bio-twobit 0.2.0 → 0.2.2

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 9584e93079bfbbd4cbf3bfeea0b5d11a638026f0cfea1a4144064c1cfbdb45b9
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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/references/ailmel1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AilMel1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "ailMel1"
+        @metadata.name = "ailMel1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/ailMel1/bigZips/ailMel1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/allmis1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AllMis1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "allMis1"
+        @metadata.name = "allMis1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/allMis1/bigZips/allMis1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/anocar2.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AnoCar2 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "anoCar2"
+        @metadata.name = "anoCar2"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/anoCar2/bigZips/anoCar2.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/anogam3.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AnoGam3 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "anoGam3"
+        @metadata.name = "anoGam3"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/anoGam3/bigZips/anoGam3.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/apimel2.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class ApiMel2 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "apiMel2"
+        @metadata.name = "apiMel2"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/apiMel2/bigZips/apiMel2.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/aplcal1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AplCal1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "aplCal1"
+        @metadata.name = "aplCal1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/aplCal1/bigZips/aplCal1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/aptman1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AptMan1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "aptMan1"
+        @metadata.name = "aptMan1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/aptMan1/bigZips/aptMan1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/aquchr2.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AquChr2 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "aquChr2"
+        @metadata.name = "aquChr2"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/aquChr2/bigZips/aquChr2.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/balacu1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class BalAcu1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "balAcu1"
+        @metadata.name = "balAcu1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/balAcu1/bigZips/balAcu1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/bostau7.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class BosTau7 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "bosTau7"
+        @metadata.name = "bosTau7"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau7/bigZips/bosTau7.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/braflo1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class BraFlo1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "braFlo1"
+        @metadata.name = "braFlo1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/braFlo1/bigZips/braFlo1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/caejap1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CaeJap1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "caeJap1"
+        @metadata.name = "caeJap1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/caeJap1/bigZips/caeJap1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/caepb2.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CaePb2 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "caePb2"
+        @metadata.name = "caePb2"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/caePb2/bigZips/caePb2.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/caerem3.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CaeRem3 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "caeRem3"
+        @metadata.name = "caeRem3"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/caeRem3/bigZips/caeRem3.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/caljac4.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CalJac4 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "calJac4"
+        @metadata.name = "calJac4"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/calJac4/bigZips/calJac4.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/calmil1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CalMil1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "calMil1"
+        @metadata.name = "calMil1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/calMil1/bigZips/calMil1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/canfam4.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CanFam4 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "canFam4"
+        @metadata.name = "canFam4"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/canFam4/bigZips/canFam4.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/canfam6.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CanFam6 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "canFam6"
+        @metadata.name = "canFam6"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/cb3.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class Cb3 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "cb3"
+        @metadata.name = "cb3"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/cb3/bigZips/cb3.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/ce11.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class Ce11 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "ce11"
+        @metadata.name = "ce11"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/cersim1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CerSim1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "cerSim1"
+        @metadata.name = "cerSim1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/cerSim1/bigZips/cerSim1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/chlsab2.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class ChlSab2 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "chlSab2"
+        @metadata.name = "chlSab2"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/chlSab2/bigZips/chlSab2.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/chohof1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class ChoHof1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "choHof1"
+        @metadata.name = "choHof1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/choHof1/bigZips/choHof1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/chrpic1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class ChrPic1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "chrPic1"
+        @metadata.name = "chrPic1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/chrPic1/bigZips/chrPic1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/ci2.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class Ci2 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "ci2"
+        @metadata.name = "ci2"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/ci2/bigZips/ci2.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end