ngs_server 0.1 → 0.2

metadata

@@ -1,8 +1,11 @@
 --- !ruby/object:Gem::Specification 
 name: ngs_server
 version: !ruby/object:Gem::Version 
-  prerelease: 
-  version: "0.1"
+  prerelease: false
+  segments: 
+  - 0
+  - 2
+  version: "0.2"
 platform: ruby
 authors: 
 - Chase Miller
@@ -10,10 +13,50 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-12-11 00:00:00 -05:00
+date: 2011-12-13 00:00:00 -05:00
 default_executable: 
-dependencies: []
-
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: sinatra
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 2
+        version: "1.2"
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: thin
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 2
+        version: "1.2"
+  type: :runtime
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: rack
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        version: "1"
+  type: :runtime
+  version_requirements: *id003
 description: "\"Converts BAM/VCF files into JSON for consumption by web apps\""
 email: 
 - chmille4@gmail.com
@@ -21,6 +64,7 @@ executables:
 - ngs_server
 extensions: 
 - ext/bamtools/extconf.rb
+- ext/vcftools/extconf.rb
 extra_rdoc_files: []
 
 files: 
@@ -304,7 +348,249 @@ files:
 - ext/bamtools/src/utils/bamtools_variant.h
 - ext/bamtools/src/utils/cmake_install.cmake
 - ext/bamtools/src/utils/utils_global.h
+- ext/vcftools/Makefile
+- ext/vcftools/README.txt
+- ext/vcftools/cpp/.svn/all-wcprops
+- ext/vcftools/cpp/.svn/dir-prop-base
+- ext/vcftools/cpp/.svn/entries
+- ext/vcftools/cpp/.svn/text-base/Makefile.svn-base
+- ext/vcftools/cpp/.svn/text-base/dgeev.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/dgeev.h.svn-base
+- ext/vcftools/cpp/.svn/text-base/output_log.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/output_log.h.svn-base
+- ext/vcftools/cpp/.svn/text-base/parameters.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/parameters.h.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcf_entry.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcf_entry.h.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcf_entry_getters.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcf_entry_setters.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcf_file.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcf_file.h.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcf_file_diff.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcf_file_filters.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcf_file_format_convert.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcf_file_index.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcf_file_output.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcftools.cpp.svn-base
+- ext/vcftools/cpp/.svn/text-base/vcftools.h.svn-base
+- ext/vcftools/cpp/Makefile
+- ext/vcftools/cpp/dgeev.cpp
+- ext/vcftools/cpp/dgeev.h
+- ext/vcftools/cpp/output_log.cpp
+- ext/vcftools/cpp/output_log.h
+- ext/vcftools/cpp/parameters.cpp
+- ext/vcftools/cpp/parameters.h
+- ext/vcftools/cpp/vcf_entry.cpp
+- ext/vcftools/cpp/vcf_entry.h
+- ext/vcftools/cpp/vcf_entry_getters.cpp
+- ext/vcftools/cpp/vcf_entry_setters.cpp
+- ext/vcftools/cpp/vcf_file.cpp
+- ext/vcftools/cpp/vcf_file.h
+- ext/vcftools/cpp/vcf_file_diff.cpp
+- ext/vcftools/cpp/vcf_file_filters.cpp
+- ext/vcftools/cpp/vcf_file_format_convert.cpp
+- ext/vcftools/cpp/vcf_file_index.cpp
+- ext/vcftools/cpp/vcf_file_output.cpp
+- ext/vcftools/cpp/vcftools.cpp
+- ext/vcftools/cpp/vcftools.h
+- ext/vcftools/examples/.svn/all-wcprops
+- ext/vcftools/examples/.svn/dir-prop-base
+- ext/vcftools/examples/.svn/entries
+- ext/vcftools/examples/.svn/prop-base/perl-api-1.pl.svn-base
+- ext/vcftools/examples/.svn/text-base/annotate-test.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/annotate.out.svn-base
+- ext/vcftools/examples/.svn/text-base/annotate.txt.svn-base
+- ext/vcftools/examples/.svn/text-base/annotate2.out.svn-base
+- ext/vcftools/examples/.svn/text-base/annotate3.out.svn-base
+- ext/vcftools/examples/.svn/text-base/cmp-test-a-3.3.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/cmp-test-a.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/cmp-test-b-3.3.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/cmp-test-b.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/cmp-test.out.svn-base
+- ext/vcftools/examples/.svn/text-base/concat-a.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/concat-b.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/concat-c.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/concat.out.svn-base
+- ext/vcftools/examples/.svn/text-base/invalid-4.0.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/isec-n2-test.vcf.out.svn-base
+- ext/vcftools/examples/.svn/text-base/merge-test-a.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/merge-test-b.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/merge-test-c.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/merge-test.vcf.out.svn-base
+- ext/vcftools/examples/.svn/text-base/perl-api-1.pl.svn-base
+- ext/vcftools/examples/.svn/text-base/query-test.out.svn-base
+- ext/vcftools/examples/.svn/text-base/shuffle-test.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/subset.SNPs.out.svn-base
+- ext/vcftools/examples/.svn/text-base/subset.indels.out.svn-base
+- ext/vcftools/examples/.svn/text-base/subset.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/valid-3.3.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/valid-4.0.vcf.stats.svn-base
+- ext/vcftools/examples/.svn/text-base/valid-4.0.vcf.svn-base
+- ext/vcftools/examples/.svn/text-base/valid-4.1.vcf.svn-base
+- ext/vcftools/examples/annotate-test.vcf
+- ext/vcftools/examples/annotate.out
+- ext/vcftools/examples/annotate.txt
+- ext/vcftools/examples/annotate2.out
+- ext/vcftools/examples/annotate3.out
+- ext/vcftools/examples/cmp-test-a-3.3.vcf
+- ext/vcftools/examples/cmp-test-a.vcf
+- ext/vcftools/examples/cmp-test-b-3.3.vcf
+- ext/vcftools/examples/cmp-test-b.vcf
+- ext/vcftools/examples/cmp-test.out
+- ext/vcftools/examples/concat-a.vcf
+- ext/vcftools/examples/concat-b.vcf
+- ext/vcftools/examples/concat-c.vcf
+- ext/vcftools/examples/concat.out
+- ext/vcftools/examples/invalid-4.0.vcf
+- ext/vcftools/examples/isec-n2-test.vcf.out
+- ext/vcftools/examples/merge-test-a.vcf
+- ext/vcftools/examples/merge-test-b.vcf
+- ext/vcftools/examples/merge-test-c.vcf
+- ext/vcftools/examples/merge-test.vcf.out
+- ext/vcftools/examples/perl-api-1.pl
+- ext/vcftools/examples/query-test.out
+- ext/vcftools/examples/shuffle-test.vcf
+- ext/vcftools/examples/subset.SNPs.out
+- ext/vcftools/examples/subset.indels.out
+- ext/vcftools/examples/subset.vcf
+- ext/vcftools/examples/valid-3.3.vcf
+- ext/vcftools/examples/valid-4.0.vcf
+- ext/vcftools/examples/valid-4.0.vcf.stats
+- ext/vcftools/examples/valid-4.1.vcf
+- ext/vcftools/extconf.rb
+- ext/vcftools/perl/.svn/all-wcprops
+- ext/vcftools/perl/.svn/entries
+- ext/vcftools/perl/.svn/prop-base/fill-aa.svn-base
+- ext/vcftools/perl/.svn/prop-base/fill-an-ac.svn-base
+- ext/vcftools/perl/.svn/prop-base/fill-ref-md5.svn-base
+- ext/vcftools/perl/.svn/prop-base/tab-to-vcf.svn-base
+- ext/vcftools/perl/.svn/prop-base/test.t.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-annotate.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-compare.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-concat.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-convert.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-fix-newlines.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-isec.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-merge.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-query.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-shuffle-cols.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-sort.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-stats.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-subset.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-to-tab.svn-base
+- ext/vcftools/perl/.svn/prop-base/vcf-validator.svn-base
+- ext/vcftools/perl/.svn/text-base/ChangeLog.svn-base
+- ext/vcftools/perl/.svn/text-base/FaSlice.pm.svn-base
+- ext/vcftools/perl/.svn/text-base/Makefile.svn-base
+- ext/vcftools/perl/.svn/text-base/Vcf.pm.svn-base
+- ext/vcftools/perl/.svn/text-base/VcfStats.pm.svn-base
+- ext/vcftools/perl/.svn/text-base/fill-aa.svn-base
+- ext/vcftools/perl/.svn/text-base/fill-an-ac.svn-base
+- ext/vcftools/perl/.svn/text-base/fill-ref-md5.svn-base
+- ext/vcftools/perl/.svn/text-base/tab-to-vcf.svn-base
+- ext/vcftools/perl/.svn/text-base/test.t.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-annotate.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-compare.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-concat.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-convert.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-fix-newlines.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-isec.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-merge.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-query.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-shuffle-cols.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-sort.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-stats.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-subset.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-to-tab.svn-base
+- ext/vcftools/perl/.svn/text-base/vcf-validator.svn-base
+- ext/vcftools/perl/ChangeLog
+- ext/vcftools/perl/FaSlice.pm
+- ext/vcftools/perl/Makefile
+- ext/vcftools/perl/Vcf.pm
+- ext/vcftools/perl/VcfStats.pm
+- ext/vcftools/perl/fill-aa
+- ext/vcftools/perl/fill-an-ac
+- ext/vcftools/perl/fill-ref-md5
+- ext/vcftools/perl/tab-to-vcf
+- ext/vcftools/perl/test.t
+- ext/vcftools/perl/vcf-annotate
+- ext/vcftools/perl/vcf-compare
+- ext/vcftools/perl/vcf-concat
+- ext/vcftools/perl/vcf-convert
+- ext/vcftools/perl/vcf-fix-newlines
+- ext/vcftools/perl/vcf-isec
+- ext/vcftools/perl/vcf-merge
+- ext/vcftools/perl/vcf-query
+- ext/vcftools/perl/vcf-shuffle-cols
+- ext/vcftools/perl/vcf-sort
+- ext/vcftools/perl/vcf-stats
+- ext/vcftools/perl/vcf-subset
+- ext/vcftools/perl/vcf-to-tab
+- ext/vcftools/perl/vcf-validator
+- ext/vcftools/website/.svn/all-wcprops
+- ext/vcftools/website/.svn/entries
+- ext/vcftools/website/.svn/prop-base/VCF-poster.pdf.svn-base
+- ext/vcftools/website/.svn/prop-base/favicon.ico.svn-base
+- ext/vcftools/website/.svn/prop-base/favicon.png.svn-base
+- ext/vcftools/website/.svn/text-base/Makefile.svn-base
+- ext/vcftools/website/.svn/text-base/README.svn-base
+- ext/vcftools/website/.svn/text-base/VCF-poster.pdf.svn-base
+- ext/vcftools/website/.svn/text-base/default.css.svn-base
+- ext/vcftools/website/.svn/text-base/favicon.ico.svn-base
+- ext/vcftools/website/.svn/text-base/favicon.png.svn-base
+- ext/vcftools/website/Makefile
+- ext/vcftools/website/README
+- ext/vcftools/website/VCF-poster.pdf
+- ext/vcftools/website/default.css
+- ext/vcftools/website/favicon.ico
+- ext/vcftools/website/favicon.png
+- ext/vcftools/website/img/.svn/all-wcprops
+- ext/vcftools/website/img/.svn/entries
+- ext/vcftools/website/img/.svn/prop-base/bg.gif.svn-base
+- ext/vcftools/website/img/.svn/prop-base/bgcode.gif.svn-base
+- ext/vcftools/website/img/.svn/prop-base/bgcontainer.gif.svn-base
+- ext/vcftools/website/img/.svn/prop-base/bgul.gif.svn-base
+- ext/vcftools/website/img/.svn/prop-base/header.gif.svn-base
+- ext/vcftools/website/img/.svn/prop-base/li.gif.svn-base
+- ext/vcftools/website/img/.svn/prop-base/quote.gif.svn-base
+- ext/vcftools/website/img/.svn/prop-base/search.gif.svn-base
+- ext/vcftools/website/img/.svn/text-base/bg.gif.svn-base
+- ext/vcftools/website/img/.svn/text-base/bgcode.gif.svn-base
+- ext/vcftools/website/img/.svn/text-base/bgcontainer.gif.svn-base
+- ext/vcftools/website/img/.svn/text-base/bgul.gif.svn-base
+- ext/vcftools/website/img/.svn/text-base/header.gif.svn-base
+- ext/vcftools/website/img/.svn/text-base/li.gif.svn-base
+- ext/vcftools/website/img/.svn/text-base/quote.gif.svn-base
+- ext/vcftools/website/img/.svn/text-base/search.gif.svn-base
+- ext/vcftools/website/img/bg.gif
+- ext/vcftools/website/img/bgcode.gif
+- ext/vcftools/website/img/bgcontainer.gif
+- ext/vcftools/website/img/bgul.gif
+- ext/vcftools/website/img/header.gif
+- ext/vcftools/website/img/li.gif
+- ext/vcftools/website/img/quote.gif
+- ext/vcftools/website/img/search.gif
+- ext/vcftools/website/src/.svn/all-wcprops
+- ext/vcftools/website/src/.svn/entries
+- ext/vcftools/website/src/.svn/text-base/docs.inc.svn-base
+- ext/vcftools/website/src/.svn/text-base/index.inc.svn-base
+- ext/vcftools/website/src/.svn/text-base/index.php.svn-base
+- ext/vcftools/website/src/.svn/text-base/license.inc.svn-base
+- ext/vcftools/website/src/.svn/text-base/links.inc.svn-base
+- ext/vcftools/website/src/.svn/text-base/options.inc.svn-base
+- ext/vcftools/website/src/.svn/text-base/perl_module.inc.svn-base
+- ext/vcftools/website/src/.svn/text-base/specs.inc.svn-base
+- ext/vcftools/website/src/docs.inc
+- ext/vcftools/website/src/index.inc
+- ext/vcftools/website/src/index.php
+- ext/vcftools/website/src/license.inc
+- ext/vcftools/website/src/links.inc
+- ext/vcftools/website/src/options.inc
+- ext/vcftools/website/src/perl_module.inc
+- ext/vcftools/website/src/specs.inc
+- lib/config.ru
 - lib/ngs_server.rb
+- lib/ngs_server/add.rb
 - lib/ngs_server/version.rb
 - ngs_server.gemspec
 has_rdoc: true
@@ -321,17 +607,21 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      segments: 
+      - 0
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      segments: 
+      - 0
       version: "0"
 requirements: []
 
 rubyforge_project: ngs_server
-rubygems_version: 1.6.2
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: "\"Ultra Lightweight NGS Data Server\""