bio-twobit 0.1.1 → 0.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: db79e13148b8b11440f1fd0bd8436af2ea10fb8291e6dcd84bb7dc3d68950783
+  metadata.gz: ec7f8c720eed6e69a7e0829e7a46237e49532a5dc3124c57ee0c574f36e79a46
+  data.tar.gz: b46dcf07bd2c34993b57a91e4743d45579285727146fe5ea269dab848e6e6a7f
 SHA512:
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-  data.tar.gz: 3047c3084492ad1ea39f73713baff896c19a095f197cb665067d64d23a2f58d80aa801a9a5319b182d36d38a0c40c708620bbeec9d84aba3dfc27fd033074048
+  metadata.gz: 071f082fca0cde51ff22be152f5b6a33837dbf9acdc39dfa9c7caa96fe141a065290febb17f1c5fc45b26a01caacd8d350334f9950885bd5f8a1fe7fae0e5ee4
+  data.tar.gz: 7a6753959f1a7bd188341e64c3dc9176de7f240cc214334ba155a9e706a5cbb997a02c2355626831435bf2b5b0755a31e412902f095a9900cd87a3413043d6cc

data/Gemfile

@@ -11,4 +11,4 @@ gem "rake-compiler"
 
 gem "test-unit"
 
-gem "rubocop"
+gem "rubocop"

data/bio-twobit.gemspec

@@ -24,6 +24,4 @@ Gem::Specification.new do |spec|
   spec.executables   = spec.files.grep(%r{\Aexe/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
   spec.extensions    = ["ext/bio/twobit/extconf.rb"]
-
-  # spec.add_dependency "example-gem", "~> 1.0"
 end

data/ext/bio/twobit/twobit.c

@@ -125,6 +125,20 @@ twobit_close(VALUE self)
   return Qnil;
 }
 
+static VALUE
+twobit_closed_question_mark(VALUE self)
+{
+  TwoBit *tb = getTwoBit(self);
+  if (tb)
+  {
+    return Qfalse;
+  }
+  else
+  {
+    return Qtrue;
+  }
+}
+
 static VALUE
 twobit_info(VALUE self)
 {
@@ -351,7 +365,8 @@ twobit_hard_masked_blocks(VALUE self, VALUE chrom, VALUE rbstart, VALUE rbend)
 {
   char *ch;
   TwoBit *tb;
-  unsigned long startl = 0, endl = 0, totalBlocks = 0, tid;
+  long tid = -1;
+  unsigned long startl = 0, endl = 0, totalBlocks = 0;
   uint32_t i, len, start, end, blockStart, blockEnd;
   VALUE val, ary;
 
@@ -428,7 +443,8 @@ twobit_soft_masked_blocks(VALUE self, VALUE chrom, VALUE rbstart, VALUE rbend)
 {
   char *ch;
   TwoBit *tb;
-  unsigned long startl = 0, endl = 0, totalBlocks = 0, tid;
+  long tid = -1;
+  unsigned long startl = 0, endl = 0, totalBlocks = 0;
   uint32_t i, len, start, end, blockStart, blockEnd;
   VALUE val, ary;
 
@@ -515,6 +531,7 @@ void Init_twobit(void)
 
   rb_define_private_method(mTwoBit, "initialize_raw", twobit_init, 2);
   rb_define_method(mTwoBit, "close", twobit_close, 0);
+  rb_define_method(mTwoBit, "closed?", twobit_closed_question_mark, 0);
   rb_define_method(mTwoBit, "info", twobit_info, 0);
   rb_define_method(mTwoBit, "chroms", twobit_chroms, 0);
   rb_define_private_method(mTwoBit, "sequence_raw", twobit_sequence, 3);

data/lib/bio/twobit/version.rb

@@ -2,6 +2,6 @@
 
 module Bio
   class TwoBit
-    VERSION = "0.1.1"
+    VERSION = "0.1.2"
   end
 end

data/lib/bio/twobit.rb

@@ -4,21 +4,40 @@ require_relative "twobit/version"
 require_relative "twobit/twobit"
 
 module Bio
+  # Reader for .2bit files (i.e., from UCSC genome browser)
   class TwoBit
-    class << self
-      alias open new
+    def self.open(*args, **kwargs)
+      file = new(*args, **kwargs)
+      return file unless block_given?
+
+      begin
+        yield file
+      ensure
+        file.close
+      end
+      file
     end
 
     def initialize(fname, masked: false)
-      mskd = masked ? 1 : 0
-      initialize_raw(fname, mskd)
-      if block_given?
-        begin
-          yield self
-        ensure
-          close
-        end
+      raise "TwoBit::new() does not take block; use TwoBit::open() instead" if block_given?
+
+      @fname = fname
+      if masked
+        mskd = 1
+        @masked = true
+      else
+        mskd = 0
+        @masked = false
       end
+      initialize_raw(fname, mskd)
+    end
+
+    def path
+      @fname
+    end
+
+    def masked?
+      @masked
     end
 
     def sequence(chrom, start = 0, stop = 0)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-twobit
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2021-12-18 00:00:00.000000000 Z
+date: 2022-01-14 00:00:00.000000000 Z
 dependencies: []
 description: This is a Ruby binding for lib2bit(https://github.com/dpryan79/lib2bit),
   which provides high-speed access to genomic data in 2bit file format.
@@ -52,7 +52,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.22
+rubygems_version: 3.3.3
 signing_key: 
 specification_version: 4
 summary: A ruby library for accessing 2bit files