ngs_server 0.7 → 0.8

data/bin/ngs_server

@@ -20,7 +20,7 @@
   }
 
   optparse = OptionParser.new do |opts|
-    opts.banner = "Usage: ngs_server start|stop|add [options]"
+    opts.banner = "Usage: ngs_server start|stop|add|find [options]"
     
     opts.on( '-h', '--help', 'display this screen' ) do
         # puts "ngs_server command options"
@@ -32,6 +32,7 @@
         puts "\tngs_server start -p 4567 -d"
         puts "\tngs_server add path_to_data_directory"
         puts "\tngs_server stop"
+        puts "\tngs_server find dir \"*bam\""
         exit
     end
     

data/lib/ngs_server.rb

@@ -22,9 +22,10 @@ class MyNgsServer < Sinatra::Base
     response['Access-Control-Allow-Origin'] = '*'; 
     
 
-    # invoke with eg: base_url/json/bam/subset22-sorted.bam?min=30000000&max=30010000&segment=22   
-    json = `#{bamtools_path} convert -in #{datapath}/#{path} -format json -region #{params["segment"]}:#{params["min"]}..#{params["max"]}`
-    json       
+    # invoke with eg: base_url/json/bam/subset22-sorted.bam?min=30000000&max=30010000&segment=22
+    json = '['
+    json += `#{bamtools_path} convert -in #{datapath}/#{path} -format json -region #{params["segment"]}:#{params["min"].to_i}..#{params["max"].to_i}`
+    json.strip().chomp(',') + ']'
 
   end
 
@@ -35,8 +36,9 @@ class MyNgsServer < Sinatra::Base
     response['Access-Control-Allow-Origin'] = '*';
 
     # invoke with eg: base_url/json/vcf/ALL.2of4intersection.20100804.sites.vcf.gz?min=6992179&max=6992190&segment=1
-    json = `#{vcftools_path} #{datapath}/#{path} #{params["segment"]}:#{params["min"]}-#{params["max"]} -f '{"reference":"%CHROM","position":%POS,"ref":"%REF","alt":"%ALT","info":%INFO},'`
-    json
+    json = '['
+    json += `#{vcftools_path} #{datapath}/#{path} #{params["segment"]}:#{params["min"].to_i}-#{params["max"].to_i} -f '{"reference":"%CHROM","position":%POS,"ref":"%REF","alt":"%ALT","info":%INFO},'`
+    json.strip().chomp(',') + ']'
 
   end
 

data/lib/ngs_server/version.rb

@@ -1,3 +1,3 @@
 module NgsServer
-  VERSION = "0.7"
+  VERSION = "0.8"
 end

metadata

@@ -2,7 +2,7 @@
 name: ngs_server
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: "0.7"
+  version: "0.8"
 platform: ruby
 authors: 
 - Chase Miller
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-01-31 00:00:00 -05:00
+date: 2012-06-04 00:00:00 -04:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency