polymarker.rb in bio-polyploid-tools-0.10.0

- old
+ new

@@ -147,12 +147,12 @@
   max = range_arr[1].to_i
   raise  Bio::DB::Exonerate::ExonerateException.new "Range #{range} is invalid!" unless max > min
   options[:flanking_size] = max
 end
 
-p options
-p ARGV
+#p options
+#p ARGV
 
 
 #TODO: Use temporary files somewhere in the file system and add traps to delete them/forward them as a result. 
 #TODO: Make all this parameters
 
@@ -190,11 +190,22 @@
   f=File.open(@status_file, "a")
   f.puts "#{Time.now.to_s},#{status}"
   f.close
 end
 
+Signal.trap("ABRT")  do
+  write_status "ERROR: Job aborted. Please try a small number of primers." 
+  Signal.trap("SIGABRT", "DEFAULT") # restore handler
+  Process.kill("ABRT", 0)   
+end
 
+Signal.trap("TERM")  do 
+  write_status "ERROR: Job terminated. Please try a small number of primers." 
+  Signal.trap("SIGTERM", "DEFAULT") # restore handler
+  Process.kill("TERM", 0)           # kill this process with correct signal
+end
+
 snps = Array.new
 
 begin
   
 write_status "Loading Reference"
@@ -375,11 +386,10 @@
 end
 
 kasp_container.add_primers_file(primer_3_output) if added_exons > 0
 header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,SNP_type,#{original_name},#{snp_in},common,primer_type,orientation,#{original_name}_TM,#{snp_in}_TM,common_TM,selected_from,product_size,errors,repetitive,total_hits"
 File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }
-
-File.open(output_to_order, "w") { |io|  io.write(kasp_container.print_primers_with_tails()) }
+File.open(output_to_order, "w") { |io|  io.write(kasp_container.print_primers_with_tails())}
 
 write_status "DONE"
 rescue StandardError => e
   write_status "ERROR\t#{e.message}"
   raise e 