gfa 0.6.0 → 0.6.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/bin/gfa-add-gaf

@@ -18,11 +18,13 @@ unless degree
     <input-gaf>  Input GAF file to read
     <output>     Output GFA file to write
     <degree>     Maximum degree of separation between the segment set in the GAF
-                 and any other included segments. If 0, only segments are
-                 included. If 1, only the target segments, records linking to
-                 them, and segments linked by those records. Any integer > 1
-                 includes additional expansion rounds for those linked segments.
-                 Use -1 to include the complete original GAF without subsetting.
+                 and any other segments included in the output GFA.
+                 - -1: include the complete original GAF without subsetting.
+                 - 0: only segments in the GAF are included.
+                 - 1: only the target segments in the GAF, records linking to
+                   them, and segments linked by those records are included.
+                 - Any integer > 1: include additional expansion rounds for
+                   those linked segments.
     <pref>       A prefix to name all recorded paths
                  By default: Based on the GAF file name
     <threads>    If passed, parallelize process with these many threads

data/lib/gfa/graph.rb

@@ -146,7 +146,7 @@ class GFA
 
   def internally_linking_records(segments, edges)
     $stderr.puts '- Gathering internally linking records'
-    segments = Hash[segments.set.map { |i| [i.name.value, true]}]
+    segments = Hash[segments.map { |i| [i.name.value, true]}]
     edges.select { |record| record.segment_names_a.all? { |s| segments[s] } }
   end
 

data/lib/gfa/version.rb

@@ -1,5 +1,5 @@
 class GFA
-  VERSION       = '0.6.0'
+  VERSION       = '0.6.1'
   VERSION_ARRAY = VERSION.split(/\./).map { |x| x.to_i } # :nodoc:
   VERSION_MAJOR = VERSION_ARRAY[0] # :nodoc:
   VERSION_MINOR = VERSION_ARRAY[1] # :nodoc:

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gfa
 version: !ruby/object:Gem::Version
-  version: 0.6.0
+  version: 0.6.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R