bio-ucsc-api 0.0.3 → 0.0.4

data/Gemfile

@@ -3,7 +3,7 @@ source "http://rubygems.org"
 # Example:
 #   gem "activesupport", ">= 2.3.5"
 gem "activerecord",         ">= 3.0.7"
-#gem "activesupport",        ">= 3.0.0"
+gem "activesupport",        ">= 3.0.7"
 gem "mysql",                ">= 2.8.1"
 gem "bio-genomic-interval", ">= 0.1.2"
 
@@ -15,5 +15,4 @@ group :development do
   gem "jeweler", "~> 1.5.2"
   gem "rcov", ">= 0"
   gem "bio", ">= 1.4.1"
-#  gem "cover_me", ">= 1.0.0.rc6"
 end

data/Gemfile.lock

@@ -33,13 +33,14 @@ GEM
     rspec-expectations (2.5.0)
       diff-lcs (~> 1.1.2)
     rspec-mocks (2.5.0)
-    tzinfo (0.3.26)
+    tzinfo (0.3.27)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
   activerecord (>= 3.0.7)
+  activesupport (>= 3.0.7)
   bio (>= 1.4.1)
   bio-genomic-interval (>= 0.1.2)
   bundler (~> 1.0.0)

data/README.rdoc

@@ -15,7 +15,7 @@ See also a paper:
 Strozzi F, Aerts J: A Ruby API to query the Ensembl database for genomic features.
 Bioinformatics 2011, 27:1013-1014.
 
-NOTE: THIS PACKAGE IS STILL VERY PRELIMINARY VERSION. 
+NOTE: THIS PACKAGE IS STILL *VERY PRELIMINARY* VERSION. 
 Your comments, suggestions and requests are welcome.
 Email to the author (missy at be.to) or create an "Issue" at
 http://github.com/misshie/bioruby-ucsc-api/issues
@@ -27,10 +27,13 @@ http://github.com/misshie/bioruby-ucsc-api/issues
 * Using the Bin index system to improve query performance (see https://github.com/misshie/UCSCBin )
 * Automatic conversion of "1-based full-closed intervals" to internal "0-based half-closed intervals" (see also bioruby-genomic-interval)
 * Supporting non-official MySql hosts (e.g. local servers)
-* NEW: Supporting locally-stored '2bit' files, which can be downloaded from the UCSC site, to retrieve referencial sequence. Now supporting unknown "N" nucleotide blocks, however, "mask-blocks", which are shown in lower-case in UCSC's DNA function, are not supported yet. 
 * Using Rspec for the testing framework
 * Trying to support whole hg19 and hg18 databases.
 
+* *UPDATE (v0.0.4)*: Almost all hg19 tables are supported. "filename" tables in ENCODE dataset are omitted. Each of them contains only single record of a path to the raw data file. Definitions of table relations are incomplete. 
+* *NEW (v0.0.3)*: Supporting locally-stored '2bit' files, which can be downloaded from the UCSC site, to retrieve referencial sequence. Now supporting unknown "N" nucleotide blocks, however, "mask-blocks", which are shown in lower-case in UCSC's DNA function, are not supported yet.
+* *MODIFIED (v0.0.3)*: For the "TABLE" class and the "column" column, TABLE.find_by_column retrives a first record, and TABLE.find_all_by_column retrieves all the records as an Array.
+
 == Install
 
  $ gem install bio-ucsc-api
@@ -43,7 +46,7 @@ http://github.com/misshie/bioruby-ucsc-api/issues
  Bio::Ucsc::Hg19::DBConnection.connect
 
  itv =  Bio::GenomicInterval.parse("chr1:1-11,000")
- Bio::Ucsc::Hg19::Snp131.find_by_interval(itv).each do |e|
+ Bio::Ucsc::Hg19::Snp131.find_all_by_interval(itv).each do |e|
    i = Bio::GenomicInterval.zero_based(e.chrom, e.chromStart, e.chromEnd)
    puts "#{i.chrom}\t#{i.chromStart}\t#{e.name}\t#{e[:class]}"
  end
@@ -58,7 +61,7 @@ http://github.com/misshie/bioruby-ucsc-api/issues
 == Copyright
 Copyright:: (c) 2011 MISHIMA, Hiroyuki (missy at be.to / hmishima at nagasaki-u.ac.jp)
 
-Copyright:: (c) 2008-2011 Francesco Strozzi, Jan Aerts
+Copyright:: (c) 2008-2010 Francesco Strozzi, Jan Aerts
 
-License:: Ruby licence (Ruby's / GPLv2 dual). See COPYING and COPYING.ja for further details.
+License:: Ruby license (Ruby's / GPLv2 dual). See COPYING and COPYING.ja for further details.
 

data/Rakefile

@@ -17,18 +17,19 @@ Jeweler::Tasks.new do |gem|
   gem.homepage = "http://github.com/misshie/bioruby-ucsc-api"
   gem.license = "Ruby (Ruby's/GPLv2 dual)"
   gem.summary = %Q{A Bioruby plugin: an API for UCSC Genome Browser (experimental)}
-  gem.description = %Q{A Bioruby plugin: an API for UCSC Genome Browser (experimental)}
+  gem.description = %Q{A Bioruby plugin: an API for UCSC Genome Browser database (experimental)}
   gem.email = "missy@be.to"
-  gem.authors = ["MISHIMA, Hiroyuki", "Francesco Strozzi", "Jan Aerts"]
+  gem.authors = ["Hiroyuki Mishima", "Francesco Strozzi", "Jan Aerts"]
   # Include your dependencies below. Runtime dependencies are required when using your gem,
   # and development dependencies are only needed for development
   # (ie running rake tasks, tests, etc)
   #  gem.add_runtime_dependency 'jabber4r', '> 0.1'
   #  gem.add_development_dependency 'rspec', '> 1.2.3'
-
-  gem.add_runtime_dependency 'activerecord',         '>= 3.0.0'
-  gem.add_runtime_dependency 'activesupport',        '>= 3.0.0'
-  gem.add_runtime_dependency 'bio-genomic-interval', '>= 0.1.2'
+  gem.files = FileList["*",
+                       "lib/**/*",
+                       "samples/**/*.rb",
+                       "spec/**/",
+                      ]
 end
 
 Jeweler::RubygemsDotOrgTasks.new
@@ -55,18 +56,3 @@ Rake::RDocTask.new do |rdoc|
   rdoc.rdoc_files.include('README*')
   rdoc.rdoc_files.include('lib/**/*.rb')
 end
-
-# namespace :cover_me do
-#   task :report do
-#     require 'cover_me'
-#     CoverMe.complete!
-#   end
-# end
-
-# task :test do
-#   Rake::Task['cover_me:report'].invoke
-# end
-
-# task :spec do
-#   Rake::Task['cover_me:report'].invoke
-# end

data/VERSION

@@ -1 +1 @@
-0.0.3
+0.0.4

data/bio-ucsc-api.gemspec

@@ -5,19 +5,17 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-ucsc-api}
-  s.version = "0.0.3"
+  s.version = "0.0.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["MISHIMA, Hiroyuki", "Francesco Strozzi", "Jan Aerts"]
-  s.date = %q{2011-04-25}
-  s.description = %q{A Bioruby plugin: an API for UCSC Genome Browser (experimental)}
+  s.authors = ["Hiroyuki Mishima", "Francesco Strozzi", "Jan Aerts"]
+  s.date = %q{2011-05-05}
+  s.description = %q{A Bioruby plugin: an API for UCSC Genome Browser database (experimental)}
   s.email = %q{missy@be.to}
   s.extra_rdoc_files = [
     "README.rdoc"
   ]
   s.files = [
-    ".document",
-    ".rspec",
     "COPYING",
     "COPYING.ja",
     "Gemfile",
@@ -42,13 +40,140 @@ Gem::Specification.new do |s|
     "lib/bio-ucsc/hg18/tables.rb",
     "lib/bio-ucsc/hg19.rb",
     "lib/bio-ucsc/hg19/activerecord.rb",
+    "lib/bio-ucsc/hg19/affyexonprobeambiguous.rb",
+    "lib/bio-ucsc/hg19/affyexonprobecore.rb",
+    "lib/bio-ucsc/hg19/affyexonprobeextended.rb",
+    "lib/bio-ucsc/hg19/affyexonprobefree.rb",
+    "lib/bio-ucsc/hg19/affyexonprobefull.rb",
+    "lib/bio-ucsc/hg19/affyexonprobesetambiguous.rb",
+    "lib/bio-ucsc/hg19/affyexonprobesetcore.rb",
+    "lib/bio-ucsc/hg19/affyexonprobesetextended.rb",
+    "lib/bio-ucsc/hg19/affyexonprobesetfree.rb",
+    "lib/bio-ucsc/hg19/affyexonprobesetfull.rb",
+    "lib/bio-ucsc/hg19/affygnf1h.rb",
+    "lib/bio-ucsc/hg19/affyu133.rb",
+    "lib/bio-ucsc/hg19/affyu133plus2.rb",
+    "lib/bio-ucsc/hg19/affyu95.rb",
+    "lib/bio-ucsc/hg19/agilentcgh1x1m.rb",
+    "lib/bio-ucsc/hg19/agilentcgh1x244k.rb",
+    "lib/bio-ucsc/hg19/agilentcgh2x105k.rb",
+    "lib/bio-ucsc/hg19/agilentcgh2x400k.rb",
+    "lib/bio-ucsc/hg19/agilentcgh4x180k.rb",
+    "lib/bio-ucsc/hg19/agilentcgh4x44k.rb",
+    "lib/bio-ucsc/hg19/agilentcgh8x60k.rb",
+    "lib/bio-ucsc/hg19/agilentcghsnp2x400k.rb",
+    "lib/bio-ucsc/hg19/agilentcghsnp4x180k.rb",
+    "lib/bio-ucsc/hg19/agilenthrd1x1m.rb",
+    "lib/bio-ucsc/hg19/all_bacends.rb",
+    "lib/bio-ucsc/hg19/all_est.rb",
+    "lib/bio-ucsc/hg19/all_fosends.rb",
+    "lib/bio-ucsc/hg19/all_mrna.rb",
+    "lib/bio-ucsc/hg19/allenbrainali.rb",
+    "lib/bio-ucsc/hg19/allenbrainurl.rb",
+    "lib/bio-ucsc/hg19/altseqhaplotypes.rb",
+    "lib/bio-ucsc/hg19/altseqliftoverpsl.rb",
+    "lib/bio-ucsc/hg19/altseqpatches.rb",
+    "lib/bio-ucsc/hg19/bacendpairs.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignadipose.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignadiposeallrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignbrain.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignbrainallrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignbreast.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignbreastallrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignbt474.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignbt474allrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperaligncolon.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperaligncolonallrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignheart.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignheartallrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignhme.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignhmeallrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignliver.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignliverallrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignlymphnode.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignlymphnodeallrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignmb435.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignmb435allrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignmcf7.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignmcf7allrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignskelmuscle.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignskelmuscleallrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignt47d.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperalignt47dallrawsignal.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperaligntestes.rb",
+    "lib/bio-ucsc/hg19/burgernaseqgemmapperaligntestesallrawsignal.rb",
     "lib/bio-ucsc/hg19/ccdsgene.rb",
+    "lib/bio-ucsc/hg19/ccdsinfo.rb",
+    "lib/bio-ucsc/hg19/ccdskgmap.rb",
+    "lib/bio-ucsc/hg19/ccdsnotes.rb",
+    "lib/bio-ucsc/hg19/cgapsage.rb",
+    "lib/bio-ucsc/hg19/cgapsagelib.rb",
+    "lib/bio-ucsc/hg19/chainailmel1.rb",
+    "lib/bio-ucsc/hg19/chainanocar1.rb",
+    "lib/bio-ucsc/hg19/chainaplcal1.rb",
+    "lib/bio-ucsc/hg19/chainbostau4.rb",
+    "lib/bio-ucsc/hg19/chaincaljac3.rb",
+    "lib/bio-ucsc/hg19/chaincanfam2.rb",
+    "lib/bio-ucsc/hg19/chaincavpor3.rb",
+    "lib/bio-ucsc/hg19/chaindanrer7.rb",
+    "lib/bio-ucsc/hg19/chainequcab2.rb",
+    "lib/bio-ucsc/hg19/chainfelcat4.rb",
+    "lib/bio-ucsc/hg19/chainfr2.rb",
+    "lib/bio-ucsc/hg19/chaingalgal3.rb",
+    "lib/bio-ucsc/hg19/chaingasacu1.rb",
+    "lib/bio-ucsc/hg19/chainhg19patch2.rb",
+    "lib/bio-ucsc/hg19/chainloxafr3.rb",
+    "lib/bio-ucsc/hg19/chainmm9.rb",
+    "lib/bio-ucsc/hg19/chainmondom5.rb",
+    "lib/bio-ucsc/hg19/chainornana1.rb",
+    "lib/bio-ucsc/hg19/chainorycun2.rb",
+    "lib/bio-ucsc/hg19/chainorylat2.rb",
+    "lib/bio-ucsc/hg19/chainoviari1.rb",
+    "lib/bio-ucsc/hg19/chainpantro3.rb",
+    "lib/bio-ucsc/hg19/chainpetmar1.rb",
+    "lib/bio-ucsc/hg19/chainponabe2.rb",
+    "lib/bio-ucsc/hg19/chainrhemac2.rb",
+    "lib/bio-ucsc/hg19/chainrn4.rb",
+    "lib/bio-ucsc/hg19/chainself.rb",
+    "lib/bio-ucsc/hg19/chainsusscr2.rb",
+    "lib/bio-ucsc/hg19/chaintaegut1.rb",
+    "lib/bio-ucsc/hg19/chaintetnig2.rb",
+    "lib/bio-ucsc/hg19/chainxentro2.rb",
+    "lib/bio-ucsc/hg19/consindelshgmmcanfam.rb",
+    "lib/bio-ucsc/hg19/consindelshgmmcanfamconf.rb",
+    "lib/bio-ucsc/hg19/cpgislandext.rb",
+    "lib/bio-ucsc/hg19/ctgpos.rb",
+    "lib/bio-ucsc/hg19/ctgpos2.rb",
     "lib/bio-ucsc/hg19/cytoband.rb",
+    "lib/bio-ucsc/hg19/darned.rb",
     "lib/bio-ucsc/hg19/db_connection.rb",
     "lib/bio-ucsc/hg19/description.rb",
     "lib/bio-ucsc/hg19/dgv.rb",
+    "lib/bio-ucsc/hg19/eiojcvinasneg.rb",
+    "lib/bio-ucsc/hg19/eiojcvinaspos.rb",
     "lib/bio-ucsc/hg19/ensgene.rb",
+    "lib/bio-ucsc/hg19/ensgtp.rb",
+    "lib/bio-ucsc/hg19/enspep.rb",
+    "lib/bio-ucsc/hg19/estorientinfo.rb",
+    "lib/bio-ucsc/hg19/evofold.rb",
+    "lib/bio-ucsc/hg19/exoniphy.rb",
+    "lib/bio-ucsc/hg19/fishclones.rb",
+    "lib/bio-ucsc/hg19/fosendpairs.rb",
+    "lib/bio-ucsc/hg19/gad.rb",
+    "lib/bio-ucsc/hg19/gap.rb",
     "lib/bio-ucsc/hg19/gbcdnainfo.rb",
+    "lib/bio-ucsc/hg19/gbmiscdiff.rb",
+    "lib/bio-ucsc/hg19/gbseq.rb",
+    "lib/bio-ucsc/hg19/gbstatus.rb",
+    "lib/bio-ucsc/hg19/gbwarn.rb",
+    "lib/bio-ucsc/hg19/gc5base.rb",
+    "lib/bio-ucsc/hg19/geneid.rb",
+    "lib/bio-ucsc/hg19/genomicsuperdups.rb",
+    "lib/bio-ucsc/hg19/genscan.rb",
+    "lib/bio-ucsc/hg19/genscanpep.rb",
+    "lib/bio-ucsc/hg19/ggburgernaseqgemmapperalignheart.rb",
+    "lib/bio-ucsc/hg19/gnfatlas2.rb",
+    "lib/bio-ucsc/hg19/gold.rb",
     "lib/bio-ucsc/hg19/gwascatalog.rb",
     "lib/bio-ucsc/hg19/hapmapalleleschimp.rb",
     "lib/bio-ucsc/hg19/hapmapallelesmacaque.rb",
@@ -63,75 +188,1389 @@ Gem::Specification.new do |s|
     "lib/bio-ucsc/hg19/hapmapsnpsmkk.rb",
     "lib/bio-ucsc/hg19/hapmapsnpstsi.rb",
     "lib/bio-ucsc/hg19/hapmapsnpsyri.rb",
+    "lib/bio-ucsc/hg19/hg19contigdiff.rb",
+    "lib/bio-ucsc/hg19/hgcentral_wikitrack.rb",
+    "lib/bio-ucsc/hg19/hgdpgeo.rb",
+    "lib/bio-ucsc/hg19/hgfixed_gladhumesotherdata.rb",
+    "lib/bio-ucsc/hg19/hgfixed_gnfhumanatlas2all.rb",
+    "lib/bio-ucsc/hg19/hgfixed_gnfhumanatlas2allratio.rb",
+    "lib/bio-ucsc/hg19/hgfixed_gnfhumanatlas2median.rb",
+    "lib/bio-ucsc/hg19/hgfixed_gnfhumanatlas2medianexps.rb",
+    "lib/bio-ucsc/hg19/hgfixed_gnfhumanatlas2medianratio.rb",
+    "lib/bio-ucsc/hg19/hgfixed_transmapsrcmrna.rb",
+    "lib/bio-ucsc/hg19/hgfixed_transmapsrcrefseq.rb",
+    "lib/bio-ucsc/hg19/hgfixed_transmapsrcsplicedest.rb",
+    "lib/bio-ucsc/hg19/hgfixed_transmapsrcucscgenes.rb",
+    "lib/bio-ucsc/hg19/hgikmc.rb",
+    "lib/bio-ucsc/hg19/hgikmcextra.rb",
+    "lib/bio-ucsc/hg19/hinv.rb",
+    "lib/bio-ucsc/hg19/hinvgenemrna.rb",
+    "lib/bio-ucsc/hg19/illuminaprobes.rb",
+    "lib/bio-ucsc/hg19/illuminaprobesalign.rb",
+    "lib/bio-ucsc/hg19/illuminaprobesseq.rb",
+    "lib/bio-ucsc/hg19/imageclone.rb",
+    "lib/bio-ucsc/hg19/intronest.rb",
+    "lib/bio-ucsc/hg19/jaxqtlasis.rb",
+    "lib/bio-ucsc/hg19/jaxqtlpadded.rb",
     "lib/bio-ucsc/hg19/kgxref.rb",
+    "lib/bio-ucsc/hg19/knownalt.rb",
     "lib/bio-ucsc/hg19/knowngene.rb",
+    "lib/bio-ucsc/hg19/knowntoensembl.rb",
+    "lib/bio-ucsc/hg19/knowntognfatlas2.rb",
+    "lib/bio-ucsc/hg19/knowntohinv.rb",
+    "lib/bio-ucsc/hg19/knowntorefseq.rb",
+    "lib/bio-ucsc/hg19/knowntou133.rb",
+    "lib/bio-ucsc/hg19/knowntou133plus2.rb",
+    "lib/bio-ucsc/hg19/knowntou95.rb",
+    "lib/bio-ucsc/hg19/laminb1lads.rb",
+    "lib/bio-ucsc/hg19/mgcfullmrna.rb",
+    "lib/bio-ucsc/hg19/mgcgenes.rb",
+    "lib/bio-ucsc/hg19/microsat.rb",
+    "lib/bio-ucsc/hg19/mrnaorientinfo.rb",
+    "lib/bio-ucsc/hg19/multiz46way.rb",
+    "lib/bio-ucsc/hg19/ncbiincidentdb.rb",
+    "lib/bio-ucsc/hg19/nestedrepeats.rb",
+    "lib/bio-ucsc/hg19/netailmel1.rb",
+    "lib/bio-ucsc/hg19/netanocar1.rb",
+    "lib/bio-ucsc/hg19/netaplcal1.rb",
+    "lib/bio-ucsc/hg19/netbostau4.rb",
+    "lib/bio-ucsc/hg19/netcaljac3.rb",
+    "lib/bio-ucsc/hg19/netcanfam2.rb",
+    "lib/bio-ucsc/hg19/netcavpor3.rb",
+    "lib/bio-ucsc/hg19/netdanrer7.rb",
+    "lib/bio-ucsc/hg19/netequcab2.rb",
+    "lib/bio-ucsc/hg19/netfelcat4.rb",
+    "lib/bio-ucsc/hg19/netfr2.rb",
+    "lib/bio-ucsc/hg19/netgalgal3.rb",
+    "lib/bio-ucsc/hg19/netgasacu1.rb",
+    "lib/bio-ucsc/hg19/nethg19patch2.rb",
+    "lib/bio-ucsc/hg19/netloxafr3.rb",
+    "lib/bio-ucsc/hg19/netmm9.rb",
+    "lib/bio-ucsc/hg19/netmondom5.rb",
+    "lib/bio-ucsc/hg19/netornana1.rb",
+    "lib/bio-ucsc/hg19/netorycun2.rb",
+    "lib/bio-ucsc/hg19/netorylat2.rb",
+    "lib/bio-ucsc/hg19/netoviari1.rb",
+    "lib/bio-ucsc/hg19/netpantro3.rb",
+    "lib/bio-ucsc/hg19/netpetmar1.rb",
+    "lib/bio-ucsc/hg19/netponabe2.rb",
+    "lib/bio-ucsc/hg19/netrhemac2.rb",
+    "lib/bio-ucsc/hg19/netrn4.rb",
+    "lib/bio-ucsc/hg19/netsusscr2.rb",
+    "lib/bio-ucsc/hg19/nettaegut1.rb",
+    "lib/bio-ucsc/hg19/nettetnig2.rb",
+    "lib/bio-ucsc/hg19/netxentro2.rb",
+    "lib/bio-ucsc/hg19/nscangene.rb",
+    "lib/bio-ucsc/hg19/nscanpep.rb",
+    "lib/bio-ucsc/hg19/nthumchimpcodingdiff.rb",
+    "lib/bio-ucsc/hg19/ntooahaplo.rb",
+    "lib/bio-ucsc/hg19/ntssssnps.rb",
+    "lib/bio-ucsc/hg19/ntssstop5p.rb",
     "lib/bio-ucsc/hg19/omimgene.rb",
+    "lib/bio-ucsc/hg19/oreganno.rb",
+    "lib/bio-ucsc/hg19/oregannoattr.rb",
+    "lib/bio-ucsc/hg19/oregannolink.rb",
+    "lib/bio-ucsc/hg19/orfeomegenes.rb",
+    "lib/bio-ucsc/hg19/orfeomemrna.rb",
+    "lib/bio-ucsc/hg19/pgna12878.rb",
+    "lib/bio-ucsc/hg19/pgna12891.rb",
+    "lib/bio-ucsc/hg19/pgna12892.rb",
+    "lib/bio-ucsc/hg19/pgna19240.rb",
+    "lib/bio-ucsc/hg19/pgsjk.rb",
+    "lib/bio-ucsc/hg19/pgventer.rb",
+    "lib/bio-ucsc/hg19/pgwatson.rb",
+    "lib/bio-ucsc/hg19/pgyh1.rb",
+    "lib/bio-ucsc/hg19/pgyoruban3.rb",
+    "lib/bio-ucsc/hg19/phastcons46way.rb",
+    "lib/bio-ucsc/hg19/phastcons46wayplacental.rb",
+    "lib/bio-ucsc/hg19/phastcons46wayprimates.rb",
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+    "lib/bio-ucsc/hg19/wgencodeuwtfbshaspctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshaspctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshbmecctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshbmecctcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshbmecctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshbmecctcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshcfaactcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshcfaactcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshcpectcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshcpectcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshcpectcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshcpectcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbsheectcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbsheectcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbsheectcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbsheectcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshek293ctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshek293ctcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshek293ctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshek293ctcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshelas3ctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshelas3ctcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshelas3ctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshelas3ctcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshepg2ctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshepg2ctcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshepg2ctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshepg2ctcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshl60ctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshl60ctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshmecctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshmecctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshmfctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshmfctcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshmfctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshmfctcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshpafctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshpafctcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshpafctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshpafctcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshpfctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshpfctcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshpfctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshpfctcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshrectcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshrectcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshrectcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshrectcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshrpectcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshrpectcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshuvecctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshuvecctcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshuvecctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbshuvecctcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbsk562ctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbsk562ctcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbsk562ctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbsk562ctcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbsnhekctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbsnhekctcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbsnhekctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbsnhekctcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbssaecctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbssaecctcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbssaecctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbssaecctcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbssknshractcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbssknshractcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbssknshractcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbssknshractcfstdpkrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbswerirb1ctcfstdhotspotsrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbswerirb1ctcfstdhotspotsrep2.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbswerirb1ctcfstdpkrep1.rb",
+    "lib/bio-ucsc/hg19/wgencodeuwtfbswerirb1ctcfstdpkrep2.rb",
     "lib/bio-ucsc/hg19/wgrna.rb",
+    "lib/bio-ucsc/hg19/xenoest.rb",
+    "lib/bio-ucsc/hg19/xenomrna.rb",
+    "lib/bio-ucsc/hg19/xenorefflat.rb",
+    "lib/bio-ucsc/hg19/xenorefgene.rb",
+    "lib/bio-ucsc/hg19/xenorefseqali.rb",
     "lib/bio-ucsc/ucsc_bin.rb",
     "samples/hg19-2bit-retrieve.rb",
     "samples/hg19-sample.rb",
-    "samples/symbol2summary.rb",
-    "spec/hg18/cnpiafrate2_spec.rb",
-    "spec/hg18/cnplocke_spec.rb",
-    "spec/hg18/cnpredon_spec.rb",
-    "spec/hg18/cnpsebat2_spec.rb",
-    "spec/hg18/cnpsharp2_spec.rb",
-    "spec/hg18/db_connection_spec.rb",
-    "spec/hg18/dgv_spec.rb",
-    "spec/hg18/reference_spec.rb",
-    "spec/hg18/refgene_spec.rb",
-    "spec/hg18/rmsk_spec.rb",
-    "spec/hg19/ccdsgene_spec.rb",
-    "spec/hg19/cytoband_spec.rb",
-    "spec/hg19/db_connection_spec.rb",
-    "spec/hg19/description_spec.rb",
-    "spec/hg19/dgv_spec.rb",
-    "spec/hg19/ensgene_spec.rb",
-    "spec/hg19/gbcdnainfo_spec.rb",
-    "spec/hg19/gwascatalog_spec.rb",
-    "spec/hg19/hapmapalleleschimp_spec.rb",
-    "spec/hg19/hapmapallelesmacaque_spec.rb",
-    "spec/hg19/hapmapsnpsasw_spec.rb",
-    "spec/hg19/hapmapsnpsceu_spec.rb",
-    "spec/hg19/hapmapsnpschb_spec.rb",
-    "spec/hg19/hapmapsnpschd_spec.rb",
-    "spec/hg19/hapmapsnpsgih_spec.rb",
-    "spec/hg19/hapmapsnpsjpt_spec.rb",
-    "spec/hg19/hapmapsnpslwk_spec.rb",
-    "spec/hg19/hapmapsnpsmex_spec.rb",
-    "spec/hg19/hapmapsnpsmkk_spec.rb",
-    "spec/hg19/hapmapsnpstsi_spec.rb",
-    "spec/hg19/hapmapsnpsyri_spec.rb",
-    "spec/hg19/kgxref_spec.rb",
-    "spec/hg19/knowngene_spec.rb",
-    "spec/hg19/omimGene_spec.rb",
-    "spec/hg19/phastconselements46wayprimates_spec.rb",
-    "spec/hg19/phyloP46wayPrimates_spec.rb",
-    "spec/hg19/reference_spec.rb",
-    "spec/hg19/refgene_spec.rb",
-    "spec/hg19/refseqsummary_spec.rb",
-    "spec/hg19/rmsk_spec.rb",
-    "spec/hg19/snp132Flagged_spec.rb",
-    "spec/hg19/snp132_spec.rb",
-    "spec/hg19/snp132codingdbsnp_spec.rb",
-    "spec/hg19/snp132common_spec.rb",
-    "spec/hg19/snp132mult_spec.rb",
-    "spec/hg19/trnas_spec.rb",
-    "spec/hg19/wgrna_spec.rb",
-    "spec/spec_helper.rb"
+    "samples/symbol2summary.rb"
   ]
   s.homepage = %q{http://github.com/misshie/bioruby-ucsc-api}
   s.licenses = ["Ruby (Ruby's/GPLv2 dual)"]
@@ -149,13 +1588,139 @@ Gem::Specification.new do |s|
     "spec/hg18/reference_spec.rb",
     "spec/hg18/refgene_spec.rb",
     "spec/hg18/rmsk_spec.rb",
+    "spec/hg19/affyexonprobeambiguous_spec.rb",
+    "spec/hg19/affyexonprobecore_spec.rb",
+    "spec/hg19/affyexonprobeextended_spec.rb",
+    "spec/hg19/affyexonprobefree_spec.rb",
+    "spec/hg19/affyexonprobefull_spec.rb",
+    "spec/hg19/affyexonprobesetambiguous_spec.rb",
+    "spec/hg19/affyexonprobesetcore_spec.rb",
+    "spec/hg19/affyexonprobesetextended_spec.rb",
+    "spec/hg19/affyexonprobesetfree_spec.rb",
+    "spec/hg19/affyexonprobesetfull_spec.rb",
+    "spec/hg19/affygnf1h_spec.rb",
+    "spec/hg19/affyu133_spec.rb",
+    "spec/hg19/affyu133plus2_spec.rb",
+    "spec/hg19/affyu95_spec.rb",
+    "spec/hg19/agilentcgh1x1m_spec.rb",
+    "spec/hg19/agilentcgh1x244k_spec.rb",
+    "spec/hg19/agilentcgh2x105k_spec.rb",
+    "spec/hg19/agilentcgh2x400k_spec.rb",
+    "spec/hg19/agilentcgh4x180k_spec.rb",
+    "spec/hg19/agilentcgh4x44k_spec.rb",
+    "spec/hg19/agilentcgh8x60k_spec.rb",
+    "spec/hg19/agilentcghsnp2x400k_spec.rb",
+    "spec/hg19/agilentcghsnp4x180k_spec.rb",
+    "spec/hg19/agilenthrd1x1m_spec.rb",
+    "spec/hg19/all_bacends_spec.rb",
+    "spec/hg19/all_est_spec.rb",
+    "spec/hg19/all_fosends_spec.rb",
+    "spec/hg19/all_mrna_spec.rb",
+    "spec/hg19/allenbrainali_spec.rb",
+    "spec/hg19/allenbrainurl_spec.rb",
+    "spec/hg19/altseqhaplotypes_spec.rb",
+    "spec/hg19/altseqliftoverpsl_spec.rb",
+    "spec/hg19/altseqpatches_spec.rb",
+    "spec/hg19/bacendpairs_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignadipose_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignadiposeallrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignbrain_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignbrainallrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignbreast_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignbreastallrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignbt474_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignbt474allrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperaligncolon_spec.rb",
+    "spec/hg19/burgernaseqgemmapperaligncolonallrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignheart_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignheartallrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignhme_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignhmeallrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignliver_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignliverallrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignlymphnode_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignlymphnodeallrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignmb435_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignmb435allrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignmcf7_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignmcf7allrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignskelmuscle_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignskelmuscleallrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignt47d_spec.rb",
+    "spec/hg19/burgernaseqgemmapperalignt47dallrawsignal_spec.rb",
+    "spec/hg19/burgernaseqgemmapperaligntestes_spec.rb",
+    "spec/hg19/burgernaseqgemmapperaligntestesallrawsignal_spec.rb",
     "spec/hg19/ccdsgene_spec.rb",
+    "spec/hg19/ccdsinfo_spec.rb",
+    "spec/hg19/ccdskgmap_spec.rb",
+    "spec/hg19/ccdsnotes_spec.rb",
+    "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/chaincaljac3_spec.rb",
+    "spec/hg19/chaincanfam2_spec.rb",
+    "spec/hg19/chaincavpor3_spec.rb",
+    "spec/hg19/chaindanrer7_spec.rb",
+    "spec/hg19/chainequcab2_spec.rb",
+    "spec/hg19/chainfelcat4_spec.rb",
+    "spec/hg19/chainfr2_spec.rb",
+    "spec/hg19/chaingalgal3_spec.rb",
+    "spec/hg19/chaingasacu1_spec.rb",
+    "spec/hg19/chainhg19patch2_spec.rb",
+    "spec/hg19/chainloxafr3_spec.rb",
+    "spec/hg19/chainmm9_spec.rb",
+    "spec/hg19/chainmondom5_spec.rb",
+    "spec/hg19/chainornana1_spec.rb",
+    "spec/hg19/chainorycun2_spec.rb",
+    "spec/hg19/chainorylat2_spec.rb",
+    "spec/hg19/chainoviari1_spec.rb",
+    "spec/hg19/chainpantro3_spec.rb",
+    "spec/hg19/chainpetmar1_spec.rb",
+    "spec/hg19/chainponabe2_spec.rb",
+    "spec/hg19/chainrhemac2_spec.rb",
+    "spec/hg19/chainrn4_spec.rb",
+    "spec/hg19/chainself_spec.rb",
+    "spec/hg19/chainsusscr2_spec.rb",
+    "spec/hg19/chaintaegut1_spec.rb",
+    "spec/hg19/chaintetnig2_spec.rb",
+    "spec/hg19/chainxentro2_spec.rb",
+    "spec/hg19/consindelshgmmcanfam_spec.rb",
+    "spec/hg19/consindelshgmmcanfamconf_spec.rb",
+    "spec/hg19/cpgislandext_spec.rb",
+    "spec/hg19/ctgpos2_spec.rb",
+    "spec/hg19/ctgpos_spec.rb",
     "spec/hg19/cytoband_spec.rb",
+    "spec/hg19/darned_spec.rb",
     "spec/hg19/db_connection_spec.rb",
     "spec/hg19/description_spec.rb",
     "spec/hg19/dgv_spec.rb",
+    "spec/hg19/eiojcvinasneg_spec.rb",
+    "spec/hg19/eiojcvinaspos_spec.rb",
     "spec/hg19/ensgene_spec.rb",
+    "spec/hg19/ensgtp_spec.rb",
+    "spec/hg19/enspep_spec.rb",
+    "spec/hg19/estorientinfo_spec.rb",
+    "spec/hg19/evofold_spec.rb",
+    "spec/hg19/exoniphy_spec.rb",
+    "spec/hg19/fishclones_spec.rb",
+    "spec/hg19/fosendpairs_spec.rb",
+    "spec/hg19/gad_spec.rb",
+    "spec/hg19/gap_spec.rb",
     "spec/hg19/gbcdnainfo_spec.rb",
+    "spec/hg19/gbmiscdiff_spec.rb",
+    "spec/hg19/gbseq_spec.rb",
+    "spec/hg19/gbstatus_spec.rb",
+    "spec/hg19/gbwarn_spec.rb",
+    "spec/hg19/gc5base_spec.rb",
+    "spec/hg19/geneid_spec.rb",
+    "spec/hg19/genomicsuperdups_spec.rb",
+    "spec/hg19/genscan_spec.rb",
+    "spec/hg19/genscanpep_spec.rb",
+    "spec/hg19/gnfatlas2_spec.rb",
+    "spec/hg19/gold_spec.rb",
     "spec/hg19/gwascatalog_spec.rb",
     "spec/hg19/hapmapalleleschimp_spec.rb",
     "spec/hg19/hapmapallelesmacaque_spec.rb",
@@ -170,22 +1735,1389 @@ Gem::Specification.new do |s|
     "spec/hg19/hapmapsnpsmkk_spec.rb",
     "spec/hg19/hapmapsnpstsi_spec.rb",
     "spec/hg19/hapmapsnpsyri_spec.rb",
+    "spec/hg19/hg19contigdiff_spec.rb",
+    "spec/hg19/hgcentral_wikitrack_spec.rb",
+    "spec/hg19/hgdpgeo_spec.rb",
+    "spec/hg19/hgfixed_gladhumesotherdata_spec.rb",
+    "spec/hg19/hgfixed_gnfhumanatlas2all_spec.rb",
+    "spec/hg19/hgfixed_gnfhumanatlas2allratio_spec.rb",
+    "spec/hg19/hgfixed_gnfhumanatlas2median_spec.rb",
+    "spec/hg19/hgfixed_gnfhumanatlas2medianexps_spec.rb",
+    "spec/hg19/hgfixed_gnfhumanatlas2medianratio_spec.rb",
+    "spec/hg19/hgfixed_transmapsrcmrna_spec.rb",
+    "spec/hg19/hgfixed_transmapsrcrefseq_spec.rb",
+    "spec/hg19/hgfixed_transmapsrcsplicedest_spec.rb",
+    "spec/hg19/hgfixed_transmapsrcucscgenes_spec.rb",
+    "spec/hg19/hgikmc_spec.rb",
+    "spec/hg19/hgikmcextra_spec.rb",
+    "spec/hg19/hinv_spec.rb",
+    "spec/hg19/hinvgenemrna_spec.rb",
+    "spec/hg19/illuminaprobes_spec.rb",
+    "spec/hg19/illuminaprobesalign_spec.rb",
+    "spec/hg19/illuminaprobesseq_spec.rb",
+    "spec/hg19/imageclone_spec.rb",
+    "spec/hg19/intronest_spec.rb",
+    "spec/hg19/jaxqtlasis_spec.rb",
+    "spec/hg19/jaxqtlpadded_spec.rb",
     "spec/hg19/kgxref_spec.rb",
+    "spec/hg19/knownalt_spec.rb",
     "spec/hg19/knowngene_spec.rb",
+    "spec/hg19/knowntoensembl_spec.rb",
+    "spec/hg19/knowntognfatlas2_spec.rb",
+    "spec/hg19/knowntohinv_spec.rb",
+    "spec/hg19/knowntorefseq_spec.rb",
+    "spec/hg19/knowntou133_spec.rb",
+    "spec/hg19/knowntou133plus2_spec.rb",
+    "spec/hg19/knowntou95_spec.rb",
+    "spec/hg19/laminb1_spec.rb",
+    "spec/hg19/laminb1lads_spec.rb",
+    "spec/hg19/mgcfullmrna_spec.rb",
+    "spec/hg19/mgcgenes_spec.rb",
+    "spec/hg19/microsat_spec.rb",
+    "spec/hg19/mrnaorinetinfo_spec.rb",
+    "spec/hg19/multiz46way_spec.rb",
+    "spec/hg19/ncbiincidentdb_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/netcaljac3_spec.rb",
+    "spec/hg19/netcanfam2_spec.rb",
+    "spec/hg19/netcavpor3_spec.rb",
+    "spec/hg19/netdanrer7_spec.rb",
+    "spec/hg19/netequcab2_spec.rb",
+    "spec/hg19/netfelcat4_spec.rb",
+    "spec/hg19/netfr2_spec.rb",
+    "spec/hg19/netgalgal3_spec.rb",
+    "spec/hg19/netgasacu1_spec.rb",
+    "spec/hg19/nethg19patch2_spec.rb",
+    "spec/hg19/netloxafr3_spec.rb",
+    "spec/hg19/netmm9_spec.rb",
+    "spec/hg19/netmondom5_spec.rb",
+    "spec/hg19/netornana1_spec.rb",
+    "spec/hg19/netorycun2_spec.rb",
+    "spec/hg19/netorylat2_spec.rb",
+    "spec/hg19/netoviari1_spec.rb",
+    "spec/hg19/netpantro3_spec.rb",
+    "spec/hg19/netpetmar1_spec.rb",
+    "spec/hg19/netponabe2_spec.rb",
+    "spec/hg19/netrhemac2_spec.rb",
+    "spec/hg19/netrn4_spec.rb",
+    "spec/hg19/netsusscr2_spec.rb",
+    "spec/hg19/nettaegut1_spec.rb",
+    "spec/hg19/nettetnig2_spec.rb",
+    "spec/hg19/netxentro2_spec.rb",
+    "spec/hg19/nscangene_spec.rb",
+    "spec/hg19/nscanpep_spec.rb",
+    "spec/hg19/nthumchimpcodingdiff_spec.rb",
+    "spec/hg19/ntooahaplo_spec.rb",
+    "spec/hg19/ntssssnps_spec.rb",
+    "spec/hg19/ntssstop5p_spec.rb",
     "spec/hg19/omimGene_spec.rb",
+    "spec/hg19/oreganno_spec.rb",
+    "spec/hg19/oregannoattr_spec.rb",
+    "spec/hg19/oregannolink_spec.rb",
+    "spec/hg19/orfeomegenes_spec.rb",
+    "spec/hg19/orfeomemrna_spec.rb",
+    "spec/hg19/pgna12878_spec.rb",
+    "spec/hg19/pgna12891_spec.rb",
+    "spec/hg19/pgna12892_spec.rb",
+    "spec/hg19/pgna19240_spec.rb",
+    "spec/hg19/pgsjk_spec.rb",
+    "spec/hg19/pgventer_spec.rb",
+    "spec/hg19/pgwatson_spec.rb",
+    "spec/hg19/pgyh1_spec.rb",
+    "spec/hg19/pgyoruban3_spec.rb",
+    "spec/hg19/phastcons46way_spec.rb",
+    "spec/hg19/phastcons46wayplacental_spec.rb",
+    "spec/hg19/phastcons46wayprimates_spec.rb",
+    "spec/hg19/phastconselements46way_spec.rb",
+    "spec/hg19/phastconselements46wayplacental_spec.rb",
     "spec/hg19/phastconselements46wayprimates_spec.rb",
-    "spec/hg19/phyloP46wayPrimates_spec.rb",
+    "spec/hg19/phylop46wayall_spec.rb",
+    "spec/hg19/phylop46wayplacental_spec.rb",
+    "spec/hg19/phylop46wayprimates_spec.rb",
+    "spec/hg19/polyadb_spec.rb",
+    "spec/hg19/polyapredict_spec.rb",
+    "spec/hg19/recombrate_spec.rb",
     "spec/hg19/reference_spec.rb",
+    "spec/hg19/refflat_spec.rb",
     "spec/hg19/refgene_spec.rb",
+    "spec/hg19/reflink_spec.rb",
+    "spec/hg19/refseqali_spec.rb",
+    "spec/hg19/refseqstatus_spec.rb",
     "spec/hg19/refseqsummary_spec.rb",
+    "spec/hg19/rgdqtl_spec.rb",
+    "spec/hg19/rgdqtllink_spec.rb",
+    "spec/hg19/rgdratqtl_spec.rb",
+    "spec/hg19/rgdratqtllink_spec.rb",
     "spec/hg19/rmsk_spec.rb",
-    "spec/hg19/snp132Flagged_spec.rb",
+    "spec/hg19/rnacluster_spec.rb",
+    "spec/hg19/seq_spec.rb",
+    "spec/hg19/sestanbrainatlas_spec.rb",
+    "spec/hg19/sgpgene_spec.rb",
+    "spec/hg19/sibtxgraph_spec.rb",
+    "spec/hg19/simplerepeat_spec.rb",
     "spec/hg19/snp132_spec.rb",
     "spec/hg19/snp132codingdbsnp_spec.rb",
     "spec/hg19/snp132common_spec.rb",
+    "spec/hg19/snp132flagged_spec.rb",
     "spec/hg19/snp132mult_spec.rb",
+    "spec/hg19/snparrayaffy250nsp_spec.rb",
+    "spec/hg19/snparrayaffy250sty_spec.rb",
+    "spec/hg19/snparrayaffy5_spec.rb",
+    "spec/hg19/snparrayaffy6_spec.rb",
+    "spec/hg19/snparrayaffy6sv_spec.rb",
+    "spec/hg19/snparrayillumina1m_spec.rb",
+    "spec/hg19/snparrayillumina300_spec.rb",
+    "spec/hg19/snparrayillumina550_spec.rb",
+    "spec/hg19/snparrayillumina650_spec.rb",
+    "spec/hg19/snparrayilluminahuman660w_quad_spec.rb",
+    "spec/hg19/snparrayilluminahumancytosnp_12_spec.rb",
+    "spec/hg19/snparrayilluminahumanomni1_quad_spec.rb",
+    "spec/hg19/spmrna_spec.rb",
+    "spec/hg19/stsalias_spec.rb",
+    "spec/hg19/stsinfo2_spec.rb",
+    "spec/hg19/stsmap_spec.rb",
+    "spec/hg19/switchdbtss_spec.rb",
+    "spec/hg19/targetscans_spec.rb",
+    "spec/hg19/tfbsconssites_spec.rb",
+    "spec/hg19/transmapalnmrna_spec.rb",
+    "spec/hg19/transmapalnrefseq_spec.rb",
+    "spec/hg19/transmapalnsplicedest_spec.rb",
+    "spec/hg19/transmapalnucscgenes_spec.rb",
+    "spec/hg19/transmapinfomrna_spec.rb",
+    "spec/hg19/transmapinforefseq_spec.rb",
+    "spec/hg19/transmapinfosplicedest_spec.rb",
+    "spec/hg19/transmapinfoucscgenes_spec.rb",
     "spec/hg19/trnas_spec.rb",
+    "spec/hg19/ucsfchipseqh3k4me3braincoverage_spec.rb",
+    "spec/hg19/ucsfmedipseqbraincoverage_spec.rb",
+    "spec/hg19/ucsfmedipseqbraincpg_spec.rb",
+    "spec/hg19/ucsfmreseqbraincpg_spec.rb",
+    "spec/hg19/ucsfrnaseqbrainallcoverage_spec.rb",
+    "spec/hg19/ucsfrnaseqbrainsmartcoverage_spec.rb",
+    "spec/hg19/umassbrainhistonepeaksinfant_spec.rb",
+    "spec/hg19/umassbrainhistonepeaksneuron_spec.rb",
+    "spec/hg19/umassbrainhistonepeakssample_spec.rb",
+    "spec/hg19/vegagene_spec.rb",
+    "spec/hg19/vegapseudogene_spec.rb",
+    "spec/hg19/vistaenhancers_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsgm12878celltotal_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsgm12878cytosollongnonpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsgm12878cytosollongpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsgm12878nucleolustotal_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsgm12878nucleuslongnonpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsgm12878nucleuslongpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragshepg2cytosollongnonpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragshepg2cytosollongpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragshepg2nucleolustotal_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragshepg2nucleuslongnonpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragshepg2nucleuslongpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsk562celltotal_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsk562chromatintotal_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsk562cytosollongnonpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsk562cytosollongpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsk562nucleolustotal_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsk562nucleoplasmtotal_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsk562nucleuslongpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsk562polysomelongnonpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragskeratinocytecytosollongnonpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragskeratinocytecytosollongpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragskeratinocytenucleuslongnonpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragskeratinocytenucleuslongpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsprostatecelllongnonpolya_spec.rb",
+    "spec/hg19/wgencodeaffyrnachipfilttransfragsprostatecelllongpolya_spec.rb",
+    "spec/hg19/wgencodebroadhistonegm12878ctcfstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonegm12878h2azstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonegm12878h3k27acstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonegm12878h3k27me3stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonegm12878h3k36me3stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonegm12878h3k4me1stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonegm12878h3k4me2stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonegm12878h3k4me3stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonegm12878h3k79me2stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonegm12878h3k9acstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonegm12878h3k9me3stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonegm12878h4k20me1stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistoneh1hescctcfstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistoneh1hesch3k27acstdpk_spec.rb",
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+    "spec/hg19/wgencodebroadhistoneh1hesch3k36me3stdpk_spec.rb",
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+    "spec/hg19/wgencodebroadhistoneh1hesch3k4me2stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistoneh1hesch3k4me3stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistoneh1hesch3k9acstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistoneh1hesch4k20me1stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehelas3ctcfstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehelas3h3k27acstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehelas3h3k27me3stdpk_spec.rb",
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+    "spec/hg19/wgencodebroadhistonehelas3h3k4me2stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehelas3h3k4me3stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehelas3h3k79me2stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehelas3h3k9acstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehelas3h4k20me1stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehelas3pol2bstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehepg2ctcfstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehepg2h2azstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehepg2h3k27acstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehepg2h3k27me3stdpk_spec.rb",
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+    "spec/hg19/wgencodebroadhistonehepg2h3k4me2stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehepg2h3k4me3stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehepg2h3k79me2stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehepg2h3k9acstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehepg2h4k20me1stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehmecctcfstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehmech3k27acstdpk_spec.rb",
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+    "spec/hg19/wgencodebroadhistonehmech4k20me1stdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonehsmmctcfstdpk_spec.rb",
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+    "spec/hg19/wgencodebroadhistonehuvecpol2bstdpk_spec.rb",
+    "spec/hg19/wgencodebroadhistonek562ctcfstdpk_spec.rb",
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+    "spec/hg19/wgencodebroadhistonenhactcfstdpk_spec.rb",
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+    "spec/hg19/wgencodeuwdnasehnpcehotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehnpcepkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehnpcepkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehpafhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehpafhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehpafpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehpafpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehpdlfhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehpdlfhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehpdlfpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehpdlfpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehpfhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehpfhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehpfpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehpfpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehrcehotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehrcehotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehrcepkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehrcepkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehrehotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehrehotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehrepkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehrepkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehrpehotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehrpehotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehrpepkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehrpepkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehuvechotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehuvecpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehvmfhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehvmfhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasehvmfpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasehvmfpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasek562hotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasek562hotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasek562pkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasek562pkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasemcf7hotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasemcf7hotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasemcf7pkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasemcf7pkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasenb4hotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasenb4hotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasenb4pkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasenb4pkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhahotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhahotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhapkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhapkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhdfadhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhdfadhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhdfadpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhdfadpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhdfneohotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhdfneohotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhdfneopkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhdfneopkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhekhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhekpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhlfhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhlfhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhlfpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasenhlfpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasepanc1hotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasepanc1hotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasepanc1pkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasepanc1pkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasesaechotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasesaechotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasesaecpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasesaecpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnaseskmchotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnaseskmchotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnaseskmcpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnaseskmcpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasesknshrahotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasesknshrahotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnasesknshrapkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnasesknshrapkrep2_spec.rb",
+    "spec/hg19/wgencodeuwdnaseth1hotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnaseth1pkrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnaseth2hotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwdnaseth2pkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag04449h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag04449h3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag04449h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag04449h3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag04450h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag04450h3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag04450h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag04450h3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag09309h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag09309h3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag09309h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag09309h3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag09319h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag09319h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag09319h3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag10803h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag10803h3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag10803h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneag10803h3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneaoafh3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneaoafh3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneaoafh3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneaoafh3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonebjh3k27me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonebjh3k27me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonebjh3k27me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonebjh3k27me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonebjh3k36me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonebjh3k36me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonebjh3k36me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonebjh3k36me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonebjh3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonebjh3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonebjh3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonebjh3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonecaco2h3k27me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonecaco2h3k27me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonecaco2h3k27me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonecaco2h3k27me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonecaco2h3k36me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonecaco2h3k36me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonecaco2h3k36me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonecaco2h3k36me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonecaco2h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonecaco2h3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonecaco2h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonecaco2h3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm06990h3k27me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm06990h3k27me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm06990h3k27me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm06990h3k27me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm06990h3k36me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm06990h3k36me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm06990h3k36me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm06990h3k36me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm06990h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm06990h3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm06990h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm06990h3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm12878h3k27me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm12878h3k27me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm12878h3k27me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm12878h3k27me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm12878h3k36me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm12878h3k36me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm12878h3k36me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm12878h3k36me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm12878h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm12878h3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm12878h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonegm12878h3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneh7esh3k27me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneh7esh3k27me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneh7esh3k27me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneh7esh3k27me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneh7esh3k36me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneh7esh3k36me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneh7esh3k36me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneh7esh3k36me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneh7esh3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneh7esh3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistoneh7esh3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistoneh7esh3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehasph3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehasph3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehasph3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehasph3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehbmech3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehbmech3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehbmech3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehbmech3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcfaah3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcfaah3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcfh3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcfh3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcfh3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcfh3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcmh3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcmh3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcmh3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcmh3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcpeh3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcpeh3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcpeh3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehcpeh3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehct116h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehct116h3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehct116h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehct116h3k4me3stdpkrep2_spec.rb",
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+    "spec/hg19/wgencodeuwhistonehek293h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehek293h3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehek293h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehek293h3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehelas3h3k27me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehelas3h3k27me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehelas3h3k27me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehelas3h3k27me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehelas3h3k36me3stdhotspotsrep1_spec.rb",
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+    "spec/hg19/wgencodeuwhistonehepg2h3k27me3stdhotspotsrep1_spec.rb",
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+    "spec/hg19/wgencodeuwhistonehreh3k27me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehreh3k27me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehreh3k36me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehreh3k36me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehreh3k36me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehreh3k36me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehreh3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehreh3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehreh3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehreh3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehrpeh3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehrpeh3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehrpeh3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehrpeh3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehuvech3k27me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehuvech3k27me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehuvech3k27me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehuvech3k27me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehuvech3k36me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehuvech3k36me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehuvech3k36me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehuvech3k36me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehuvech3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehuvech3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehuvech3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehuvech3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehvmfh3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehvmfh3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonehvmfh3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonehvmfh3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonejurkath3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonejurkath3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonejurkath3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonejurkath3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonek562h3k27me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonek562h3k27me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonek562h3k27me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonek562h3k27me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonek562h3k36me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonek562h3k36me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonek562h3k36me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonek562h3k36me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonek562h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonek562h3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonek562h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonek562h3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonemcf7h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonemcf7h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonenb4h3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonenb4h3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhdfneoh3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhdfneoh3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhdfneoh3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhdfneoh3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhekh3k27me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhekh3k27me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhekh3k27me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhekh3k27me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhekh3k36me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhekh3k36me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhekh3k36me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhekh3k36me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhekh3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhekh3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhekh3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonenhekh3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonesaech3k27me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonesaech3k27me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonesaech3k27me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonesaech3k27me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonesaech3k36me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonesaech3k36me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonesaech3k36me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonesaech3k36me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonesaech3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonesaech3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonesaech3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonesaech3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonesknshrah3k27me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonesknshrah3k27me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonesknshrah3k27me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonesknshrah3k27me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonesknshrah3k36me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonesknshrah3k36me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonesknshrah3k36me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonesknshrah3k36me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonesknshrah3k4me3stdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonesknshrah3k4me3stdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwhistonesknshrah3k4me3stdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwhistonesknshrah3k4me3stdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag04449ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag04449ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag04449ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag04449ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag04450ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag04450ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag09309ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag09309ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag09309ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag09309ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag09319ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag09319ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag09319ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag09319ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag10803ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag10803ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag10803ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsag10803ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsaoafctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsaoafctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsaoafctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsaoafctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsbjctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsbjctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsbjctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsbjctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbscaco2ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbscaco2ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbscaco2ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbscaco2ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm06990ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm06990ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm06990ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm06990ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12801ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12801ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12864ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12864ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12864ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12864ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12865ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12865ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12865ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12865ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12872ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12872ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12872ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12872ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12873ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12873ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12873ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12873ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12874ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12874ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12874ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12874ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12875ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12875ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12875ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12875ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12878ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12878ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12878ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsgm12878ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshaspctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshaspctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshbmecctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshbmecctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshbmecctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshbmecctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshcfaactcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshcfaactcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshcpectcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshcpectcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshcpectcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshcpectcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsheectcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsheectcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsheectcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsheectcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshek293ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshek293ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshek293ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshek293ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshelas3ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshelas3ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshelas3ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshelas3ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshepg2ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshepg2ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshepg2ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshepg2ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshl60ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshl60ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshmecctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshmecctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshmfctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshmfctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshmfctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshmfctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshpafctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshpafctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshpafctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshpafctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshpfctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshpfctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshpfctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshpfctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshrectcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshrectcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshrectcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshrectcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshrpectcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshrpectcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshuvecctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshuvecctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbshuvecctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbshuvecctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsk562ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsk562ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsk562ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsk562ctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsnhekctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsnhekctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbsnhekctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbsnhekctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbssaecctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbssaecctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbssaecctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbssaecctcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbssknshractcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbssknshractcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbssknshractcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbssknshractcfstdpkrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbswerirb1ctcfstdhotspotsrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbswerirb1ctcfstdhotspotsrep2_spec.rb",
+    "spec/hg19/wgencodeuwtfbswerirb1ctcfstdpkrep1_spec.rb",
+    "spec/hg19/wgencodeuwtfbswerirb1ctcfstdpkrep2_spec.rb",
     "spec/hg19/wgrna_spec.rb",
+    "spec/hg19/xenoest_spec.rb",
+    "spec/hg19/xenomrna_spec.rb",
+    "spec/hg19/xenorefflat_spec.rb",
+    "spec/hg19/xenorefgene_spec.rb",
+    "spec/hg19/xenorefseqali_spec.rb",
     "spec/spec_helper.rb"
   ]
 
@@ -194,6 +3126,7 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<activerecord>, [">= 3.0.7"])
+      s.add_runtime_dependency(%q<activesupport>, [">= 3.0.7"])
       s.add_runtime_dependency(%q<mysql>, [">= 2.8.1"])
       s.add_runtime_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
       s.add_development_dependency(%q<rspec>, ["~> 2.5.0"])
@@ -201,11 +3134,9 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
       s.add_development_dependency(%q<rcov>, [">= 0"])
       s.add_development_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_runtime_dependency(%q<activerecord>, [">= 3.0.0"])
-      s.add_runtime_dependency(%q<activesupport>, [">= 3.0.0"])
-      s.add_runtime_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
     else
       s.add_dependency(%q<activerecord>, [">= 3.0.7"])
+      s.add_dependency(%q<activesupport>, [">= 3.0.7"])
       s.add_dependency(%q<mysql>, [">= 2.8.1"])
       s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
       s.add_dependency(%q<rspec>, ["~> 2.5.0"])
@@ -213,12 +3144,10 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
       s.add_dependency(%q<rcov>, [">= 0"])
       s.add_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_dependency(%q<activerecord>, [">= 3.0.0"])
-      s.add_dependency(%q<activesupport>, [">= 3.0.0"])
-      s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
     end
   else
     s.add_dependency(%q<activerecord>, [">= 3.0.7"])
+    s.add_dependency(%q<activesupport>, [">= 3.0.7"])
     s.add_dependency(%q<mysql>, [">= 2.8.1"])
     s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
     s.add_dependency(%q<rspec>, ["~> 2.5.0"])
@@ -226,9 +3155,6 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
     s.add_dependency(%q<rcov>, [">= 0"])
     s.add_dependency(%q<bio>, [">= 1.4.1"])
-    s.add_dependency(%q<activerecord>, [">= 3.0.0"])
-    s.add_dependency(%q<activesupport>, [">= 3.0.0"])
-    s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
   end
 end