bio-sambamba 0.0.1 → 0.0.2

data/README.md

@@ -14,10 +14,29 @@ Note: this software is under active development!
 ```
 
 In order to use the gem, you also need <code>sambamba</code> tool installed.
-For that, do the following:
+
+If you use Debian, you can download a package for your architecture from
+[github downloads](http://github.com/lomereiter/sambamba/downloads).
+
+Otherwise, you need to do the following:
 
 * install [DMD compiler](http://dlang.org/download.html)
 * install [Ragel](http://www.complang.org/ragel/) finite state machine compiler
+
+* On Mac OS X you can install [homebrew](http://mxcl.github.com/homebrew/) package manager, 
+then install dmd and ragel easily with 
+
+```sh
+    brew install dmd
+    brew install ragel
+```
+
+* On Arch Linux you can use pacman to install dmd and ragel
+
+```sh
+    pacman -S dmd libphobos ragel
+```
+
 * clone sambamba repository and compile the tool
 
 ```sh

data/VERSION

@@ -1 +1 @@
-0.0.1
+0.0.2

data/lib/bio-sambamba/bamfile.rb

@@ -18,7 +18,7 @@ module Bio
 
       # Returns an AlignmentIterator object for iterating over all alignments in the file
       def alignments
-        Bio::Bam::AlignmentIterator.new ['sambamba', '--format=json', @filename]
+        Bio::Bam::AlignmentIterator.new ['sambamba', 'view', '--format=json', @filename]
       end
 
       # True if index file was found 
@@ -35,9 +35,9 @@ module Bio
       # * _chr_: reference sequence
       # * _region_: a Range representing an interval. Coordinates are 1-based.
       def fetch(chr, region)
-        Bio::Bam::AlignmentIterator.new ['sambamba', '--format=json', 
+        Bio::Bam::AlignmentIterator.new ['sambamba', 'view', '--format=json', 
                                          @filename,
-                                          "#{chr}:#{region.min}-#{region.max}"]
+                                         "#{chr}:#{region.min}-#{region.max}"]
       end
     end
     

data/lib/bio-sambamba/samfile.rb

@@ -17,7 +17,7 @@ module Bio
 
       # Returns an AlignmentIterator object for iterating over all alignments in the file
       def alignments
-        Bio::Bam::AlignmentIterator.new ['sambamba', '--format=json', '-S', @filename]
+        Bio::Bam::AlignmentIterator.new ['sambamba', 'view', '--format=json', '-S', @filename]
       end
     end
 

data/lib/bio-sambamba/samheader.rb

@@ -14,7 +14,7 @@ module Bio
       # Raw text of SAM header
       def raw_contents
         if @raw_contents.nil? then
-          @raw_contents = Bio::Command.query_command(['sambamba', '-H', @filename] + @opts)
+          @raw_contents = Bio::Command.query_command(['sambamba', 'view', '-H', @filename] + @opts)
           if @raw_contents.start_with? "sambamba" then
             raise @raw_contents
           end
@@ -46,7 +46,7 @@ module Bio
         @sq_lines ||= @json['rg_lines'].map{|json| RGLine.new(json)}
       end
 
-      # An array of PGLine objects
+      # @return [PGLine] array of @PG lines
       def pg_lines
         @json ||= get_json
         @sq_lines ||= @json['pg_lines'].map{|json| PGLine.new(json)}
@@ -55,7 +55,7 @@ module Bio
       private
       # Calls sambamba to get underlying JSON object
       def get_json
-        command = ['sambamba', '-H', '--format=json', @filename] + @opts
+        command = ['sambamba', 'view', '-H', '--format=json', @filename] + @opts
         line = Bio::Command.query_command(command)
         raise line if line[0] != '{'
         @json = Oj.load(line)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-sambamba
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-06-27 00:00:00.000000000 Z
+date: 2012-07-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -168,7 +168,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 3091856073334228890
+      hash: 1006609026242934180
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: