rbbt-util 5.23.24 → 5.23.25

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8d51c26a41d1234eec3ba11ccbe095c1a1d414df
-  data.tar.gz: 2d540336dedf30e7e6c421255225d2963b907303
+  metadata.gz: 625721aa410028657ae453a55d77e57782e3d7c5
+  data.tar.gz: 30a323d757baade804120a648538a5f7669aa053
 SHA512:
-  metadata.gz: e93235dd166bef8a2648ffddb161808630022396a7d0555d11a1d079899a3034e3c0a74db25e9cb48af0290cbaa9d206431b3c82e8743add5b196471773cc693
-  data.tar.gz: 7015cb56c57717aa854c84d35ffdcba3a4448f40990fb42909b708b9281e23d7d3ceed9d6d8812204064d0cfc6bc32cfcb329d392013d734b45f5cec3634eec5
+  metadata.gz: 3e6ca02574ebf885b77e0d380dfdc84be134fa651f11fe13e011b36b06e944e7d6bcb1ee15338a287096835cb84f2ee9b9f41f594c4b975013888552638f20b2
+  data.tar.gz: f605dff38ff692d99d438a1082071abbb890a209ffb27cf51f9e9c40e1a431aa2a17f3759dc4cebe723af8d047d4cc4d79304927c06cecf2845404467e8590f5

data/lib/rbbt/util/cmd.rb

@@ -189,6 +189,7 @@ module CMD
       end
     end
     io.join
+
     nil
   end
 end

data/lib/rbbt/util/misc.rb

@@ -84,7 +84,7 @@ module Misc
     tokens[nil] = tokens[default]
     tokens[""] = tokens[default]
     time = 0
-    str.scan(/(\d+)(\w?)/).each do |amount, measure|
+    str.scan(/(\d+)(\w*)/).each do |amount, measure|
       time += amount.to_i * tokens[measure]
     end
     time

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

@@ -7,7 +7,7 @@ module AbortedStream
 end
 
 module ConcurrentStream
-  attr_accessor :threads, :pids, :callback, :abort_callback, :filename, :joined, :aborted, :autojoin, :lockfile, :no_fail, :pair, :thread
+  attr_accessor :threads, :pids, :callback, :abort_callback, :filename, :joined, :aborted, :autojoin, :lockfile, :no_fail, :pair, :thread, :stream_exception
 
   def self.setup(stream, options = {}, &block)
     
@@ -125,6 +125,7 @@ module ConcurrentStream
     ensure
       @joined = true
       lockfile.unlock if lockfile and lockfile.locked?
+      raise stream_exception if stream_exception
     end
   end
 
@@ -224,6 +225,7 @@ module ConcurrentStream
     threads.each do |thread|
       thread.raise exception
     end
+    self.stream_exception = exception
 
     self.abort
   end

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

@@ -270,7 +270,7 @@ module Misc
               obj + " (file missing)"
             end
           when String
-            if Misc.is_filename?(obj)
+            if Misc.is_filename?(obj) 
               obj2str Path.setup(obj.dup)
             else
               obj = obj.chomp if String === obj

data/test/rbbt/util/test_misc.rb

@@ -428,9 +428,6 @@ eum fugiat quo voluptas nulla pariatur?"
     assert_equal [737407, ["-----", "-----G", "-----GTTAAT"]], Misc.correct_vcf_mutation(737406, "GTTAAT", "G,GG,GGTTAAT")
   end
 
-  def test_mutation_to_ensembl_format
-    assert_equal Misc.mutation_to_ensembl_format("1:100:T", "A"), %w(1 100 100 A/T)
-  end
 
   def test_fingerprint
     assert_equal '{:a=>1}', Misc.fingerprint({:a => 1})
@@ -487,9 +484,11 @@ eum fugiat quo voluptas nulla pariatur?"
 
   def test_obj2md5
     str = "string" *  1000000
-    obj1 = [1,2,"test", 0.3, [1,2,3], {:a => [1,2], :b => str}]
-    obj2 = [1,2,"test", 0.3, [1,2,3], {:a => [1,2,3], :b => str}]
-    obj3 = [1,2,:test, 0.3, [1,2,3], {:a => [1,2,"3"], :b => str}]
+    obj1 = [1,2,"test_str", 0.3, [1,2,3], {:a => [1,2], :b => str}]
+
+    obj2 = [1,2,"test_str", 0.3, [1,2,3], {:a => [1,2,3], :b => str}]
+    obj3 = [1,2,:test_str, 0.3, [1,2,3], {:a => [1,2,"3"], :b => str}]
+
     assert_not_equal Misc.obj2md5(obj1), Misc.obj2md5(obj2)
     assert_equal Misc.obj2md5(obj2), Misc.obj2md5(obj3)
     hash = Hash[*(0..obj1.length).zip(obj1).flatten]

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.23.24
+  version: 5.23.25
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-10-02 00:00:00.000000000 Z
+date: 2018-10-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake