bio-samtools 2.3.0 → 2.3.1
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/bio-samtools.gemspec +3 -3
- data/ext/Rakefile +7 -7
- data/lib/bio/db/sam.rb +1 -2
- data/test/test_sam.rb +12 -0
- metadata +2 -2
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA1:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: 8b8fc60d0e2728d7069923ed6c1efa52e5bafe85
|
|
4
|
+
data.tar.gz: 3e190a21f82d735ddf376c85586df45bd7c60b28
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: 999c438419b28abcab58633c24e16937ee267671384762a5d81d24650d95daa04a1789053302adc4eebf3984b9b8d4acbb72c604fedfc26c182c20216af704fb
|
|
7
|
+
data.tar.gz: 048b2fb95ebbf7ada3f34ed1701f24bc4897a89da8efdfe018a9b441ae9cacb3d0e89b52affa38b779823f64167ad7dc15c99dd791e78b061f0df77f20cbd7b4
|
data/VERSION
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
2.3.
|
|
1
|
+
2.3.1
|
data/bio-samtools.gemspec
CHANGED
|
@@ -2,17 +2,17 @@
|
|
|
2
2
|
# DO NOT EDIT THIS FILE DIRECTLY
|
|
3
3
|
# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
|
|
4
4
|
# -*- encoding: utf-8 -*-
|
|
5
|
-
# stub: bio-samtools 2.3.
|
|
5
|
+
# stub: bio-samtools 2.3.1 ruby lib
|
|
6
6
|
# stub: ext/mkrf_conf.rb
|
|
7
7
|
|
|
8
8
|
Gem::Specification.new do |s|
|
|
9
9
|
s.name = "bio-samtools"
|
|
10
|
-
s.version = "2.3.
|
|
10
|
+
s.version = "2.3.1"
|
|
11
11
|
|
|
12
12
|
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
|
13
13
|
s.require_paths = ["lib"]
|
|
14
14
|
s.authors = ["Ricardo Ramirez-Gonzalez", "Dan MacLean", "Raoul J.P. Bonnal"]
|
|
15
|
-
s.date = "2015-02-
|
|
15
|
+
s.date = "2015-02-25"
|
|
16
16
|
s.description = "Binder of samtools for ruby, on the top of FFI. \n\n This project was born from the need to add support of BAM files to \n the gee_fu genome browser (http://github.com/danmaclean/gee_fu)."
|
|
17
17
|
s.email = "ilpuccio.febo@gmail.com"
|
|
18
18
|
s.executables = ["bam_consensus.rb"]
|
data/ext/Rakefile
CHANGED
|
@@ -24,24 +24,24 @@ task :compile do
|
|
|
24
24
|
when /linux/
|
|
25
25
|
#sh "CFLAGS='-g -Wall -O2 -fPIC' make -e"
|
|
26
26
|
sh "make"
|
|
27
|
-
cp("libbam.a","/
|
|
27
|
+
cp("libbam.a","/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
|
|
28
28
|
#sh "CFLAGS='-g -Wall -O2 -fPIC' make -e libbam.so.1-local"
|
|
29
29
|
sh "make libbam.so.1-local"
|
|
30
|
-
cp("samtools", "/
|
|
31
|
-
cp("libbam.so.1","/
|
|
30
|
+
cp("samtools", "/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
|
|
31
|
+
cp("libbam.so.1","/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
|
|
32
32
|
when /darwin/
|
|
33
33
|
sh "make"
|
|
34
|
-
cp("libbam.a","/
|
|
34
|
+
cp("libbam.a","/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
|
|
35
35
|
sh "make libbam.1.dylib-local"
|
|
36
|
-
cp("libbam.1.dylib","/
|
|
36
|
+
cp("libbam.1.dylib","/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
|
|
37
37
|
sh "make"
|
|
38
|
-
cp('samtools', "/
|
|
38
|
+
cp('samtools', "/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
|
|
39
39
|
when /mswin|mingw/ then raise NotImplementedError, "BWA library is not available for Windows platform"
|
|
40
40
|
end #case
|
|
41
41
|
end #cd
|
|
42
42
|
cd("samtools-0.1.19/bcftools") do
|
|
43
43
|
sh "make"
|
|
44
|
-
cp('bcftools', "/
|
|
44
|
+
cp('bcftools', "/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
|
|
45
45
|
end
|
|
46
46
|
end
|
|
47
47
|
|
data/lib/bio/db/sam.rb
CHANGED
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
require 'open3'
|
|
2
1
|
module Bio
|
|
3
2
|
class DB
|
|
4
3
|
class Sam
|
|
@@ -25,7 +24,7 @@ module Bio
|
|
|
25
24
|
|
|
26
25
|
@last_command = nil
|
|
27
26
|
raise ArgumentError, "Need Fasta and at least one BAM or SAM" if not @fasta or not @bam
|
|
28
|
-
raise IOError, "File not found #{files}" if not files_ok?
|
|
27
|
+
raise IOError, "File not found #{@files}" if not files_ok?
|
|
29
28
|
@bams = [@bams] if @bams.instance_of? String
|
|
30
29
|
|
|
31
30
|
end
|
data/test/test_sam.rb
CHANGED
|
@@ -43,6 +43,18 @@ class TestBioDbSam < Test::Unit::TestCase
|
|
|
43
43
|
|
|
44
44
|
def test_new
|
|
45
45
|
assert_kind_of(Bio::DB::Sam, @sam)
|
|
46
|
+
|
|
47
|
+
assert_raise(IOError) do
|
|
48
|
+
Bio::DB::Sam.new(
|
|
49
|
+
:fasta => @testReference,
|
|
50
|
+
:bam => @testBAMFile + "ads"
|
|
51
|
+
)
|
|
52
|
+
|
|
53
|
+
end
|
|
54
|
+
assert_raise(ArgumentError) do
|
|
55
|
+
Bio::DB::Sam.new()
|
|
56
|
+
end
|
|
57
|
+
|
|
46
58
|
end
|
|
47
59
|
|
|
48
60
|
def test_index
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: bio-samtools
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 2.3.
|
|
4
|
+
version: 2.3.1
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Ricardo Ramirez-Gonzalez
|
|
@@ -10,7 +10,7 @@ authors:
|
|
|
10
10
|
autorequire:
|
|
11
11
|
bindir: bin
|
|
12
12
|
cert_chain: []
|
|
13
|
-
date: 2015-02-
|
|
13
|
+
date: 2015-02-25 00:00:00.000000000 Z
|
|
14
14
|
dependencies:
|
|
15
15
|
- !ruby/object:Gem::Dependency
|
|
16
16
|
name: bio-svgenes
|