bio-twobit 0.1.2 → 0.1.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -18,8 +18,7 @@ gem install bio-twobit
 Downlaod BSgenome.Hsapiens.UCSC.hg38
 
 ```sh
-wget https://bioconductor.org/packages/release/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.4.tar.gz
-tar xvf BSgenome.Hsapiens.UCSC.hg38_1.4.4.tar.gz
+wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit
 ```
 
 Quick Start
@@ -27,7 +26,10 @@ Quick Start
 ```ruby
 require 'bio/twobit'
 
-hg38 = Bio::TwoBit.open("BSgenome.Hsapiens.UCSC.hg38/inst/extdata/single_sequences.2bit")
+hg38 = Bio::TwoBit.open("hg38.2bit")
+
+hg38.path
+# "hg38.2bit"
 
 hg38.info
 # {"file_size"=>818064875,
@@ -75,6 +77,10 @@ Bio::TwoBit.open("test/fixtures/foo.2bit") do |t|
 end
 ```
 
+```ruby
+tb.closed? # true / false
+```
+
 If you would like to include information about soft-masked bases, you need to manually specify `masked: true`
 
 ```ruby
@@ -89,10 +95,18 @@ tb.soft_masked_blocks("chr1")
 # => [[62, 70]]
 ```
 
+```ruby
+tb.masked? # true / false
+```
+
 ## Development
 
 Bug reports and pull requests are welcome on GitHub at https://github.com/ruby-on-bioc/bio-twobit.
 
+    Do you need commit rights to my repository?
+    Do you want to get admin rights and take over the project?
+    If so, please feel free to contact us @kojix2.
+
 ## License
 
 The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

data/bio-twobit.gemspec

@@ -10,7 +10,7 @@ Gem::Specification.new do |spec|
 
   spec.summary       = "A ruby library for accessing 2bit files"
   spec.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."
+                       "which provides high-speed access to genomic data in 2bit file format."
   spec.homepage      = "https://github.com/ruby-on-bioc/bio-twobit"
   spec.license       = "MIT"
   spec.required_ruby_version = ">= 2.6.0"
@@ -20,8 +20,6 @@ Gem::Specification.new do |spec|
       (f == __FILE__) || f.match(%r{\A(?:(?:test|spec|features)/|\.(?:git|travis|circleci)|appveyor)})
     end
   end
-  spec.bindir        = "exe"
-  spec.executables   = spec.files.grep(%r{\Aexe/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
   spec.extensions    = ["ext/bio/twobit/extconf.rb"]
 end

data/ext/bio/twobit/2bit.c

@@ -278,6 +278,7 @@ uint8_t getByteMaskFromOffset(int offset) {
 void *twobitBasesWorker(TwoBit *tb, uint32_t tid, uint32_t start, uint32_t end, int fraction) {
     void *out;
     uint32_t tmp[4] = {0, 0, 0, 0}, len = end - start + (start % 4), i = 0, j = 0;
+    uint32_t seqLen = end - start;
     uint32_t blockStart, blockEnd, maskIdx = (uint32_t) -1, maskStart, maskEnd, foo;
     uint8_t *bytes = NULL, mask = 0, offset;
 
@@ -375,10 +376,10 @@ void *twobitBasesWorker(TwoBit *tb, uint32_t tid, uint32_t start, uint32_t end,
     //out is in TCAG order, since that's how 2bit is stored.
     //However, for whatever reason I went with ACTG in the first release...
     if(fraction) {
-        ((double*) out)[0] = ((double) tmp[2])/((double) len);
-        ((double*) out)[1] = ((double) tmp[1])/((double) len);
-        ((double*) out)[2] = ((double) tmp[0])/((double) len);
-        ((double*) out)[3] = ((double) tmp[3])/((double) len);
+        ((double*) out)[0] = ((double) tmp[2])/((double) seqLen);
+        ((double*) out)[1] = ((double) tmp[1])/((double) seqLen);
+        ((double*) out)[2] = ((double) tmp[0])/((double) seqLen);
+        ((double*) out)[3] = ((double) tmp[3])/((double) seqLen);
     } else {
         ((uint32_t*) out)[0] = tmp[2];
         ((uint32_t*) out)[1] = tmp[1];

data/lib/bio/twobit/version.rb

@@ -2,6 +2,6 @@
 
 module Bio
   class TwoBit
-    VERSION = "0.1.2"
+    VERSION = "0.1.3"
   end
 end

data/lib/bio/twobit.rb

@@ -40,19 +40,33 @@ module Bio
       @masked
     end
 
+    # Since "end" is a reserved word in Ruby, use "stop" instead.
+
     def sequence(chrom, start = 0, stop = 0)
+      raise ArgumentError, "negative start position" if start.negative?
+      raise ArgumentError, "negative stop position" if stop.negative?
+
       sequence_raw(chrom, start, stop)
     end
 
     def bases(chrom, start = 0, stop = 0, fraction: true)
+      raise ArgumentError, "negative start position" if start.negative?
+      raise ArgumentError, "negative stop position" if stop.negative?
+
       bases_raw(chrom, start, stop, fraction ? 1 : 0)
     end
 
     def hard_masked_blocks(chrom, start = 0, stop = 0)
+      raise ArgumentError, "negative start position" if start.negative?
+      raise ArgumentError, "negative stop position" if stop.negative?
+
       hard_masked_blocks_raw(chrom, start, stop)
     end
 
     def soft_masked_blocks(chrom, start = 0, stop = 0)
+      raise ArgumentError, "negative start position" if start.negative?
+      raise ArgumentError, "negative stop position" if stop.negative?
+
       soft_masked_blocks_raw(chrom, start, stop)
     end
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-twobit
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.1.3
 platform: ruby
 authors:
 - kojix2
 autorequire: 
-bindir: exe
+bindir: bin
 cert_chain: []
-date: 2022-01-14 00:00:00.000000000 Z
+date: 2022-07-29 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: 3.3.3
+rubygems_version: 3.3.7
 signing_key: 
 specification_version: 4
 summary: A ruby library for accessing 2bit files