bio-sambamba 0.0.1 → 0.0.2

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.
data/README.md CHANGED
@@ -14,10 +14,29 @@ Note: this software is under active development!
14
14
  ```
15
15
 
16
16
  In order to use the gem, you also need <code>sambamba</code> tool installed.
17
- For that, do the following:
17
+
18
+ If you use Debian, you can download a package for your architecture from
19
+ [github downloads](http://github.com/lomereiter/sambamba/downloads).
20
+
21
+ Otherwise, you need to do the following:
18
22
 
19
23
  * install [DMD compiler](http://dlang.org/download.html)
20
24
  * install [Ragel](http://www.complang.org/ragel/) finite state machine compiler
25
+
26
+ * On Mac OS X you can install [homebrew](http://mxcl.github.com/homebrew/) package manager,
27
+ then install dmd and ragel easily with
28
+
29
+ ```sh
30
+ brew install dmd
31
+ brew install ragel
32
+ ```
33
+
34
+ * On Arch Linux you can use pacman to install dmd and ragel
35
+
36
+ ```sh
37
+ pacman -S dmd libphobos ragel
38
+ ```
39
+
21
40
  * clone sambamba repository and compile the tool
22
41
 
23
42
  ```sh
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.0.1
1
+ 0.0.2
@@ -18,7 +18,7 @@ module Bio
18
18
 
19
19
  # Returns an AlignmentIterator object for iterating over all alignments in the file
20
20
  def alignments
21
- Bio::Bam::AlignmentIterator.new ['sambamba', '--format=json', @filename]
21
+ Bio::Bam::AlignmentIterator.new ['sambamba', 'view', '--format=json', @filename]
22
22
  end
23
23
 
24
24
  # True if index file was found
@@ -35,9 +35,9 @@ module Bio
35
35
  # * _chr_: reference sequence
36
36
  # * _region_: a Range representing an interval. Coordinates are 1-based.
37
37
  def fetch(chr, region)
38
- Bio::Bam::AlignmentIterator.new ['sambamba', '--format=json',
38
+ Bio::Bam::AlignmentIterator.new ['sambamba', 'view', '--format=json',
39
39
  @filename,
40
- "#{chr}:#{region.min}-#{region.max}"]
40
+ "#{chr}:#{region.min}-#{region.max}"]
41
41
  end
42
42
  end
43
43
 
@@ -17,7 +17,7 @@ module Bio
17
17
 
18
18
  # Returns an AlignmentIterator object for iterating over all alignments in the file
19
19
  def alignments
20
- Bio::Bam::AlignmentIterator.new ['sambamba', '--format=json', '-S', @filename]
20
+ Bio::Bam::AlignmentIterator.new ['sambamba', 'view', '--format=json', '-S', @filename]
21
21
  end
22
22
  end
23
23
 
@@ -14,7 +14,7 @@ module Bio
14
14
  # Raw text of SAM header
15
15
  def raw_contents
16
16
  if @raw_contents.nil? then
17
- @raw_contents = Bio::Command.query_command(['sambamba', '-H', @filename] + @opts)
17
+ @raw_contents = Bio::Command.query_command(['sambamba', 'view', '-H', @filename] + @opts)
18
18
  if @raw_contents.start_with? "sambamba" then
19
19
  raise @raw_contents
20
20
  end
@@ -46,7 +46,7 @@ module Bio
46
46
  @sq_lines ||= @json['rg_lines'].map{|json| RGLine.new(json)}
47
47
  end
48
48
 
49
- # An array of PGLine objects
49
+ # @return [PGLine] array of @PG lines
50
50
  def pg_lines
51
51
  @json ||= get_json
52
52
  @sq_lines ||= @json['pg_lines'].map{|json| PGLine.new(json)}
@@ -55,7 +55,7 @@ module Bio
55
55
  private
56
56
  # Calls sambamba to get underlying JSON object
57
57
  def get_json
58
- command = ['sambamba', '-H', '--format=json', @filename] + @opts
58
+ command = ['sambamba', 'view', '-H', '--format=json', @filename] + @opts
59
59
  line = Bio::Command.query_command(command)
60
60
  raise line if line[0] != '{'
61
61
  @json = Oj.load(line)
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-sambamba
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.0.1
4
+ version: 0.0.2
5
5
  prerelease:
6
6
  platform: ruby
7
7
  authors:
@@ -9,7 +9,7 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2012-06-27 00:00:00.000000000 Z
12
+ date: 2012-07-17 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: bio
@@ -168,7 +168,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
168
168
  version: '0'
169
169
  segments:
170
170
  - 0
171
- hash: 3091856073334228890
171
+ hash: 1006609026242934180
172
172
  required_rubygems_version: !ruby/object:Gem::Requirement
173
173
  none: false
174
174
  requirements: