bio-twobit 0.2.1 → 0.2.2

checksums.yaml

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

@@ -1,12 +1,17 @@
 # bio-twobit
 
 [![Gem Version](https://badge.fury.io/rb/bio-twobit.svg)](https://badge.fury.io/rb/bio-twobit)
-[![test](https://github.com/ruby-on-bioc/bio-twobit/actions/workflows/ci.yml/badge.svg)](https://github.com/ruby-on-bioc/bio-twobit/actions/workflows/ci.yml)
+[![test](https://github.com/kojix2/bio-twobit/actions/workflows/ci.yml/badge.svg)](https://github.com/kojix2/bio-twobit/actions/workflows/ci.yml)
 [![dics](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/bio-twobit)
 [![DOI](https://zenodo.org/badge/436454379.svg)](https://zenodo.org/badge/latestdoi/436454379)
 
+Bio::TwoBit is a Ruby interface to 2bit files.
+
 Ruby bindings to [lib2bit](https://github.com/dpryan79/lib2bit) / [py2bit](https://github.com/deeptools/py2bit).
 
+
+2bit files are used to store and index DNA sequences, usually of entire reference genomes. [The 2bit format](https://genome.ucsc.edu/goldenPath/help/twoBit.html) is a compact binary representation of DNA sequences that is used by the UCSC Genome Browser.
+
 ## Installation
 
 ```sh
@@ -16,20 +21,13 @@ gem install bio-twobit
 Linux and macOS are supported.
 Windows is currently not supported.
 
-## Usage
-
-Downlaod BSgenome.Hsapiens.UCSC.hg38
-
-```sh
-wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit
-```
-
-### Quick Start
+### Usage
 
 ```ruby
 require 'bio/twobit'
 
-hg38 = Bio::TwoBit.open("hg38.2bit")
+# hg38 = Bio::TwoBit.open("hg38.2bit")
+hg38 = Bio::TwoBit::Hg38.new
 
 hg38.path
 # "hg38.2bit"
@@ -56,7 +54,7 @@ hg38.sequence("chr1", 50000, 50050)
 # "AAACAGGTTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCC" # length 50
 ```
 
-* The first number is the **(0-based)** position on the chromosome/contig where the sequence should begin. 
+* The first number is the **(0-based)** position on the chromosome/contig where the sequence should begin.
 * The second number is the **(1-based)** position on the chromosome where the sequence should end.
 
 ```ruby
@@ -121,22 +119,22 @@ hg38 = Bio::TwoBit::Hg38.new
 hs1  = Bio::TwoBit::Hs1.new
 ```
 
-Adding a new reference genome is easy. Add [here](https://github.com/ruby-on-bioc/bio-twobit/blob/main/lib/bio/twobit/references/template.erb) the id of the genome you want to use. 
+Adding a new reference genome is easy. Add the id of the genome you want to use [here](https://github.com/kojix2/bio-twobit/blob/main/lib/bio/twobit/references/template.erb). 
 
 ```
-git clone https://github.com/ruby-on-bioc/bio-twobit
+git clone https://github.com/kojix2/bio-twobit
 vi lib/bio/twobit/references/template.erb # Add your id to ids list.
 ruby lib/bio/twobit/references/template.erb
 rake install
 ```
 
-If you want to use 2-bit files from locations other than UCSC, create your own classes [here](https://github.com/ruby-on-bioc/bio-twobit/tree/main/lib/bio/twobit/references).
+If you want to use 2-bit files from locations other than UCSC, create your own classes [here](https://github.com/kojix2/bio-twobit/tree/main/lib/bio/twobit/references).
 
 Pull requests are welcome.
 
 ## Development
 
-Bug reports and pull requests are welcome on GitHub at https://github.com/ruby-on-bioc/bio-twobit.
+Bug reports and pull requests are welcome on GitHub at https://github.com/kojix2/bio-twobit.
 
     Do you need commit rights to my repository?
     Do you want to get admin rights and take over the project?
@@ -147,4 +145,3 @@ Bug reports and pull requests are welcome on GitHub at https://github.com/ruby-o
 The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
 
 Code from [Red Datasets](https://github.com/red-data-tools/red-datasets) is used for automatic file download and caching. (The MIT license)
-

data/ext/bio/twobit/twobit.c

@@ -48,12 +48,12 @@ static void TwoBit_free(void *ptr);
 static size_t TwoBit_memsize(const void *ptr);
 
 static const rb_data_type_t TwoBit_type = {
-	.wrap_struct_name = "TwoBit",
-	.function = {
-		.dfree = TwoBit_free,
-		.dsize = TwoBit_memsize,
-	},
-	.flags = RUBY_TYPED_FREE_IMMEDIATELY,
+		.wrap_struct_name = "TwoBit",
+		.function = {
+				.dfree = TwoBit_free,
+				.dsize = TwoBit_memsize,
+		},
+		.flags = RUBY_TYPED_FREE_IMMEDIATELY,
 };
 
 static void
@@ -100,7 +100,6 @@ twobit_init(VALUE klass, VALUE fpath, VALUE storeMasked)
 	tb = twobitOpen(path, mask);
 	if (!tb)
 	{
-		twobitClose(tb);
 		rb_raise(rb_eRuntimeError, "Could not open file %s", path);
 		return Qnil;
 	}
@@ -251,8 +250,8 @@ twobit_sequence(VALUE self, VALUE chrom, VALUE rbstart, VALUE rbend)
 	TwoBit *tb;
 
 	ch = StringValueCStr(chrom);
-	startl = NUM2UINT32(rbstart);
-	endl = NUM2UINT32(rbend);
+	startl = NUM2ULONG(rbstart);
+	endl = NUM2ULONG(rbend);
 	tb = getTwoBit(self);
 
 	if (!tb)
@@ -278,8 +277,14 @@ twobit_sequence(VALUE self, VALUE chrom, VALUE rbstart, VALUE rbend)
 	start = (uint32_t)startl;
 
 	str = twobitSequence(tb, ch, start, end);
-
-	return rb_str_new2(str);
+	if (!str)
+	{
+		rb_raise(rb_eRuntimeError, "Failed to retrieve the sequence for %s:%u-%u", ch, start, end);
+		return Qnil;
+	}
+	VALUE result = rb_str_new2(str);
+	free(str);
+	return result;
 }
 
 static VALUE
@@ -290,6 +295,7 @@ twobit_bases(VALUE self, VALUE chrom, VALUE start, VALUE end, VALUE fraction)
 	TwoBit *tb;
 	void *o = NULL;
 	VALUE val, hash;
+	const char *bases[4] = {"A", "C", "T", "G"};
 
 	tb = getTwoBit(self);
 	if (!tb)
@@ -312,48 +318,20 @@ twobit_bases(VALUE self, VALUE chrom, VALUE start, VALUE end, VALUE fraction)
 
 	hash = rb_hash_new();
 
-	if (fr)
+	for (int i = 0; i < 4; i++)
 	{
-		val = DBL2NUM(((double *)o)[0]);
-	}
-	else
-	{
-		val = UINT32_2NUM(((uint32_t *)o)[0]);
-	}
-	rb_hash_aset(hash, rb_str_new2("A"), val);
-
-	if (fr)
-	{
-		val = DBL2NUM(((double *)o)[1]);
-	}
-	else
-	{
-		val = UINT32_2NUM(((uint32_t *)o)[1]);
-	}
-	rb_hash_aset(hash, rb_str_new2("C"), val);
-
-	if (fr)
-	{
-		val = DBL2NUM(((double *)o)[2]);
-	}
-	else
-	{
-		val = UINT32_2NUM(((uint32_t *)o)[2]);
-	}
-	rb_hash_aset(hash, rb_str_new2("T"), val);
-
-	if (fr)
-	{
-		val = DBL2NUM(((double *)o)[3]);
-	}
-	else
-	{
-		val = UINT32_2NUM(((uint32_t *)o)[3]);
+		if (fr)
+		{
+			val = DBL2NUM(((double *)o)[i]);
+		}
+		else
+		{
+			val = UINT32_2NUM(((uint32_t *)o)[i]);
+		}
+		rb_hash_aset(hash, rb_str_new2(bases[i]), val);
 	}
-	rb_hash_aset(hash, rb_str_new2("G"), val);
 
 	free(o);
-
 	return hash;
 }
 

data/lib/bio/twobit/version.rb

@@ -2,6 +2,6 @@
 
 module Bio
   class TwoBit
-    VERSION = "0.2.1"
+    VERSION = "0.2.2"
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-twobit
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.2.2
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-01-12 00:00:00.000000000 Z
+date: 2024-09-19 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.
@@ -142,11 +142,11 @@ files:
 - lib/bio/twobit/references/wuhcor1.rb
 - lib/bio/twobit/references/xentro10.rb
 - lib/bio/twobit/version.rb
-homepage: https://github.com/ruby-on-bioc/bio-twobit
+homepage: https://github.com/kojix2/bio-twobit
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -161,8 +161,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.26
-signing_key: 
+rubygems_version: 3.5.16
+signing_key:
 specification_version: 4
 summary: A ruby library for accessing 2bit files
 test_files: []