gfa 0.8.0 → 0.9.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 13cc01c1ed08457fc0a4cf409e87ab0e0c52e6de6f9a9019bb15de87d462bac7
-  data.tar.gz: 9013cf534626775e09c9aa2006ff47d5f03fc5c5580cde1d0f325124de911a79
+  metadata.gz: '084129ba7579aabba911f329cd32d5e4d1dbed66c4a2aa303a5763ced7bddd15'
+  data.tar.gz: ee74a43738762876c4dd342f5bed89e4a8a0a275b2f9923dcd8b4a4cc8543241
 SHA512:
-  metadata.gz: fe4dfc8fa6e24fcc734a91d5101c9d9ab3315ddf5cc26ef943ae01695e573c367d31ae53a7a1325a809f0eedcaaae97d0453fd590f079c0f6a63eecdf89cc10f
-  data.tar.gz: 3957432e59163f82cce3eddc240a03b70ffe1693c3dad9d7f373655108c454f04b5dbe618f4f65adcaf7c98ed8327323c3d2b1fee97083685612a02678780ac8
+  metadata.gz: 878db0eeee212745e68ec7c08107e9730a4f46f33b78f91037c8b728df851d595e98996c57fdc8c4673d16905c6bc194abca04d083e914f6be345345c138e4c6
+  data.tar.gz: 5f3c2266559b6cb959711c1d59c629c345236a36cf038241affe9e3b7761f4ac58d8d9a0989326b5f98de9c02e7b6259cf8b08e4c31de68b26baaf1c59d431e8

data/bin/gfa-add-gaf

@@ -20,7 +20,8 @@ unless degree
     <degree>     Maximum degree of separation between the segment set in the GAF
                  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.
+                 - 0: only segments in the GAF and strictly internal edges 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

data/lib/gfa/graph.rb

@@ -120,9 +120,7 @@ class GFA
       raise "Unrecognised class: #{segments.class}"
     end
 
-    return [] if degree <= 0
-
-    edge_matrix # Just to trigger matrix calculation
+    edge_matrix unless degree == 0 # Just to trigger matrix calculation
     degree.times do |round|
       $stderr.puts "- Expansion round #{round + 1}"
       self.class.advance_bar(segments.size)

data/lib/gfa/matrix.rb

@@ -62,10 +62,10 @@ class GFA::Matrix
   def index(row = nil, col = nil)
     if row.nil? && col.nil?
       # All values
-      (0 .. values.size - 1) # .to_a
+      (0 .. values.size - 1).to_a
     elsif row.nil?
       # Entire column
-      (col_offset(col) .. col_offset(col) + rows - 1) # .to_a
+      (col_offset(col) .. col_offset(col) + rows - 1).to_a
     elsif col.nil?
       # Entire row
       ric = row_in_column(row)

data/lib/gfa/version.rb

@@ -1,5 +1,5 @@
 class GFA
-  VERSION       = '0.8.0'
+  VERSION       = '0.9.1'
   VERSION_ARRAY = VERSION.split(/\./).map { |x| x.to_i } # :nodoc:
   VERSION_MAJOR = VERSION_ARRAY[0] # :nodoc:
   VERSION_MINOR = VERSION_ARRAY[1] # :nodoc:

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: gfa
 version: !ruby/object:Gem::Version
-  version: 0.8.0
+  version: 0.9.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-10-11 00:00:00.000000000 Z
+date: 2023-10-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rgl