rbbt-util 5.14.4 → 5.14.5

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 7763cbe7760e56fc1faeba8d117ec7deddd25f88
+  metadata.gz: f1fa2f550e7cac4d0ccdfe338c6a5012288bbdff
+  data.tar.gz: af4d638b5f65f37eac8279b3f6be21f87fd71b65
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+  metadata.gz: b4695a330e812a45fc5f1bdcf0bf36752b49161b408022da3f37f64133e2c9ba5b7ed4754861ef189f588601e81f5a5f2d32008d464ed3bc98846a066dd3171e
+  data.tar.gz: 4475cf87c50919517a7a56e32e9d4fbb653b65adf9fe7e3935f8db24562d72ae2d4e5ea991bba6c1db441aa643abf11e0e6e4cacc3974d54422745b742d034e2

data/lib/rbbt/annotations.rb

@@ -260,7 +260,7 @@ module Annotation
     annotations.each_with_index do |name,i|
       value = values[i]
 
-      value = value.split("|") if String === value and value.index "|"
+      value = value.split("|") if String === value and value.include? "|"
 
       annotation_values[name] = value
     end

data/lib/rbbt/resource/path.rb

@@ -123,6 +123,10 @@ module Path
         sub('{SUBPATH}', subpath).
         sub('{PATH}', self).
         sub('{LIBDIR}', libdir) #, @pkgdir, @resource, @search_paths
+
+      path = path + '.gz' if File.exists? path + '.gz'
+      path = path + '.bgz' if File.exists? path + '.bgz'
+
       self.annotate path
     end
   end
@@ -150,19 +154,21 @@ module Path
     self.find
   end
 
+  def _exists?
+    Open.exists? self.find.to_s
+  end
+
   def exists?
     begin
       self.produce
-      File.exists? self.find
+      _exists?
     rescue Exception
       false
     end
   end
 
   def produce(force = false)
-    path = self.find
-
-    return self if Open.exists?(path.to_s) and not force
+    return self if _exists? and not force
 
     raise "No resource defined to produce file: #{ self }" if resource.nil?
 

data/lib/rbbt/util/misc/bgzf.rb

@@ -33,17 +33,20 @@ module Bgzf
 
   def _index
     @_index ||= begin
-                 index = []
-                 pos = 0
-                 while true do
-                   blockdata_offset = tell
-                   block = read_block
-                   break unless block
-                   index << [pos, blockdata_offset]
-                   pos += block.length
-                 end
-                 @block_cache_size = Math.log(index.length).to_i + 1
-                 index
+                  index = Persist.persist("BGZF index" + filename.sub(/.bgz$/,''), :marshal, :dir => Rbbt.var.bgzf_index) do
+                    index = []
+                    pos = 0
+                    while true do
+                      blockdata_offset = tell
+                      block = read_block
+                      break unless block
+                      index << [pos, blockdata_offset]
+                      pos += block.length
+                    end
+                    index
+                  end
+                  @block_cache_size = Math.log(index.length).to_i + 1
+                  index
                end
   end
 
@@ -131,6 +134,10 @@ module Bgzf
     end
   end
 
+  def getc
+    read(1)
+  end
+
   def gets
     str = nil
     current = @data_offset

data/lib/rbbt/workflow/accessor.rb

@@ -449,16 +449,16 @@ module Workflow
   end
 
   def task_from_dep(dep)
-    case dep
-    when Array
-      dep.first.tasks[dep.last] 
-    when String
-      tasks[dep.to_sym]
-    when Symbol
-      tasks[dep.to_sym]
-    else
-      raise "Unknown dependency: #{Misc.fingerprint dep}"
-    end
+    task = case dep
+           when Array
+             dep.first.tasks[dep[1]] 
+           when String
+             tasks[dep.to_sym]
+           when Symbol
+             tasks[dep.to_sym]
+           end
+    raise "Unknown dependency: #{Misc.fingerprint dep}" if task.nil?
+    task
   end
 
   def rec_inputs(taskname)
@@ -467,28 +467,28 @@ module Workflow
 
   def rec_input_defaults(taskname)
     [taskname].concat(rec_dependencies(taskname)).inject(IndiferentHash.setup({})){|acc, tn|
-      new = (Array === tn ? tn.first.tasks[tn.last.to_sym] : tasks[tn.to_sym]).input_defaults
+      new = (Array === tn ? tn.first.tasks[tn[1].to_sym] : tasks[tn.to_sym]).input_defaults
       acc = new.merge(acc) 
     }.tap{|h| IndiferentHash.setup(h)}
   end
 
   def rec_input_types(taskname)
     [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn|
-      new = (Array === tn ? tn.first.tasks[tn.last.to_sym] : tasks[tn.to_sym]).input_types
+      new = (Array === tn ? tn.first.tasks[tn[1].to_sym] : tasks[tn.to_sym]).input_types
       acc = new.merge(acc) 
     }.tap{|h| IndiferentHash.setup(h)}
   end
 
   def rec_input_descriptions(taskname)
     [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn|
-      new = (Array === tn ? tn.first.tasks[tn.last.to_sym] : tasks[tn.to_sym]).input_descriptions
+      new = (Array === tn ? tn.first.tasks[tn[1].to_sym] : tasks[tn.to_sym]).input_descriptions
       acc = new.merge(acc) 
     }.tap{|h| IndiferentHash.setup(h)}
   end
 
   def rec_input_options(taskname)
     [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn|
-      new = (Array === tn ? tn.first.tasks[tn.last.to_sym] : tasks[tn.to_sym]).input_options
+      new = (Array === tn ? tn.first.tasks[tn[1].to_sym] : tasks[tn.to_sym]).input_options
       acc = new.merge(acc) 
     }.tap{|h| IndiferentHash.setup(h)}
   end
@@ -498,7 +498,18 @@ module Workflow
     dependencies.each do |dependency|
       real_dependencies << case dependency
       when Array
-        dependency.first.job(dependency.last, jobname, inputs)
+        inputs = inputs.dup
+        options = dependency.last if Hash === dependency.last
+        options.each{|i,v|
+          case v
+          when Symbol
+            rec_dependency = real_dependencies.select{|d| d.task.name == v }.first
+            inputs[i] = rec_dependency
+          else
+            inputs[i] = v
+          end
+        } if options
+        dependency.first.job(dependency[1], jobname, inputs)
       when Step
         dependency
       when Symbol

data/lib/rbbt/workflow/definition.rb

@@ -36,7 +36,7 @@ module Workflow
 
   def dep(*dependency_list, &block)
     @dependencies ||= []
-    if Array === dependency_list and Module === dependency_list.first
+    if Module === dependency_list.first or Hash === dependency_list.last
       @dependencies << dependency_list
     else
       @dependency_list ||= []

data/lib/rbbt/workflow/usage.rb

@@ -31,9 +31,11 @@ module Task
       deps.each do |dep|
         next if seen.include? dep.name
         seen << dep.name
+        new_inputs = (dep.inputs - self.inputs)
+        next unless new_inputs.any?
         puts "  #{Log.color :yellow, dep.name.to_s}:"
         puts
-        puts SOPT.input_doc((dep.inputs - self.inputs), dep.input_types, dep.input_descriptions, dep.input_defaults, true)
+        puts SOPT.input_doc(new_inputs, dep.input_types, dep.input_descriptions, dep.input_defaults, true)
         puts
       end
     end
@@ -77,7 +79,7 @@ module Workflow
         task = self.tasks[task_name]
       end
 
-      dependencies = self.rec_dependencies(task_name).collect{|dep_name| Array === dep_name ? dep_name.first.tasks[dep_name.last.to_sym] : self.tasks[dep_name.to_sym]}
+      dependencies = self.rec_dependencies(task_name).collect{|dep_name| Array === dep_name ? dep_name.first.tasks[dep_name[1].to_sym] : self.tasks[dep_name.to_sym]}
 
       task.doc(dependencies)
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.14.4
+  version: 5.14.5
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-10 00:00:00.000000000 Z
+date: 2014-07-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake