bio-ucsc-api 0.3.1 → 0.4.0

data/spec/ornana1_spec.rb

@@ -67,40 +67,40 @@ describe "Bio::Ucsc::OrnAna1" do
     end
   end 
 
-  describe "Bio::Ucsc::OrnAna1::ChainAnoCar1" do
+  describe "Bio::Ucsc::OrnAna1::ChainAnoCar2" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::OrnAna1::ChainAnoCar1.first
+        result = Bio::Ucsc::OrnAna1::ChainAnoCar2.first
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::OrnAna1::ChainAnoCar1Link" do
+  describe "Bio::Ucsc::OrnAna1::ChainAnoCar2Link" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::OrnAna1::ChainAnoCar1Link.first
+        result = Bio::Ucsc::OrnAna1::ChainAnoCar2Link.first
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::OrnAna1::ChainBosTau4" do
+  describe "Bio::Ucsc::OrnAna1::ChainBosTau6" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::OrnAna1::ChainBosTau4.first
+        result = Bio::Ucsc::OrnAna1::ChainBosTau6.first
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::OrnAna1::ChainBosTau4Link" do
+  describe "Bio::Ucsc::OrnAna1::ChainBosTau6Link" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::OrnAna1::ChainBosTau4Link.first
+        result = Bio::Ucsc::OrnAna1::ChainBosTau6Link.first
         pp result
         result.should be_true
       end
@@ -577,20 +577,20 @@ describe "Bio::Ucsc::OrnAna1" do
     end
   end 
 
-  describe "Bio::Ucsc::OrnAna1::NetAnoCar1" do
+  describe "Bio::Ucsc::OrnAna1::NetAnoCar2" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::OrnAna1::NetAnoCar1.first
+        result = Bio::Ucsc::OrnAna1::NetAnoCar2.first
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::OrnAna1::NetBosTau4" do
+  describe "Bio::Ucsc::OrnAna1::NetBosTau6" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::OrnAna1::NetBosTau4.first
+        result = Bio::Ucsc::OrnAna1::NetBosTau6.first
         pp result
         result.should be_true
       end

data/spec/{named_scope_spec.rb → relation_objects_spec.rb}

@@ -7,6 +7,20 @@ describe "Bio::Ucsc::Hg19" do
     Bio::Ucsc::Hg19::DBConnection.connect
   end
 
+  describe "HapmapSnpsJPT (BED table)" do
+    describe ".with_interval" do
+      context "given 'chr1:50,000-100,00000'" do
+        it 'returns records' do
+          gi = Bio::GenomicInterval.parse("chr1:50,000-100,000")
+          results = Bio::Ucsc::Hg19::HapmapSnpsJPT.
+            with_interval(gi).all
+          pp results
+          results.should be_kind_of(Array)
+        end
+      end
+    end
+  end
+    
   describe "Snp132 (BED table)" do
     describe ".with_interval" do
       context "given 'chr17:7,579,614-7,579,700' and class='in-del'" do

data/spec/rhemac2_spec.rb

@@ -97,6 +97,16 @@ describe "Bio::Ucsc::RheMac2" do
     end
   end 
 
+  describe "Bio::Ucsc::RheMac2::ChainMm9" do
+    context ".find_by_interval using interval String" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::RheMac2::ChainMm9.find_by_interval("chrX:1-10,000,000")
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
   describe "Bio::Ucsc::RheMac2::ChainMm9" do
     context ".find_by_interval" do
       it 'returns the first records' do
@@ -139,22 +149,22 @@ describe "Bio::Ucsc::RheMac2" do
     end
   end 
 
-  describe "Bio::Ucsc::RheMac2::ChainPanTro2" do
+  describe "Bio::Ucsc::RheMac2::ChainPanTro3" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
-        result = Bio::Ucsc::RheMac2::ChainPanTro2.find_by_interval gi
+        result = Bio::Ucsc::RheMac2::ChainPanTro3.find_by_interval gi
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::RheMac2::ChainPanTro2Link" do
+  describe "Bio::Ucsc::RheMac2::ChainPanTro3Link" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
-        result = Bio::Ucsc::RheMac2::ChainPanTro2Link.find_by_interval gi
+        result = Bio::Ucsc::RheMac2::ChainPanTro3Link.find_by_interval gi
         pp result
         result.should be_true
       end
@@ -575,10 +585,10 @@ describe "Bio::Ucsc::RheMac2" do
     end
   end 
 
-  describe "Bio::Ucsc::RheMac2::NetPanTro2" do
+  describe "Bio::Ucsc::RheMac2::NetPanTro3" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::RheMac2::NetPanTro2.first
+        result = Bio::Ucsc::RheMac2::NetPanTro3.first
         pp result
         result.should be_true
       end

data/spec/rn4_spec.rb

@@ -247,22 +247,22 @@ describe "Bio::Ucsc::Rn4" do
     end
   end 
 
-  describe "Bio::Ucsc::Rn4::ChainBosTau3" do
+  describe "Bio::Ucsc::Rn4::ChainBosTau6" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
-        result = Bio::Ucsc::Rn4::ChainBosTau3.find_by_interval gi
+        result = Bio::Ucsc::Rn4::ChainBosTau6.find_by_interval gi
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::Rn4::ChainBosTau3Link" do
+  describe "Bio::Ucsc::Rn4::ChainBosTau6Link" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
-        result = Bio::Ucsc::Rn4::ChainBosTau3Link.find_by_interval gi
+        result = Bio::Ucsc::Rn4::ChainBosTau6Link.find_by_interval gi
         pp result
         result.should be_true
       end
@@ -487,22 +487,22 @@ describe "Bio::Ucsc::Rn4" do
     end
   end 
 
-  describe "Bio::Ucsc::Rn4::ChainXenTro2" do
+  describe "Bio::Ucsc::Rn4::ChainXenTro3" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
-        result = Bio::Ucsc::Rn4::ChainXenTro2.find_by_interval gi
+        result = Bio::Ucsc::Rn4::ChainXenTro3.find_by_interval gi
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::Rn4::ChainXenTro2Link" do
+  describe "Bio::Ucsc::Rn4::ChainXenTro3Link" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
-        result = Bio::Ucsc::Rn4::ChainXenTro2Link.find_by_interval gi
+        result = Bio::Ucsc::Rn4::ChainXenTro3Link.find_by_interval gi
         pp result
         result.should be_true
       end
@@ -1304,10 +1304,10 @@ describe "Bio::Ucsc::Rn4" do
     end
   end 
 
-  describe "Bio::Ucsc::Rn4::NetBosTau3" do
+  describe "Bio::Ucsc::Rn4::NetBosTau6" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::Rn4::NetBosTau3.first
+        result = Bio::Ucsc::Rn4::NetBosTau6.first
         pp result
         result.should be_true
       end
@@ -1414,10 +1414,10 @@ describe "Bio::Ucsc::Rn4" do
     end
   end 
 
-  describe "Bio::Ucsc::Rn4::NetXenTro2" do
+  describe "Bio::Ucsc::Rn4::NetXenTro3" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::Rn4::NetXenTro2.first
+        result = Bio::Ucsc::Rn4::NetXenTro3.first
         pp result
         result.should be_true
       end

data/spec/spec_helper.rb

@@ -1,7 +1,9 @@
+require 'simplecov'
+SimpleCov.start
+
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'rspec'
-#require 'cover_me'
 
 # Requires supporting files with custom matchers and macros, etc,
 # in ./support/ and its subdirectories.

data/spec/susscr2_spec.rb

@@ -67,20 +67,20 @@ describe "Bio::Ucsc::SusScr2" do
     end
   end 
 
-  describe "Bio::Ucsc::SusScr2::ChainBosTau4" do
+  describe "Bio::Ucsc::SusScr2::ChainBosTau6" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::SusScr2::ChainBosTau4.first
+        result = Bio::Ucsc::SusScr2::ChainBosTau6.first
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::SusScr2::ChainBosTau4Link" do
+  describe "Bio::Ucsc::SusScr2::ChainBosTau6Link" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::SusScr2::ChainBosTau4Link.first
+        result = Bio::Ucsc::SusScr2::ChainBosTau6Link.first
         pp result
         result.should be_true
       end
@@ -470,10 +470,10 @@ describe "Bio::Ucsc::SusScr2" do
     end
   end 
 
-  describe "Bio::Ucsc::SusScr2::NetBosTau4" do
+  describe "Bio::Ucsc::SusScr2::NetBosTau6" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::SusScr2::NetBosTau4.first
+        result = Bio::Ucsc::SusScr2::NetBosTau6.first
         pp result
         result.should be_true
       end

data/spec/taegut1_spec.rb

@@ -70,7 +70,7 @@ describe "Bio::Ucsc::TaeGut1" do
   describe "Bio::Ucsc::TaeGut1::ChainGalGal3" do
     context ".find_by_interval" do
       it 'returns the first records' do
-        gi = Bio::GenomicInterval.parse("chrW:1-10,000,000")
+        gi = Bio::GenomicInterval.parse("chrUn:1-10,000,000")
         result = Bio::Ucsc::TaeGut1::ChainGalGal3.find_by_interval gi
         pp result
         result.should be_true
@@ -81,7 +81,7 @@ describe "Bio::Ucsc::TaeGut1" do
   describe "Bio::Ucsc::TaeGut1::ChainGalGal3Link" do
     context ".find_by_interval" do
       it 'returns the first records' do
-        gi = Bio::GenomicInterval.parse("chrW:1-10,000,000")
+        gi = Bio::GenomicInterval.parse("chrUn:1-10,000,000")
         result = Bio::Ucsc::TaeGut1::ChainGalGal3Link.find_by_interval gi
         pp result
         result.should be_true
@@ -172,7 +172,7 @@ describe "Bio::Ucsc::TaeGut1" do
   describe "Bio::Ucsc::TaeGut1::Est" do
     context ".find_by_interval" do
       it 'returns the first records' do
-        gi = Bio::GenomicInterval.parse("chrW:1-10,000,000")
+        gi = Bio::GenomicInterval.parse("chrUn:1-10,000,000")
         result = Bio::Ucsc::TaeGut1::Est.find_by_interval gi
         pp result
         result.should be_true
@@ -193,7 +193,7 @@ describe "Bio::Ucsc::TaeGut1" do
   describe "Bio::Ucsc::TaeGut1::Gap" do
     context ".find_by_interval" do
       it 'returns the first records' do
-        gi = Bio::GenomicInterval.parse("chrW:1-10,000,000")
+        gi = Bio::GenomicInterval.parse("chrUn:1-10,000,000")
         result = Bio::Ucsc::TaeGut1::Gap.find_by_interval gi
         pp result
         result.should be_true
@@ -324,7 +324,7 @@ describe "Bio::Ucsc::TaeGut1" do
   describe "Bio::Ucsc::TaeGut1::Gold" do
     context ".find_by_interval" do
       it 'returns the first records' do
-        gi = Bio::GenomicInterval.parse("chrW:1-10,000,000")
+        gi = Bio::GenomicInterval.parse("chrUn:1-10,000,000")
         result = Bio::Ucsc::TaeGut1::Gold.find_by_interval gi
         pp result
         result.should be_true
@@ -375,7 +375,7 @@ describe "Bio::Ucsc::TaeGut1" do
   describe "Bio::Ucsc::TaeGut1::IntronEst" do
     context ".find_by_interval" do
       it 'returns the first records' do
-        gi = Bio::GenomicInterval.parse("chrW:1-10,000,000")
+        gi = Bio::GenomicInterval.parse("chrUn:1-10,000,000")
         result = Bio::Ucsc::TaeGut1::IntronEst.find_by_interval gi
         pp result
         result.should be_true
@@ -406,7 +406,7 @@ describe "Bio::Ucsc::TaeGut1" do
   describe "Bio::Ucsc::TaeGut1::Mrna" do
     context ".find_by_interval" do
       it 'returns the first records' do
-        gi = Bio::GenomicInterval.parse("chrW:1-10,000,000")
+        gi = Bio::GenomicInterval.parse("chrUn:1-10,000,000")
         result = Bio::Ucsc::TaeGut1::Mrna.find_by_interval gi
         pp result
         result.should be_true
@@ -567,7 +567,7 @@ describe "Bio::Ucsc::TaeGut1" do
   describe "Bio::Ucsc::TaeGut1::Rmsk" do
     context ".find_by_interval" do
       it 'returns the first records' do
-        gi = Bio::GenomicInterval.parse("chrW:1-10,000,000")
+        gi = Bio::GenomicInterval.parse("chrUn:1-10,000,000")
         result = Bio::Ucsc::TaeGut1::Rmsk.find_by_interval gi
         pp result
         result.should be_true

data/spec/xentro2_spec.rb

@@ -67,20 +67,20 @@ describe "Bio::Ucsc::XenTro2" do
     end
   end 
 
-  describe "Bio::Ucsc::XenTro2::ChainAnoCar1" do
+  describe "Bio::Ucsc::XenTro2::ChainAnoCar2" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::XenTro2::ChainAnoCar1.first
+        result = Bio::Ucsc::XenTro2::ChainAnoCar2.first
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::XenTro2::ChainAnoCar1Link" do
+  describe "Bio::Ucsc::XenTro2::ChainAnoCar2Link" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::XenTro2::ChainAnoCar1Link.first
+        result = Bio::Ucsc::XenTro2::ChainAnoCar2Link.first
         pp result
         result.should be_true
       end
@@ -577,10 +577,10 @@ describe "Bio::Ucsc::XenTro2" do
     end
   end 
 
-  describe "Bio::Ucsc::XenTro2::NetAnoCar1" do
+  describe "Bio::Ucsc::XenTro2::NetAnoCar2" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::XenTro2::NetAnoCar1.first
+        result = Bio::Ucsc::XenTro2::NetAnoCar2.first
         pp result
         result.should be_true
       end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ucsc-api
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.4.0
   prerelease: 
 platform: ruby
 authors:
@@ -10,33 +10,33 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-09-06 00:00:00.000000000Z
+date: 2012-03-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &156765300 !ruby/object:Gem::Requirement
+  requirement: &138717880 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 3.0.7
   type: :runtime
   prerelease: false
-  version_requirements: *156765300
+  version_requirements: *138717880
 - !ruby/object:Gem::Dependency
   name: activesupport
-  requirement: &156764820 !ruby/object:Gem::Requirement
+  requirement: &138717400 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 3.0.7
   type: :runtime
   prerelease: false
-  version_requirements: *156764820
+  version_requirements: *138717400
 - !ruby/object:Gem::Dependency
   name: mysql
-  requirement: &156764340 !ruby/object:Gem::Requirement
+  requirement: &138716920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -44,10 +44,10 @@ dependencies:
         version: 2.8.1
   type: :runtime
   prerelease: false
-  version_requirements: *156764340
+  version_requirements: *138716920
 - !ruby/object:Gem::Dependency
   name: bio-genomic-interval
-  requirement: &156763840 !ruby/object:Gem::Requirement
+  requirement: &138716440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,21 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *156763840
+  version_requirements: *138716440
+- !ruby/object:Gem::Dependency
+  name: safe_attributes
+  requirement: &138715960 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.8
+  type: :runtime
+  prerelease: false
+  version_requirements: *138715960
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &156763360 !ruby/object:Gem::Requirement
+  requirement: &138715480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +77,10 @@ dependencies:
         version: 2.5.0
   type: :development
   prerelease: false
-  version_requirements: *156763360
+  version_requirements: *138715480
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &156762880 !ruby/object:Gem::Requirement
+  requirement: &138715000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +88,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *156762880
+  version_requirements: *138715000
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &156762400 !ruby/object:Gem::Requirement
+  requirement: &138714520 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +99,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *156762400
+  version_requirements: *138714520
 - !ruby/object:Gem::Dependency
-  name: rcov
-  requirement: &156761920 !ruby/object:Gem::Requirement
+  name: simplecov
+  requirement: &138730400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -99,10 +110,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *156761920
+  version_requirements: *138730400
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &156761440 !ruby/object:Gem::Requirement
+  requirement: &138729920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,10 +121,10 @@ dependencies:
         version: 1.4.1
   type: :development
   prerelease: false
-  version_requirements: *156761440
+  version_requirements: *138729920
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &156760960 !ruby/object:Gem::Requirement
+  requirement: &138729440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -121,32 +132,29 @@ dependencies:
         version: 3.9.1
   type: :development
   prerelease: false
-  version_requirements: *156760960
+  version_requirements: *138729440
 description: ! 'Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
 email: missy@be.to
 executables: []
 extensions: []
 extra_rdoc_files:
-- README.rdoc
+- README.md
 files:
 - COPYING
 - COPYING.ja
 - Gemfile
 - Gemfile.lock
-- README.rdoc
+- README.md
 - Rakefile
 - VERSION
 - bio-ucsc-api.gemspec
 - lib/bio-ucsc-api.rb
 - lib/bio-ucsc.rb
 - lib/bio-ucsc/ailmel1.rb
-- lib/bio-ucsc/ailmel1/db_connection.rb
 - lib/bio-ucsc/anocar2.rb
-- lib/bio-ucsc/anocar2/db_connection.rb
 - lib/bio-ucsc/anogam1.rb
 - lib/bio-ucsc/anogam1/chaindm3.rb
 - lib/bio-ucsc/anogam1/chaindm3link.rb
-- lib/bio-ucsc/anogam1/db_connection.rb
 - lib/bio-ucsc/anogam1/est.rb
 - lib/bio-ucsc/anogam1/gap.rb
 - lib/bio-ucsc/anogam1/gold.rb
@@ -156,7 +164,6 @@ files:
 - lib/bio-ucsc/apimel2.rb
 - lib/bio-ucsc/apimel2/chaindm2.rb
 - lib/bio-ucsc/apimel2/chaindm2link.rb
-- lib/bio-ucsc/apimel2/db_connection.rb
 - lib/bio-ucsc/aplcal1.rb
 - lib/bio-ucsc/aplcal1/chaincaepb1.rb
 - lib/bio-ucsc/aplcal1/chaincaepb1link.rb
@@ -166,12 +173,10 @@ files:
 - lib/bio-ucsc/aplcal1/chaincb3link.rb
 - lib/bio-ucsc/aplcal1/chaince6.rb
 - lib/bio-ucsc/aplcal1/chaince6link.rb
-- lib/bio-ucsc/aplcal1/db_connection.rb
 - lib/bio-ucsc/aplcal1/gap.rb
 - lib/bio-ucsc/aplcal1/gold.rb
 - lib/bio-ucsc/aplcal1/rmsk.rb
 - lib/bio-ucsc/bostau4.rb
-- lib/bio-ucsc/bostau4/db_connection.rb
 - lib/bio-ucsc/braflo1.rb
 - lib/bio-ucsc/braflo1/chaingalgal3.rb
 - lib/bio-ucsc/braflo1/chaingalgal3link.rb
@@ -181,29 +186,24 @@ files:
 - lib/bio-ucsc/braflo1/chainmm9link.rb
 - lib/bio-ucsc/braflo1/chainpetmar1.rb
 - lib/bio-ucsc/braflo1/chainpetmar1link.rb
-- lib/bio-ucsc/braflo1/db_connection.rb
 - lib/bio-ucsc/braflo1/gap.rb
 - lib/bio-ucsc/braflo1/gold.rb
 - lib/bio-ucsc/caejap1.rb
 - lib/bio-ucsc/caejap1/chaince6.rb
 - lib/bio-ucsc/caejap1/chaince6link.rb
-- lib/bio-ucsc/caejap1/db_connection.rb
 - lib/bio-ucsc/caejap1/gap.rb
 - lib/bio-ucsc/caejap1/gold.rb
 - lib/bio-ucsc/caepb2.rb
 - lib/bio-ucsc/caepb2/chaince6.rb
 - lib/bio-ucsc/caepb2/chaince6link.rb
-- lib/bio-ucsc/caepb2/db_connection.rb
 - lib/bio-ucsc/caepb2/gap.rb
 - lib/bio-ucsc/caepb2/gold.rb
 - lib/bio-ucsc/caerem3.rb
 - lib/bio-ucsc/caerem3/chaince6.rb
 - lib/bio-ucsc/caerem3/chaince6link.rb
-- lib/bio-ucsc/caerem3/db_connection.rb
 - lib/bio-ucsc/caerem3/gap.rb
 - lib/bio-ucsc/caerem3/gold.rb
 - lib/bio-ucsc/caljac3.rb
-- lib/bio-ucsc/caljac3/db_connection.rb
 - lib/bio-ucsc/canfam2.rb
 - lib/bio-ucsc/canfam2/chainbostau4.rb
 - lib/bio-ucsc/canfam2/chainbostau4link.rb
@@ -213,7 +213,6 @@ files:
 - lib/bio-ucsc/canfam2/chainrn4link.rb
 - lib/bio-ucsc/canfam2/chainself.rb
 - lib/bio-ucsc/canfam2/chainselflink.rb
-- lib/bio-ucsc/canfam2/db_connection.rb
 - lib/bio-ucsc/canfam2/est.rb
 - lib/bio-ucsc/canfam2/gap.rb
 - lib/bio-ucsc/canfam2/gold.rb
@@ -221,7 +220,6 @@ files:
 - lib/bio-ucsc/canfam2/mrna.rb
 - lib/bio-ucsc/canfam2/rmsk.rb
 - lib/bio-ucsc/cavpor3.rb
-- lib/bio-ucsc/cavpor3/db_connection.rb
 - lib/bio-ucsc/cb3.rb
 - lib/bio-ucsc/cb3/chaincaepb1.rb
 - lib/bio-ucsc/cb3/chaincaepb1link.rb
@@ -231,7 +229,6 @@ files:
 - lib/bio-ucsc/cb3/chaince6link.rb
 - lib/bio-ucsc/cb3/chainpripac1.rb
 - lib/bio-ucsc/cb3/chainpripac1link.rb
-- lib/bio-ucsc/cb3/db_connection.rb
 - lib/bio-ucsc/cb3/est.rb
 - lib/bio-ucsc/cb3/gap.rb
 - lib/bio-ucsc/cb3/gold.rb
@@ -251,7 +248,6 @@ files:
 - lib/bio-ucsc/ce6/chainpripac1link.rb
 - lib/bio-ucsc/ce6/chainself.rb
 - lib/bio-ucsc/ce6/chainselflink.rb
-- lib/bio-ucsc/ce6/db_connection.rb
 - lib/bio-ucsc/ce6/est.rb
 - lib/bio-ucsc/ce6/gap.rb
 - lib/bio-ucsc/ce6/gold.rb
@@ -260,9 +256,8 @@ files:
 - lib/bio-ucsc/ce6/rmsk.rb
 - lib/bio-ucsc/ce6/t25mersrepeats.rb
 - lib/bio-ucsc/ci2.rb
-- lib/bio-ucsc/ci2/db_connection.rb
 - lib/bio-ucsc/danrer7.rb
-- lib/bio-ucsc/danrer7/db_connection.rb
+- lib/bio-ucsc/db_connector.rb
 - lib/bio-ucsc/dm3.rb
 - lib/bio-ucsc/dm3/chainanogam1.rb
 - lib/bio-ucsc/dm3/chainanogam1link.rb
@@ -282,7 +277,6 @@ files:
 - lib/bio-ucsc/dm3/chaindrosim1link.rb
 - lib/bio-ucsc/dm3/chaindroyak2.rb
 - lib/bio-ucsc/dm3/chaindroyak2link.rb
-- lib/bio-ucsc/dm3/db_connection.rb
 - lib/bio-ucsc/dm3/est.rb
 - lib/bio-ucsc/dm3/gap.rb
 - lib/bio-ucsc/dm3/gold.rb
@@ -292,7 +286,6 @@ files:
 - lib/bio-ucsc/dp3.rb
 - lib/bio-ucsc/dp3/chaindm3.rb
 - lib/bio-ucsc/dp3/chaindm3link.rb
-- lib/bio-ucsc/dp3/db_connection.rb
 - lib/bio-ucsc/dp3/est.rb
 - lib/bio-ucsc/dp3/gap.rb
 - lib/bio-ucsc/dp3/gold.rb
@@ -300,21 +293,14 @@ files:
 - lib/bio-ucsc/dp3/mrna.rb
 - lib/bio-ucsc/dp3/rmsk.rb
 - lib/bio-ucsc/droana2.rb
-- lib/bio-ucsc/droana2/db_connection.rb
 - lib/bio-ucsc/droere1.rb
-- lib/bio-ucsc/droere1/db_connection.rb
 - lib/bio-ucsc/drogri1.rb
-- lib/bio-ucsc/drogri1/db_connection.rb
 - lib/bio-ucsc/dromoj2.rb
-- lib/bio-ucsc/dromoj2/db_connection.rb
 - lib/bio-ucsc/droper1.rb
-- lib/bio-ucsc/droper1/db_connection.rb
 - lib/bio-ucsc/drosec1.rb
-- lib/bio-ucsc/drosec1/db_connection.rb
 - lib/bio-ucsc/drosim1.rb
 - lib/bio-ucsc/drosim1/chaindm3.rb
 - lib/bio-ucsc/drosim1/chaindm3link.rb
-- lib/bio-ucsc/drosim1/db_connection.rb
 - lib/bio-ucsc/drosim1/est.rb
 - lib/bio-ucsc/drosim1/gap.rb
 - lib/bio-ucsc/drosim1/gold.rb
@@ -322,11 +308,9 @@ files:
 - lib/bio-ucsc/drosim1/mrna.rb
 - lib/bio-ucsc/drosim1/rmsk.rb
 - lib/bio-ucsc/drovir2.rb
-- lib/bio-ucsc/drovir2/db_connection.rb
 - lib/bio-ucsc/droyak2.rb
 - lib/bio-ucsc/droyak2/chaindm3.rb
 - lib/bio-ucsc/droyak2/chaindm3link.rb
-- lib/bio-ucsc/droyak2/db_connection.rb
 - lib/bio-ucsc/droyak2/est.rb
 - lib/bio-ucsc/droyak2/gap.rb
 - lib/bio-ucsc/droyak2/gold.rb
@@ -334,7 +318,6 @@ files:
 - lib/bio-ucsc/droyak2/mrna.rb
 - lib/bio-ucsc/droyak2/rmsk.rb
 - lib/bio-ucsc/equcab2.rb
-- lib/bio-ucsc/equcab2/db_connection.rb
 - lib/bio-ucsc/equcab2/est.rb
 - lib/bio-ucsc/equcab2/gap.rb
 - lib/bio-ucsc/equcab2/gold.rb
@@ -342,7 +325,9 @@ files:
 - lib/bio-ucsc/equcab2/mrna.rb
 - lib/bio-ucsc/equcab2/rmsk.rb
 - lib/bio-ucsc/felcat4.rb
-- lib/bio-ucsc/felcat4/db_connection.rb
+- lib/bio-ucsc/file.rb
+- lib/bio-ucsc/file/bytequeue.rb
+- lib/bio-ucsc/file/twobit.rb
 - lib/bio-ucsc/fr2.rb
 - lib/bio-ucsc/fr2/chaingalgal3.rb
 - lib/bio-ucsc/fr2/chaingalgal3link.rb
@@ -352,7 +337,6 @@ files:
 - lib/bio-ucsc/fr2/chainmm9link.rb
 - lib/bio-ucsc/fr2/chainorylat2.rb
 - lib/bio-ucsc/fr2/chainorylat2link.rb
-- lib/bio-ucsc/fr2/db_connection.rb
 - lib/bio-ucsc/fr2/est.rb
 - lib/bio-ucsc/fr2/gap.rb
 - lib/bio-ucsc/fr2/gold.rb
@@ -384,7 +368,6 @@ files:
 - lib/bio-ucsc/galgal3/chaintaegut1link.rb
 - lib/bio-ucsc/galgal3/chainxentro2.rb
 - lib/bio-ucsc/galgal3/chainxentro2link.rb
-- lib/bio-ucsc/galgal3/db_connection.rb
 - lib/bio-ucsc/galgal3/est.rb
 - lib/bio-ucsc/galgal3/gap.rb
 - lib/bio-ucsc/galgal3/gold.rb
@@ -402,14 +385,13 @@ files:
 - lib/bio-ucsc/gasacu1/chainmm9link.rb
 - lib/bio-ucsc/gasacu1/chainorylat2.rb
 - lib/bio-ucsc/gasacu1/chainorylat2link.rb
-- lib/bio-ucsc/gasacu1/db_connection.rb
 - lib/bio-ucsc/gasacu1/est.rb
 - lib/bio-ucsc/gasacu1/intronest.rb
 - lib/bio-ucsc/gasacu1/mrna.rb
 - lib/bio-ucsc/gasacu1/rmsk.rb
 - lib/bio-ucsc/genomic-interval-bin.rb
+- lib/bio-ucsc/gi.rb
 - lib/bio-ucsc/go.rb
-- lib/bio-ucsc/go/db_connection.rb
 - lib/bio-ucsc/hg18.rb
 - lib/bio-ucsc/hg18/chainanocar1.rb
 - lib/bio-ucsc/hg18/chainbostau4.rb
@@ -437,25 +419,17 @@ files:
 - lib/bio-ucsc/hg18/chaintaegut1.rb
 - lib/bio-ucsc/hg18/chaintetnig2.rb
 - lib/bio-ucsc/hg18/chainxentro2.rb
-- lib/bio-ucsc/hg18/db_connection.rb
 - lib/bio-ucsc/hg18/gap.rb
 - lib/bio-ucsc/hg18/gold.rb
 - lib/bio-ucsc/hg18/intronest.rb
 - lib/bio-ucsc/hg18/rmsk.rb
 - lib/bio-ucsc/hg18/rmskrm327.rb
 - lib/bio-ucsc/hg19.rb
-- lib/bio-ucsc/hg19/db_connection.rb
 - lib/bio-ucsc/hg19/description.rb
 - lib/bio-ucsc/hg19/gbcdnainfo.rb
 - lib/bio-ucsc/hgfixed.rb
-- lib/bio-ucsc/hgfixed/db_connection.rb
 - lib/bio-ucsc/loxafr3.rb
-- lib/bio-ucsc/loxafr3/db_connection.rb
 - lib/bio-ucsc/mm9.rb
-- lib/bio-ucsc/mm9/chainanocar1.rb
-- lib/bio-ucsc/mm9/chainanocar1link.rb
-- lib/bio-ucsc/mm9/chainbostau4.rb
-- lib/bio-ucsc/mm9/chainbostau4link.rb
 - lib/bio-ucsc/mm9/chainbraflo1.rb
 - lib/bio-ucsc/mm9/chainbraflo1link.rb
 - lib/bio-ucsc/mm9/chaincanfam2.rb
@@ -472,8 +446,6 @@ files:
 - lib/bio-ucsc/mm9/chainornana1link.rb
 - lib/bio-ucsc/mm9/chainorylat2.rb
 - lib/bio-ucsc/mm9/chainorylat2link.rb
-- lib/bio-ucsc/mm9/chainpantro2.rb
-- lib/bio-ucsc/mm9/chainpantro2link.rb
 - lib/bio-ucsc/mm9/chainpetmar1.rb
 - lib/bio-ucsc/mm9/chainpetmar1link.rb
 - lib/bio-ucsc/mm9/chainponabe2.rb
@@ -482,9 +454,6 @@ files:
 - lib/bio-ucsc/mm9/chainrhemac2link.rb
 - lib/bio-ucsc/mm9/chainrn4.rb
 - lib/bio-ucsc/mm9/chainrn4link.rb
-- lib/bio-ucsc/mm9/chainxentro2.rb
-- lib/bio-ucsc/mm9/chainxentro2link.rb
-- lib/bio-ucsc/mm9/db_connection.rb
 - lib/bio-ucsc/mm9/est.rb
 - lib/bio-ucsc/mm9/gap.rb
 - lib/bio-ucsc/mm9/gold.rb
@@ -492,19 +461,12 @@ files:
 - lib/bio-ucsc/mm9/mrna.rb
 - lib/bio-ucsc/mm9/rmsk.rb
 - lib/bio-ucsc/mondom5.rb
-- lib/bio-ucsc/mondom5/db_connection.rb
 - lib/bio-ucsc/ornana1.rb
-- lib/bio-ucsc/ornana1/db_connection.rb
 - lib/bio-ucsc/orycun2.rb
-- lib/bio-ucsc/orycun2/db_connection.rb
 - lib/bio-ucsc/orylat2.rb
-- lib/bio-ucsc/orylat2/db_connection.rb
 - lib/bio-ucsc/oviari1.rb
-- lib/bio-ucsc/oviari1/db_connection.rb
 - lib/bio-ucsc/pantro3.rb
-- lib/bio-ucsc/pantro3/db_connection.rb
 - lib/bio-ucsc/petmar1.rb
-- lib/bio-ucsc/petmar1/db_connection.rb
 - lib/bio-ucsc/ponabe2.rb
 - lib/bio-ucsc/ponabe2/chainmm9.rb
 - lib/bio-ucsc/ponabe2/chainmm9link.rb
@@ -512,7 +474,6 @@ files:
 - lib/bio-ucsc/ponabe2/chainornana1link.rb
 - lib/bio-ucsc/ponabe2/chainrhemac2.rb
 - lib/bio-ucsc/ponabe2/chainrhemac2link.rb
-- lib/bio-ucsc/ponabe2/db_connection.rb
 - lib/bio-ucsc/ponabe2/est.rb
 - lib/bio-ucsc/ponabe2/gap.rb
 - lib/bio-ucsc/ponabe2/gold.rb
@@ -528,26 +489,19 @@ files:
 - lib/bio-ucsc/pripac1/chaincb3link.rb
 - lib/bio-ucsc/pripac1/chaince6.rb
 - lib/bio-ucsc/pripac1/chaince6link.rb
-- lib/bio-ucsc/pripac1/db_connection.rb
 - lib/bio-ucsc/pripac1/gap.rb
 - lib/bio-ucsc/pripac1/gold.rb
 - lib/bio-ucsc/pripac1/rmsk.rb
 - lib/bio-ucsc/proteome.rb
-- lib/bio-ucsc/proteome/db_connection.rb
 - lib/bio-ucsc/reference.rb
 - lib/bio-ucsc/rhemac2.rb
 - lib/bio-ucsc/rhemac2/chainmm9.rb
 - lib/bio-ucsc/rhemac2/chainmm9link.rb
-- lib/bio-ucsc/rhemac2/chainpantro2.rb
-- lib/bio-ucsc/rhemac2/chainpantro2link.rb
 - lib/bio-ucsc/rhemac2/chainponabe2.rb
 - lib/bio-ucsc/rhemac2/chainponabe2link.rb
 - lib/bio-ucsc/rhemac2/chainrn4.rb
 - lib/bio-ucsc/rhemac2/chainrn4link.rb
-- lib/bio-ucsc/rhemac2/db_connection.rb
 - lib/bio-ucsc/rn4.rb
-- lib/bio-ucsc/rn4/chainbostau3.rb
-- lib/bio-ucsc/rn4/chainbostau3link.rb
 - lib/bio-ucsc/rn4/chaincanfam2.rb
 - lib/bio-ucsc/rn4/chaincanfam2link.rb
 - lib/bio-ucsc/rn4/chaincavpor3.rb
@@ -566,9 +520,6 @@ files:
 - lib/bio-ucsc/rn4/chainpantro2link.rb
 - lib/bio-ucsc/rn4/chainrhemac2.rb
 - lib/bio-ucsc/rn4/chainrhemac2link.rb
-- lib/bio-ucsc/rn4/chainxentro2.rb
-- lib/bio-ucsc/rn4/chainxentro2link.rb
-- lib/bio-ucsc/rn4/db_connection.rb
 - lib/bio-ucsc/rn4/est.rb
 - lib/bio-ucsc/rn4/gap.rb
 - lib/bio-ucsc/rn4/gold.rb
@@ -576,7 +527,6 @@ files:
 - lib/bio-ucsc/rn4/mrna.rb
 - lib/bio-ucsc/rn4/rmsk.rb
 - lib/bio-ucsc/saccer2.rb
-- lib/bio-ucsc/saccer2/db_connection.rb
 - lib/bio-ucsc/saccer2/est.rb
 - lib/bio-ucsc/saccer2/gap.rb
 - lib/bio-ucsc/saccer2/gold.rb
@@ -588,19 +538,7 @@ files:
 - lib/bio-ucsc/saccer2/t2micron_intronEst.rb
 - lib/bio-ucsc/saccer2/t2micron_mrna.rb
 - lib/bio-ucsc/strpur2.rb
-- lib/bio-ucsc/strpur2/chaingalgal3.rb
-- lib/bio-ucsc/strpur2/chaingalgal3link.rb
-- lib/bio-ucsc/strpur2/chainhg18.rb
-- lib/bio-ucsc/strpur2/chainhg18link.rb
-- lib/bio-ucsc/strpur2/chainmm9.rb
-- lib/bio-ucsc/strpur2/chainmm9link.rb
-- lib/bio-ucsc/strpur2/chainpetmar1.rb
-- lib/bio-ucsc/strpur2/chainpetmar1link.rb
-- lib/bio-ucsc/strpur2/db_connection.rb
-- lib/bio-ucsc/strpur2/gap.rb
-- lib/bio-ucsc/strpur2/gold.rb
 - lib/bio-ucsc/susscr2.rb
-- lib/bio-ucsc/susscr2/db_connection.rb
 - lib/bio-ucsc/susscr2/est.rb
 - lib/bio-ucsc/susscr2/intronest.rb
 - lib/bio-ucsc/susscr2/mrna.rb
@@ -608,7 +546,6 @@ files:
 - lib/bio-ucsc/taegut1.rb
 - lib/bio-ucsc/taegut1/chaingalgal3.rb
 - lib/bio-ucsc/taegut1/chaingalgal3link.rb
-- lib/bio-ucsc/taegut1/db_connection.rb
 - lib/bio-ucsc/taegut1/est.rb
 - lib/bio-ucsc/taegut1/gap.rb
 - lib/bio-ucsc/taegut1/gold.rb
@@ -616,23 +553,11 @@ files:
 - lib/bio-ucsc/taegut1/mrna.rb
 - lib/bio-ucsc/taegut1/rmsk.rb
 - lib/bio-ucsc/tetnig2.rb
-- lib/bio-ucsc/tetnig2/db_connection.rb
 - lib/bio-ucsc/tetnig2/mrna.rb
 - lib/bio-ucsc/ucsc_bin.rb
 - lib/bio-ucsc/uniprot.rb
-- lib/bio-ucsc/uniprot/db_connection.rb
 - lib/bio-ucsc/visigene.rb
-- lib/bio-ucsc/visigene/db_connection.rb
 - lib/bio-ucsc/xentro2.rb
-- lib/bio-ucsc/xentro2/chaingalgal3.rb
-- lib/bio-ucsc/xentro2/chaingalgal3link.rb
-- lib/bio-ucsc/xentro2/db_connection.rb
-- lib/bio-ucsc/xentro2/est.rb
-- lib/bio-ucsc/xentro2/gap.rb
-- lib/bio-ucsc/xentro2/gold.rb
-- lib/bio-ucsc/xentro2/intronest.rb
-- lib/bio-ucsc/xentro2/mrna.rb
-- lib/bio-ucsc/xentro2/rmsk.rb
 - samples/bed2refseq.rb
 - samples/hg19-2bit-retrieve.rb
 - samples/hg19-sample.rb
@@ -670,6 +595,7 @@ files:
 - spec/droyak2_spec.rb
 - spec/equcab2_spec.rb
 - spec/felcat4_spec.rb
+- spec/file/twobit.rb
 - spec/find_by_and_spec.rb
 - spec/fr2_spec.rb
 - spec/galgal3_spec.rb
@@ -4088,9 +4014,8 @@ files:
 - spec/hg19/cgapsage_spec.rb
 - spec/hg19/cgapsagelib_spec.rb
 - spec/hg19/chainailmel1_spec.rb
-- spec/hg19/chainanocar1_spec.rb
-- spec/hg19/chainaplcal1_spec.rb
-- spec/hg19/chainbostau4_spec.rb
+- spec/hg19/chainanocar2_spec.rb
+- spec/hg19/chainbostau6_spec.rb
 - spec/hg19/chaincaljac3_spec.rb
 - spec/hg19/chaincanfam2_spec.rb
 - spec/hg19/chaincavpor3_spec.rb
@@ -4117,7 +4042,8 @@ files:
 - spec/hg19/chainsusscr2_spec.rb
 - spec/hg19/chaintaegut1_spec.rb
 - spec/hg19/chaintetnig2_spec.rb
-- spec/hg19/chainxentro2_spec.rb
+- spec/hg19/chainxentro3_spec.rb
+- spec/hg19/connect_spec.rb
 - spec/hg19/consindelshgmmcanfam_spec.rb
 - spec/hg19/consindelshgmmcanfamconf_spec.rb
 - spec/hg19/cpgislandext_spec.rb
@@ -4201,9 +4127,8 @@ files:
 - spec/hg19/multiz46way_spec.rb
 - spec/hg19/nestedrepeats_spec.rb
 - spec/hg19/netailmel1_spec.rb
-- spec/hg19/netanocar1_spec.rb
-- spec/hg19/netaplcal1_spec.rb
-- spec/hg19/netbostau4_spec.rb
+- spec/hg19/netanocar2_spec.rb
+- spec/hg19/netbostau6_spec.rb
 - spec/hg19/netcaljac3_spec.rb
 - spec/hg19/netcanfam2_spec.rb
 - spec/hg19/netcavpor3_spec.rb
@@ -4229,7 +4154,7 @@ files:
 - spec/hg19/netsusscr2_spec.rb
 - spec/hg19/nettaegut1_spec.rb
 - spec/hg19/nettetnig2_spec.rb
-- spec/hg19/netxentro2_spec.rb
+- spec/hg19/netxentro3_spec.rb
 - spec/hg19/nscangene_spec.rb
 - spec/hg19/nscanpep_spec.rb
 - spec/hg19/nthumchimpcodingdiff_spec.rb
@@ -5560,7 +5485,6 @@ files:
 - spec/loxafr3_spec.rb
 - spec/mm9_spec.rb
 - spec/mondom5_spec.rb
-- spec/named_scope_spec.rb
 - spec/ornana1_spec.rb
 - spec/orycun2_spec.rb
 - spec/orylat2_spec.rb
@@ -5571,6 +5495,7 @@ files:
 - spec/pripac1_spec.rb
 - spec/proteome_spec.rb
 - spec/reference_spec.rb
+- spec/relation_objects_spec.rb
 - spec/rhemac2_spec.rb
 - spec/rn4_spec.rb
 - spec/saccer2_spec.rb
@@ -5597,7 +5522,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1643967241848508000
+      hash: -2016024275931778348
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -5606,7 +5531,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.6
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: ! 'The Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
@@ -5642,6 +5567,7 @@ test_files:
 - spec/droyak2_spec.rb
 - spec/equcab2_spec.rb
 - spec/felcat4_spec.rb
+- spec/file/twobit.rb
 - spec/find_by_and_spec.rb
 - spec/fr2_spec.rb
 - spec/galgal3_spec.rb
@@ -9060,9 +8986,8 @@ test_files:
 - spec/hg19/cgapsage_spec.rb
 - spec/hg19/cgapsagelib_spec.rb
 - spec/hg19/chainailmel1_spec.rb
-- spec/hg19/chainanocar1_spec.rb
-- spec/hg19/chainaplcal1_spec.rb
-- spec/hg19/chainbostau4_spec.rb
+- spec/hg19/chainanocar2_spec.rb
+- spec/hg19/chainbostau6_spec.rb
 - spec/hg19/chaincaljac3_spec.rb
 - spec/hg19/chaincanfam2_spec.rb
 - spec/hg19/chaincavpor3_spec.rb
@@ -9089,7 +9014,8 @@ test_files:
 - spec/hg19/chainsusscr2_spec.rb
 - spec/hg19/chaintaegut1_spec.rb
 - spec/hg19/chaintetnig2_spec.rb
-- spec/hg19/chainxentro2_spec.rb
+- spec/hg19/chainxentro3_spec.rb
+- spec/hg19/connect_spec.rb
 - spec/hg19/consindelshgmmcanfam_spec.rb
 - spec/hg19/consindelshgmmcanfamconf_spec.rb
 - spec/hg19/cpgislandext_spec.rb
@@ -9173,9 +9099,8 @@ test_files:
 - spec/hg19/multiz46way_spec.rb
 - spec/hg19/nestedrepeats_spec.rb
 - spec/hg19/netailmel1_spec.rb
-- spec/hg19/netanocar1_spec.rb
-- spec/hg19/netaplcal1_spec.rb
-- spec/hg19/netbostau4_spec.rb
+- spec/hg19/netanocar2_spec.rb
+- spec/hg19/netbostau6_spec.rb
 - spec/hg19/netcaljac3_spec.rb
 - spec/hg19/netcanfam2_spec.rb
 - spec/hg19/netcavpor3_spec.rb
@@ -9201,7 +9126,7 @@ test_files:
 - spec/hg19/netsusscr2_spec.rb
 - spec/hg19/nettaegut1_spec.rb
 - spec/hg19/nettetnig2_spec.rb
-- spec/hg19/netxentro2_spec.rb
+- spec/hg19/netxentro3_spec.rb
 - spec/hg19/nscangene_spec.rb
 - spec/hg19/nscanpep_spec.rb
 - spec/hg19/nthumchimpcodingdiff_spec.rb
@@ -10532,7 +10457,6 @@ test_files:
 - spec/loxafr3_spec.rb
 - spec/mm9_spec.rb
 - spec/mondom5_spec.rb
-- spec/named_scope_spec.rb
 - spec/ornana1_spec.rb
 - spec/orycun2_spec.rb
 - spec/orylat2_spec.rb
@@ -10543,6 +10467,7 @@ test_files:
 - spec/pripac1_spec.rb
 - spec/proteome_spec.rb
 - spec/reference_spec.rb
+- spec/relation_objects_spec.rb
 - spec/rhemac2_spec.rb
 - spec/rn4_spec.rb
 - spec/saccer2_spec.rb