htslib 0.0.6 → 0.1.0
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 +69 -28
- data/lib/hts/bam/aux.rb +39 -0
- data/lib/hts/bam/cigar.rb +5 -7
- data/lib/hts/bam/flag.rb +22 -58
- data/lib/hts/bam/header.rb +17 -9
- data/lib/hts/bam/record.rb +102 -56
- data/lib/hts/bam.rb +99 -55
- data/lib/hts/bcf/format.rb +108 -16
- data/lib/hts/bcf/header.rb +24 -3
- data/lib/hts/bcf/info.rb +80 -34
- data/lib/hts/bcf/record.rb +58 -26
- data/lib/hts/bcf.rb +98 -35
- data/lib/hts/faidx.rb +5 -6
- data/lib/hts/ffi_ext/pointer.rb +18 -0
- data/lib/hts/hts.rb +74 -0
- data/lib/hts/libhts/bgzf.rb +10 -5
- data/lib/hts/libhts/constants.rb +25 -7
- data/lib/hts/libhts/cram.rb +292 -0
- data/lib/hts/libhts/hfile.rb +19 -11
- data/lib/hts/libhts/hts.rb +3 -3
- data/lib/hts/libhts/sam_funcs.rb +2 -1
- data/lib/hts/libhts/thread_pool.rb +139 -0
- data/lib/hts/libhts/vcf.rb +14 -0
- data/lib/hts/libhts.rb +9 -3
- data/lib/hts/tbx.rb +46 -0
- data/lib/hts/version.rb +1 -1
- data/lib/htslib.rb +5 -5
- metadata +13 -8
- data/lib/hts/tabix.rb +0 -28
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: htslib
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.0
|
|
4
|
+
version: 0.1.0
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- kojix2
|
|
8
|
-
autorequire:
|
|
8
|
+
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2022-
|
|
11
|
+
date: 2022-05-06 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: ffi
|
|
@@ -122,7 +122,7 @@ dependencies:
|
|
|
122
122
|
- - ">="
|
|
123
123
|
- !ruby/object:Gem::Version
|
|
124
124
|
version: '0'
|
|
125
|
-
description:
|
|
125
|
+
description:
|
|
126
126
|
email:
|
|
127
127
|
- 2xijok@gmail.com
|
|
128
128
|
executables: []
|
|
@@ -132,6 +132,7 @@ files:
|
|
|
132
132
|
- LICENSE.txt
|
|
133
133
|
- README.md
|
|
134
134
|
- lib/hts/bam.rb
|
|
135
|
+
- lib/hts/bam/aux.rb
|
|
135
136
|
- lib/hts/bam/cigar.rb
|
|
136
137
|
- lib/hts/bam/flag.rb
|
|
137
138
|
- lib/hts/bam/header.rb
|
|
@@ -143,10 +144,13 @@ files:
|
|
|
143
144
|
- lib/hts/bcf/record.rb
|
|
144
145
|
- lib/hts/faidx.rb
|
|
145
146
|
- lib/hts/ffi_ext/README.md
|
|
147
|
+
- lib/hts/ffi_ext/pointer.rb
|
|
146
148
|
- lib/hts/ffi_ext/struct.rb
|
|
149
|
+
- lib/hts/hts.rb
|
|
147
150
|
- lib/hts/libhts.rb
|
|
148
151
|
- lib/hts/libhts/bgzf.rb
|
|
149
152
|
- lib/hts/libhts/constants.rb
|
|
153
|
+
- lib/hts/libhts/cram.rb
|
|
150
154
|
- lib/hts/libhts/faidx.rb
|
|
151
155
|
- lib/hts/libhts/hfile.rb
|
|
152
156
|
- lib/hts/libhts/hts.rb
|
|
@@ -154,16 +158,17 @@ files:
|
|
|
154
158
|
- lib/hts/libhts/sam.rb
|
|
155
159
|
- lib/hts/libhts/sam_funcs.rb
|
|
156
160
|
- lib/hts/libhts/tbx.rb
|
|
161
|
+
- lib/hts/libhts/thread_pool.rb
|
|
157
162
|
- lib/hts/libhts/vcf.rb
|
|
158
163
|
- lib/hts/libhts/vcf_funcs.rb
|
|
159
|
-
- lib/hts/
|
|
164
|
+
- lib/hts/tbx.rb
|
|
160
165
|
- lib/hts/version.rb
|
|
161
166
|
- lib/htslib.rb
|
|
162
167
|
homepage: https://github.com/kojix2/ruby-htslib
|
|
163
168
|
licenses:
|
|
164
169
|
- MIT
|
|
165
170
|
metadata: {}
|
|
166
|
-
post_install_message:
|
|
171
|
+
post_install_message:
|
|
167
172
|
rdoc_options: []
|
|
168
173
|
require_paths:
|
|
169
174
|
- lib
|
|
@@ -178,8 +183,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
178
183
|
- !ruby/object:Gem::Version
|
|
179
184
|
version: '0'
|
|
180
185
|
requirements: []
|
|
181
|
-
rubygems_version: 3.3.
|
|
182
|
-
signing_key:
|
|
186
|
+
rubygems_version: 3.3.7
|
|
187
|
+
signing_key:
|
|
183
188
|
specification_version: 4
|
|
184
189
|
summary: HTSlib bindings for Ruby
|
|
185
190
|
test_files: []
|
data/lib/hts/tabix.rb
DELETED
|
@@ -1,28 +0,0 @@
|
|
|
1
|
-
# frozen_string_literal: true
|
|
2
|
-
|
|
3
|
-
# Based on hts-python
|
|
4
|
-
# https://github.com/quinlan-lab/hts-python
|
|
5
|
-
|
|
6
|
-
module HTS
|
|
7
|
-
class Tabix
|
|
8
|
-
class << self
|
|
9
|
-
alias open new
|
|
10
|
-
end
|
|
11
|
-
def initialize
|
|
12
|
-
# IO like API
|
|
13
|
-
if block_given?
|
|
14
|
-
begin
|
|
15
|
-
yield self
|
|
16
|
-
ensure
|
|
17
|
-
close
|
|
18
|
-
end
|
|
19
|
-
end
|
|
20
|
-
end
|
|
21
|
-
|
|
22
|
-
def build; end
|
|
23
|
-
|
|
24
|
-
def sequences; end
|
|
25
|
-
|
|
26
|
-
# def __call__\
|
|
27
|
-
end
|
|
28
|
-
end
|