ngs_server 0.1

data/.gitignore

@@ -0,0 +1,4 @@
+*.gem
+.bundle
+Gemfile.lock
+pkg/*

data/Gemfile

@@ -0,0 +1,4 @@
+source "http://rubygems.org"
+
+# Specify your gem's dependencies in ngs_server.gemspec
+gemspec

data/Rakefile

@@ -0,0 +1,2 @@
+require 'bundler'
+Bundler::GemHelper.install_tasks

data/bin/ngs_server

@@ -0,0 +1,58 @@
+#!/usr/bin/env ruby
+
+command = ARGV[0]
+path = `which ngs_server`
+
+puts Dir.pwd
+`ls ext/bamtools/binw`
+
+if command == 'start'
+  require 'rubygems'
+  require 'sinatra'
+  require 'json'
+
+  set :public, '.'
+  set :port, "4569"
+
+  bamtools_path = "ext/bamtools/bin/bamtools"
+  vcftools_path = "~/Tools/vcftools_0.1.7/bin/vcf-query"
+
+
+  get '/json/bam/*' do |path|
+
+    content_type :json
+    response['Access-Control-Allow-Origin'] = '*';
+
+    # invoke with eg: base_url/json/bam/file=subset22-sorted.bam?min=30000000&max=30010000&segment=22   
+    json = `#{bamtools_path} convert -in data/#{path} -format json -region #{params["segment"]}:#{params["min"]}..#{params["max"]}`
+    json       
+
+  end
+
+  get '/json/vcf/*' do |path|
+
+    content_type :json
+    response['Access-Control-Allow-Origin'] = '*';
+
+    # invoke with eg: base_url/json/vcf/file=ALL.2of4intersection.20100804.sites.vcf.gz?min=6992179&max=6992190&segment=1
+    json = `#{vcftools_path} data/#{path} #{params["segment"]}:#{params["min"]}-#{params["max"]} -f '{"reference":"%CHROM","position":%POS,"ref":"%REF","alt":"%ALT","info":%INFO},'`
+    json
+
+  end
+
+  get '/json/sources/:extension' do
+
+    content_type :json
+    response['Access-Control-Allow-Origin'] = '*';
+
+    # invoke with eg: base_url/json/vcf/file=ALL.2of4intersection.20100804.sites.vcf.gz?min=6992179&max=6992190&segment=1
+    list = `find -L data -name *#{params['extension']} | awk -F/ '{ for(i=2; i<NF; i++) {printf("%s/", $i)} print $NF }'`
+    list
+
+  end
+
+  
+elsif command == 'add-data'
+  
+  
+end

data/ext/bamtools/CMakeLists.txt

@@ -0,0 +1,49 @@
+# ==========================
+# BamTools CMakeLists.txt
+# (c) 2010 Derek Barnett
+#
+# top-level
+# ==========================
+
+# set project name
+project (BamTools)
+
+# Cmake requirements
+cmake_minimum_required (VERSION 2.6.4)
+
+# Force the build directory to be different from source directory
+# macro (ENSURE_OUT_OF_SOURCE_BUILD MSG)
+#     string (COMPARE EQUAL "${CMAKE_SOURCE_DIR}" "${CMAKE_BINARY_DIR}" insource)
+#     get_filename_component (PARENTDIR ${CMAKE_SOURCE_DIR} PATH)
+#     string (COMPARE EQUAL "${CMAKE_SOURCE_DIR}" "${PARENTDIR}" insourcesubdir)
+#     IF (insource OR insourcesubdir)
+#         message (FATAL_ERROR "${MSG}")
+#     ENDIF (insource OR insourcesubdir)
+# endmacro (ENSURE_OUT_OF_SOURCE_BUILD)
+
+# ensure_out_of_source_build ("
+#   ${PROJECT_NAME} requires an out of source build.
+#   $ mkdir build 
+#   $ cd build
+#   $ cmake ..
+#   $ make 
+# (or the Windows equivalent)\n")
+
+# set BamTools version information
+set (BamTools_VERSION_MAJOR 1)
+set (BamTools_VERSION_MINOR 0)
+set (BamTools_VERSION_BUILD 2)
+
+# set our library and executable destination dirs
+set (EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin")
+set (LIBRARY_OUTPUT_PATH    "${CMAKE_SOURCE_DIR}/lib")
+
+# define compiler flags for all code
+set (CMAKE_BUILD_TYPE Release)
+add_definitions (-Wall -D_FILE_OFFSET_BITS=64)
+
+# add our includes root path
+include_directories (src)
+
+# list subdirectories to build in
+add_subdirectory (src)

data/ext/bamtools/LICENSE

@@ -0,0 +1,22 @@
+The MIT License
+
+Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+

data/ext/bamtools/README

@@ -0,0 +1,60 @@
+--------------------------------------------------------------------------------
+README : BAMTOOLS
+--------------------------------------------------------------------------------
+
+BamTools provides both a programmer's API and an end-user's toolkit for handling
+BAM files.
+
+I.   Learn More
+
+II.  License
+
+III. Acknowledgements
+
+IV.  Contact
+
+--------------------------------------------------------------------------------
+I. Learn More:
+--------------------------------------------------------------------------------
+
+Installation steps, tutorial, API documentation, etc. are all now available 
+through the BamTools project wiki:
+
+https://github.com/pezmaster31/bamtools/wiki
+
+Join the mailing list(s) to stay informed of updates or get involved with 
+contributing:
+
+https://github.com/pezmaster31/bamtools/wiki/Mailing-lists
+
+--------------------------------------------------------------------------------
+II. License :
+--------------------------------------------------------------------------------
+
+Both the BamTools API and toolkit are released under the MIT License.
+Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth,
+    Michael Stromberg
+
+See included file LICENSE for details.
+
+--------------------------------------------------------------------------------
+III. Acknowledgements :
+--------------------------------------------------------------------------------
+
+ * Aaron Quinlan for several key feature ideas and bug fix contributions
+ * Baptiste Lepilleur for the public-domain JSON parser (JsonCPP)
+ * Heng Li, author of SAMtools - the original C-language BAM API/toolkit.
+
+--------------------------------------------------------------------------------
+IV. Contact :
+--------------------------------------------------------------------------------
+
+Feel free to contact me with any questions, comments, suggestions, bug reports,
+    etc.
+
+Derek Barnett
+Marth Lab
+Biology Dept., Boston College
+
+Email: derekwbarnett@gmail.com
+Project Website: http://github.com/pezmaster31/bamtools