bio-cgranges 0.0.1 → 0.0.3
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/README.md +12 -4
- data/Rakefile +0 -5
- data/ext/bio/cgranges/cgranges.c +7 -10
- data/lib/bio/cgranges/version.rb +1 -1
- metadata +7 -7
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA256:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: d8994f59d1b67dd6aedd82baea6a0f844788e37d05cb3d461a838eb225f74d04
|
|
4
|
+
data.tar.gz: 764537c8f8227f05fbe4e7641da56aa539759f39937db6c8a28aac0caaf69ff9
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: bab3e61e0f9d7da8a59e5d521db8638db8d47270d3ced8b7b3a39171c4179e16ca1cf9154cd975d8625a7e41a3bcefe6d71cbe06bcad7ff5670c75c5d044ac42
|
|
7
|
+
data.tar.gz: b641fa455ac81b6bcbf8962ff0cf56af57a211bbfeeedcd41c8283917cf3ad123d176584b98e50a36cbd1d930a36377a202ad6e2a0416d2a019f0a298b15ebef
|
data/README.md
CHANGED
|
@@ -1,9 +1,10 @@
|
|
|
1
1
|
# bio-cgranges
|
|
2
2
|
|
|
3
3
|
[](https://badge.fury.io/rb/bio-cgranges)
|
|
4
|
-
[](https://github.com/kojix2/bio-cgranges/actions/workflows/ci.yml)
|
|
5
5
|
[](https://rubydoc.info/gems/bio-cgranges)
|
|
6
|
-
[](https://
|
|
6
|
+
[](https://kojix2.github.io/bio-cgranges/)
|
|
7
|
+
[](https://zenodo.org/badge/latestdoi/491354623)
|
|
7
8
|
|
|
8
9
|
Ruby bindings to [lh3/cgranges](https://github.com/lh3/cgranges).
|
|
9
10
|
|
|
@@ -60,11 +61,18 @@ granges.coverage("chr1", 12, 22, mode: :contain)
|
|
|
60
61
|
# [5, 1]
|
|
61
62
|
```
|
|
62
63
|
|
|
63
|
-
See [](https://
|
|
64
|
+
See [](https://kojix2.github.io/bio-cgranges/) for details.
|
|
64
65
|
|
|
65
66
|
## Development
|
|
66
67
|
|
|
67
|
-
|
|
68
|
+
```sh
|
|
69
|
+
git clone https://github.com/kojix2/bio-cgranges
|
|
70
|
+
bundle install
|
|
71
|
+
bundle exec rake compile
|
|
72
|
+
bundle exec rake test
|
|
73
|
+
```
|
|
74
|
+
|
|
75
|
+
Bug reports and pull requests are welcome on GitHub at https://github.com/kojix2/bio-cgranges.
|
|
68
76
|
|
|
69
77
|
Do you need commit rights to this repository?
|
|
70
78
|
Do you want to get admin rights and take over the project?
|
data/Rakefile
CHANGED
|
@@ -9,10 +9,6 @@ Rake::TestTask.new(:test) do |t|
|
|
|
9
9
|
t.test_files = FileList["test/**/*_test.rb"]
|
|
10
10
|
end
|
|
11
11
|
|
|
12
|
-
require "rubocop/rake_task"
|
|
13
|
-
|
|
14
|
-
RuboCop::RakeTask.new
|
|
15
|
-
|
|
16
12
|
require "rake/extensiontask"
|
|
17
13
|
|
|
18
14
|
task build: :compile
|
|
@@ -34,7 +30,6 @@ task default: %i[
|
|
|
34
30
|
compile
|
|
35
31
|
remove_object_file
|
|
36
32
|
test
|
|
37
|
-
rubocop
|
|
38
33
|
]
|
|
39
34
|
|
|
40
35
|
task cleanall: %i[
|
data/ext/bio/cgranges/cgranges.c
CHANGED
|
@@ -32,7 +32,7 @@
|
|
|
32
32
|
#define NUM2INT64 NUM2LONG
|
|
33
33
|
#define UINT64_2NUM ULONG2NUM
|
|
34
34
|
#define INT64_2NUM LONG2NUM
|
|
35
|
-
#elif
|
|
35
|
+
#elif SIZEOF_LONG_LONG == SIZEOF_INT64
|
|
36
36
|
#define NUM2UINT64 NUM2ULL
|
|
37
37
|
#define NUM2INT64 NUM2LL
|
|
38
38
|
#define UINT64_2NUM ULL2NUM
|
|
@@ -50,15 +50,12 @@ static void cgranges_free(void *ptr);
|
|
|
50
50
|
static size_t cgranges_memsize(const void *ptr);
|
|
51
51
|
|
|
52
52
|
static const rb_data_type_t cgranges_type = {
|
|
53
|
-
"cgranges",
|
|
54
|
-
{
|
|
55
|
-
|
|
56
|
-
|
|
57
|
-
cgranges_memsize,
|
|
53
|
+
.wrap_struct_name = "cgranges",
|
|
54
|
+
.function = {
|
|
55
|
+
.dfree = cgranges_free,
|
|
56
|
+
.dsize = cgranges_memsize,
|
|
58
57
|
},
|
|
59
|
-
|
|
60
|
-
0,
|
|
61
|
-
RUBY_TYPED_FREE_IMMEDIATELY,
|
|
58
|
+
.flags = RUBY_TYPED_FREE_IMMEDIATELY,
|
|
62
59
|
};
|
|
63
60
|
|
|
64
61
|
static void
|
|
@@ -467,4 +464,4 @@ void Init_cgranges(void)
|
|
|
467
464
|
rb_define_method(rb_CGRanges, "count_contain", cgranges_count_contain, 3);
|
|
468
465
|
rb_define_method(rb_CGRanges, "coverage_overlap", cgranges_coverage_overlap, 3);
|
|
469
466
|
rb_define_method(rb_CGRanges, "coverage_contain", cgranges_coverage_contain, 3);
|
|
470
|
-
}
|
|
467
|
+
}
|
data/lib/bio/cgranges/version.rb
CHANGED
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: bio-cgranges
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.0.
|
|
4
|
+
version: 0.0.3
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- kojix2
|
|
8
|
-
autorequire:
|
|
8
|
+
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date:
|
|
11
|
+
date: 2023-09-25 00:00:00.000000000 Z
|
|
12
12
|
dependencies: []
|
|
13
13
|
description: Genomic interval overlap queries
|
|
14
14
|
email:
|
|
@@ -31,11 +31,11 @@ files:
|
|
|
31
31
|
- ext/bio/cgranges/extconf.rb
|
|
32
32
|
- lib/bio/cgranges.rb
|
|
33
33
|
- lib/bio/cgranges/version.rb
|
|
34
|
-
homepage: https://github.com/
|
|
34
|
+
homepage: https://github.com/kojix2/bio-cgranges
|
|
35
35
|
licenses:
|
|
36
36
|
- MIT
|
|
37
37
|
metadata: {}
|
|
38
|
-
post_install_message:
|
|
38
|
+
post_install_message:
|
|
39
39
|
rdoc_options: []
|
|
40
40
|
require_paths:
|
|
41
41
|
- lib
|
|
@@ -50,8 +50,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
50
50
|
- !ruby/object:Gem::Version
|
|
51
51
|
version: '0'
|
|
52
52
|
requirements: []
|
|
53
|
-
rubygems_version: 3.
|
|
54
|
-
signing_key:
|
|
53
|
+
rubygems_version: 3.4.10
|
|
54
|
+
signing_key:
|
|
55
55
|
specification_version: 4
|
|
56
56
|
summary: Ruby bindings for lh3/cgranges
|
|
57
57
|
test_files: []
|