if @hts_file[:is_cram] == 1
|
30
|
+
LibHTS.cram_seek(@hts_file[:fp][:cram], offset, IO::SEEK_SET)
|
31
|
+
elsif @hts_file[:is_bgzf] == 1
|
32
|
+
LibHTS.bgzf_seek(@hts_file[:fp][:bgzf], offset, IO::SEEK_SET)
|
33
|
+
else
|
34
|
+
LibHTS.hseek(@hts_file[:fp][:hfile], offset, IO::SEEK_SET)
|
35
|
+
end
|
36
|
+
end
|
37
|
+
|
38
|
+
def tell
|
39
|
+
if @hts_file[:is_cram] == 1
|
40
|
+
# LibHTS.cram_tell(@hts_file[:fp][:cram])
|
41
|
+
# warn 'cram_tell is not implemented in c htslib'
|
42
|
+
nil
|
43
|
+
elsif @hts_file[:is_bgzf] == 1
|
44
|
+
LibHTS.bgzf_tell(@hts_file[:fp][:bgzf])
|
45
|
+
else
|
46
|
+
LibHTS.htell(@hts_file[:fp][:hfile])
|
47
|
+
end
|
48
|
+
end
|
49
|
+
|
50
|
+
def rewind
|
51
|
+
r = seek(@start_position) if @start_position
|
52
|
+
raise "Failed to rewind: #{r}" if r < 0
|
53
|
+
r
|
54
|
+
end
|
55
|
+
end
|
56
|
+
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,
|
@@ -75,6 +75,11 @@ module HTS
|
|
75
75
|
[BGZF],
|
76
76
|
:int
|
77
77
|
|
78
|
+
# Return a virtual file pointer to the current location in the file.
|
79
|
+
def self.bgzf_tell(fp)
|
80
|
+
(fp[:block_address] << 16) | (fp[:block_offset] & 0xFFFF)
|
81
|
+
end
|
82
|
+
|
78
83
|
# Set the file to read from the location specified by _pos_.
|
79
84
|
attach_function \
|
80
85
|
:bgzf_seek,
|
@@ -176,7 +181,7 @@ module HTS
|
|
176
181
|
# Load BGZF index from an hFILE
|
177
182
|
attach_function \
|
178
183
|
:bgzf_index_load_hfile,
|
179
|
-
[BGZF,
|
184
|
+
[BGZF, HFILE, :string],
|
180
185
|
:int
|
181
186
|
|
182
187
|
# Save BGZF index
|
@@ -188,7 +193,7 @@ module HTS
|
|
188
193
|
# Write a BGZF index to an hFILE
|
189
194
|
attach_function \
|
190
195
|
:bgzf_index_dump_hfile,
|
191
|
-
[BGZF,
|
196
|
+
[BGZF, HFILE, :string],
|
192
197
|
:int
|
193
198
|
end
|
194
199
|
end
|
data/lib/hts/libhts/constants.rb
CHANGED
@@ -2,7 +2,6 @@
|
|
2
2
|
|
3
3
|
module HTS
|
4
4
|
module LibHTS
|
5
|
-
typedef :pointer, :HFILE
|
6
5
|
typedef :int64, :hts_pos_t
|
7
6
|
typedef :pointer, :bam_plp_auto_f
|
8
7
|
|
@@ -25,6 +24,25 @@ module HTS
|
|
25
24
|
:f, :pointer # kstream_t
|
26
25
|
end
|
27
26
|
|
27
|
+
# HFILE
|
28
|
+
|
29
|
+
class HFILE < FFI::BitStruct
|
30
|
+
layout \
|
31
|
+
:buffer, :string,
|
32
|
+
:begin, :string,
|
33
|
+
:end, :string,
|
34
|
+
:limit, :string,
|
35
|
+
:backend, :pointer,
|
36
|
+
:offset, :size_t,
|
37
|
+
:_flags, :uint,
|
38
|
+
:has_errno, :int
|
39
|
+
|
40
|
+
bit_fields :_flags,
|
41
|
+
:at_eof, 1,
|
42
|
+
:mobile, 1,
|
43
|
+
:readonly, 1
|
44
|
+
end
|
45
|
+
|
28
46
|
# BGZF
|
29
47
|
class BGZF < FFI::BitStruct
|
30
48
|
layout \
|
@@ -38,7 +56,7 @@ module HTS
|
|
38
56
|
:uncompressed_block, :pointer,
|
39
57
|
:compressed_block, :pointer,
|
40
58
|
:cache, :pointer,
|
41
|
-
:fp,
|
59
|
+
:fp, HFILE.ptr,
|
42
60
|
:mt, :pointer,
|
43
61
|
:idx, :pointer,
|
44
62
|
:idx_build_otf, :int,
|
@@ -198,8 +216,8 @@ module HTS
|
|
198
216
|
:fp,
|
199
217
|
union_layout(
|
200
218
|
:bgzf, BGZF.ptr,
|
201
|
-
:cram, :pointer,
|
202
|
-
:hfile,
|
219
|
+
:cram, :pointer, # cram_fd
|
220
|
+
:hfile, HFILE.ptr
|
203
221
|
),
|
204
222
|
:state, :pointer,
|
205
223
|
:format, HtsFormat,
|
@@ -218,7 +236,7 @@ module HTS
|
|
218
236
|
|
219
237
|
SamFile = HtsFile
|
220
238
|
|
221
|
-
class
|
239
|
+
class HtsTpool < FFI::Struct
|
222
240
|
layout \
|
223
241
|
:pool, :pointer,
|
224
242
|
:qsize, :int
|