Support writing compressed .jplace files

checked via:

    pplacer -p -c vaginal_16s.refpkg src/p4z1r36.fasta.gz -o test.jplace.gz

common_src/ppatteries.ml

@@ -234,15 +234,24 @@ module MaybeZipped = struct
   let lines_of name =
     open_in name |> IO.lines_of
 
-  (*let open_out name =
+  let open_out name =
     if is_gzipped name then
       let out_chan = Gzip.open_out name in
+      (* Gzip.output doesn't return the number of characters written,
+       * hence the Buffer wrapping *)
       IO.create_out
         ~write:(Gzip.output_char out_chan)
-        ~output:(Gzip.output out_chan)
+        ~output:(fun s p l ->
+          let buf = Buffer.create l in
+          Buffer.add_substring buf s p l;
+          Gzip.output out_chan (Buffer.contents buf) 0 (Buffer.length buf);
+          Buffer.length buf)
         ~close:(fun () -> Gzip.close_out out_chan)
+        (* Gzip.flush disposes of the Gzip stream and prevents further writes -
+         * we don't want that, so no action here. *)
+        ~flush:(fun () -> ())
     else
-      File.open_out name*)
+      File.open_out name
 end
 
 (* parsing *)

json_src/json.ml

@@ -70,6 +70,10 @@ let to_string o =
   Buffer.contents buf
 
 let to_file name o =
-  let file = open_out name in
-  to_formatter (Format.formatter_of_out_channel file) o;
+  let file = MaybeZipped.open_out name in
+  let formatter= Format.make_formatter
+    (fun s p l -> let _ = IO.output file s p l in ())
+    (fun () -> IO.flush file)
+  in
+  to_formatter formatter o;
   close_out file

pplacer_src/guppy_cmdobjs.ml

@@ -234,7 +234,7 @@ object (self)
 
   method private write_placefile fname pr =
     if fname.[0] = '@' then
-      let name = Filename.chop_extension
+      let name = MaybeZipped.chop_extension
         (String.sub fname 1 ((String.length fname) - 1))
       in
       placerun_map := SM.add fname (Placerun.set_name pr name) !placerun_map