gfa 0.9.3 → 0.9.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 8919a697174aabef8c92bf7024d855c31c2adce2402e05474882cc03754e9ce2
-  data.tar.gz: 3a03b9fd5446938df35974eb0e225a35ecdc69539546ff0c6873fdba0cb28928
+  metadata.gz: 77b3aea84dc5c5a0411e66da4947f418c051550c62c401a3eadb50043ec6ae0c
+  data.tar.gz: 9e901a36a7a22fa368b17e91b330dc4848dac8b647c684753618e7acef2ae1f1
 SHA512:
-  metadata.gz: f72d49eb2fa08a89a8bf919cbc73161f65a1c2d083aa783856f33a5d872895a450d6de87a52977bfe69e5de35b0677cd00473b73d6a515449407c3705cfa3744
-  data.tar.gz: b57b09ffd99e0744fbf686d328acf778d4dcb502ae88cb79cfc3722d2c0b0d415569db0a9cce27367e6c16048ac3788efd7d4af3bfa2f3bbce7e66fad8b0f776
+  metadata.gz: 84e37302e32e089c7644a2934bf3a101e064faff9fbbf2b36c82d24b3a99e2333a73fb0858a739f8857b08a464ad60858edf8ff074247490133ff40410099cc8
+  data.tar.gz: ec3c85a3da565babb7a0f1538a52321e567366cc56fcde09a82367b683669a57259a0603045b979205c763ad3198d7432edbe452fcdd20e66406036ed846fb3d

data/lib/gfa/parser.rb

@@ -11,6 +11,8 @@ class GFA
   # - index_id: If the records should also be index by ID (default: false)
   # - comments: If the comment records should be saved (default: false)
   # - line_range: Two-integer array indicating the first and last lines to read
+  # - file_seek:  Seek to this file position before start reading
+  # - until_line: Read until reaching this line only
   #   (default: nil, read the entire file)
   def self.load(file, opts = {})
     gfa = GFA.new(opts)
@@ -23,11 +25,11 @@ class GFA
   def self.read_records(file, opts = {})
     rng = opts[:line_range]
     File.open(file, 'r') do |fh|
-      lno = -1
-      fh.each do |ln|
-        lno += 1
-        next if !rng.nil? && (lno < rng[0] || lno > rng[1])
-        next if !opts[:comments] && ln[0] == '#'
+      fh.seek(opts[:file_seek], :SET) unless opts[:file_seek].nil?
+      fh.each_with_index do |ln, lno|
+        next  if !rng.nil? && (lno < rng[0] || lno > rng[1])
+        break if !opts[:until_line].nil? && (lno == opts[:until_line])
+        next  if !opts[:comments] && ln[0] == '#'
 
         yield(GFA::Record[ln])
       end
@@ -42,10 +44,10 @@ class GFA
     return self.load(file, opts) if thr < 1
 
     # Prepare data
-    lno = 0
-    File.open(file, 'r') { |fh| fh.each { lno += 1 } }
-    thr = lno if thr > lno
-    blk = (lno.to_f / thr).ceil
+    lsize = []
+    File.open(file, 'r') { |fh| fh.each { |ln| lsize << ln.size } }
+    thr = [lsize.size, thr].min
+    blk = (lsize.size.to_f / thr).ceil
 
     # Launch children processes
     advance_bar(blk + 1)
@@ -55,7 +57,8 @@ class GFA
       io[i] = IO.pipe
       pid << fork do
         io[i][0].close
-        o = opts.merge(line_range: [i * blk, (i + 1) * blk - 1])
+        o = opts.merge(file_seek: lsize[0, blk * i].inject(:+), until_line: blk)
+        #o = opts.merge(line_range: [i * blk, (i + 1) * blk - 1])
         records = []
         read_records(file, o) do |record|
           records << record

data/lib/gfa/version.rb

@@ -1,5 +1,5 @@
 class GFA
-  VERSION       = '0.9.3'
+  VERSION       = '0.9.4'
   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: 0.9.3
+  version: 0.9.4
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-08-30 00:00:00.000000000 Z
+date: 2024-09-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rgl