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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/pplacer">Debian Med / pplacer</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pplacer/-/commit/770e5caee97a2d7d62f7d3f179f88d050965cf36">770e5cae</a></strong>
<div>
<span>by Ralf Treinen</span>
<i>at 2020-06-13T17:05:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add patch to replace Pervasives by Stdlib
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pplacer/-/commit/b35a959570d746cf009b164a5d9723e98eddf90c">b35a9595</a></strong>
<div>
<span>by Ralf Treinen</span>
<i>at 2020-06-13T18:52:38+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">patch for read-only strings in recent ocaml
</pre>
</li>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#a4416d0924d117bd51912929ec975e7d1e789fd2">
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+
debian/patches/ocaml_bytes
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<li class="file-stats">
<a href="#ff9c563dedb94407025694ae4311cf34844a98b5">
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+
debian/patches/ocaml_stdlib
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<li class="file-stats">
<a href="#ac9a0fb7ed09d8775c7899149574abe3381357dd">
debian/patches/ocamlbuild
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="a4416d0924d117bd51912929ec975e7d1e789fd2">
<a href="https://salsa.debian.org/med-team/pplacer/-/compare/8f6f9aac2953129d004aef65a21c864c88a7a72b...b35a959570d746cf009b164a5d9723e98eddf90c#a4416d0924d117bd51912929ec975e7d1e789fd2"><strong>debian/patches/ocaml_bytes</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Ralf Treinen <treinen@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: ocaml strings are immutable in recent ocaml versions,</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> replace them by Bytes.t where necessary</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Index: pplacer/common_src/ppatteries.ml</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/common_src/ppatteries.ml 2020-06-13 18:46:39.674407130 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/common_src/ppatteries.ml 2020-06-13 18:46:39.670407109 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -60,7 +60,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> let maybe_cons o l = maybe_map_cons identity o l</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> let to_csv_out ch =</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (ch :> <close_out: unit -> unit; output: string -> int -> int -> int>)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (ch :> <close_out: unit -> unit; output: Bytes.t -> int -> int -> int>)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> let csv_out_channel ch = new IO.out_channel ch |> to_csv_out</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> let to_csv_in ch = object</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -243,8 +243,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> ~write:(Gzip.output_char out_chan)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> ~output:(fun s p l -></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> let buf = Buffer.create l in</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Buffer.add_substring buf s p l;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Gzip.output out_chan (Buffer.contents buf) 0 (Buffer.length buf);</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Buffer.add_subbytes buf s p l;</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Gzip.output out_chan (Bytes.of_string (Buffer.contents buf)) 0 (Buffer.length buf);</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> Buffer.length buf)</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> ~close:(fun () -> Gzip.close_out out_chan)</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> (* Gzip.flush disposes of the Gzip stream and prevents further writes -</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="p">@@ -714,8 +714,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> let left_pad pad_width c s =</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> assert(pad_width >= 0);</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> let len = String.length s in</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- let new_s = String.make (len+pad_width) c in</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String.blit s 0 new_s pad_width len;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ let new_s = Bytes.make (len+pad_width) c in</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Bytes.blit_string s 0 new_s pad_width len;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> new_s</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> end</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/json_src/json.ml</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/json_src/json.ml 2020-06-13 18:46:39.674407130 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/json_src/json.ml 2020-06-13 18:46:39.670407109 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -72,7 +72,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> let to_file name o =</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> let file = MaybeZipped.open_out name in</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> let formatter= Format.make_formatter</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (fun s p l -> let _ = IO.output file s p l in ())</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (fun s p l -> let _ = IO.output file (Bytes.of_string s) p l in ())</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> (fun () -> IO.flush file)</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> in</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> to_formatter formatter o;</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/common_src/alignment.ml</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/common_src/alignment.ml 2020-06-13 18:46:39.674407130 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/common_src/alignment.ml 2020-06-13 18:46:39.670407109 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="p">@@ -102,7 +102,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> Printf.fprintf ch "%d %d\n" (n_seqs align) (length align);</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> Array.iter (</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> fun (name, seq) -></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Printf.fprintf ch "%s %s\n" (StringFuns.left_pad 14 ' ' name) seq;</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Printf.fprintf ch "%s %s\n" (Bytes.to_string (StringFuns.left_pad 14 ' ' name)) seq;</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> ) align;</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> close_out ch</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/pplacer_src/string_matrix.ml</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/pplacer_src/string_matrix.ml 2020-06-13 18:46:39.674407130 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/pplacer_src/string_matrix.ml 2020-06-13 18:46:39.670407109 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="p">@@ -50,7 +50,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> let m = add_names [|"a";"b"|] [|[|"0";"1"|];[|"2";"3"|]|]</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> let row_to_str delim row =</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String.concat delim (Array.to_list row)</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Bytes.to_string (Bytes.concat (Bytes.of_string delim) (Array.to_list row))</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> let write_row ch row =</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> Printf.fprintf ch "%s\n" (row_to_str " " row)</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/pplacer_src/pplacer_run.ml</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/pplacer_src/pplacer_run.ml 2020-06-13 18:46:39.674407130 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/pplacer_src/pplacer_run.ml 2020-06-13 18:46:39.670407109 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="p">@@ -118,7 +118,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> (seq'.[!pos] <- seq.[e];</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> incr pos))</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> mask;</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name, seq'</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ name, (Bytes.to_string seq')</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> in</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> dprintf "sequence length cut from %d to %d.\n" n_sites masklen;</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> let effective_length = match seq_type with</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="p">@@ -372,7 +372,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> |> Array.append</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> [|[|"node"; "tree_likelihood"; "slow_tree_like"; "supernode_like"|]|]</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> |> String_matrix.pad</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- |> Array.iter (Array.iter (dprintf "%s ") %> tap (fun () -> dprint "\n"))</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ |> Array.iter (Array.iter (function b -> (dprintf "%s ") (Bytes.to_string b)) %> tap (fun () -> dprint "\n"))</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> end;</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> </span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/json_src/jsonparse.mly</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/json_src/jsonparse.mly 2020-06-13 18:46:39.674407130 +0200</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/json_src/jsonparse.mly 2020-06-13 18:46:39.670407109 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="p">@@ -42,7 +42,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> | "t" -> "\t"</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> | _ -></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> let escape = Str.replace_matched "\\2" s in</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- utf8_encode (int_of_string ("0x" ^ escape))</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (Bytes.to_string (utf8_encode (int_of_string ("0x" ^ escape))))</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> ) s</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> let add_to_hash h (s, v) = Hashtbl.add h s v; h</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/pplacer_src/multiprocessing.ml</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/pplacer_src/multiprocessing.ml 2020-06-13 18:46:39.674407130 +0200</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/pplacer_src/multiprocessing.ml 2020-06-13 18:48:07.406882567 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="p">@@ -71,11 +71,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> in aux pipe_map</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> type buffer = {</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- buf: string;</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ buf: Bytes.t;</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> mutable pos: int;</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> length: int;</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> }</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-let buffer n = {buf = String.create n; pos = 0; length = n}</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+let buffer n = {buf = Bytes.create n; pos = 0; length = n}</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> type buffer_state =</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> | Needs_more</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> | Done of string</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="p">@@ -87,7 +87,7 @@</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> | n -></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> let n_read = b.pos + n in</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> if n_read = b.length then</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Done b.buf</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Done (Bytes.to_string b.buf)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> else begin</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> b.pos <- n_read;</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> Needs_more</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="p">@@ -184,7 +184,7 @@</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> in match fill_buffer b h.ch, marshal_state with</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> | Needs_more, _ -> ()</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> | Done header, Needs_header _ -></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- marshal_state <- Needs_data (header, buffer (Marshal.data_size header 0))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ marshal_state <- Needs_data (header, buffer (Marshal.data_size (Bytes.of_string header) 0))</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> | Done body, Needs_data (header, _) -></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> let obj = Marshal.from_string (header ^ body) 0 in</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> self#obj_received obj;</span></pre>
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<li id="ff9c563dedb94407025694ae4311cf34844a98b5">
<a href="https://salsa.debian.org/med-team/pplacer/-/compare/8f6f9aac2953129d004aef65a21c864c88a7a72b...b35a959570d746cf009b164a5d9723e98eddf90c#ff9c563dedb94407025694ae4311cf34844a98b5"><strong>debian/patches/ocaml_stdlib</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Ralf Treinen <treinen@debian.org></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Pervasives has become Stdlib in ocaml 4.07</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Index: pplacer/common_src/mapsSets.ml</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/common_src/mapsSets.ml 2020-06-13 17:04:45.732114513 +0200</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/common_src/mapsSets.ml 2020-06-13 17:04:45.728116096 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> module OrderedFloat = struct</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> type t = float</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- let compare = Pervasives.compare</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ let compare = Stdlib.compare</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> end</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> module OrderedInt = struct</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/common_src/number.ml</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/common_src/number.ml 2020-06-13 17:04:45.732114513 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/common_src/number.ml 2020-06-13 17:04:45.728116096 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -44,7 +44,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> let max = ( || )</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> let pow x y = if y then x else true</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> let indic = ( = )</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- let compare = Pervasives.compare</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ let compare = Stdlib.compare</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> let succ = not</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> let abs x = x</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> let inv _ = false</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -80,7 +80,7 @@</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> aux y</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> let indic x y =</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> if x = y then 1 else 0</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- let compare = Pervasives.compare</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ let compare = Stdlib.compare</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> let succ = (+) 1</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> let abs = abs</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> let conv_float_fun f =</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -118,7 +118,7 @@</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> let max = bcheck max</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> let pow = bcheck ( ** )</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> let indic = bcheck (fun x y -> if x = y then 1. else 0.)</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- let compare = Pervasives.compare</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ let compare = Stdlib.compare</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> let succ = (+.) 1.</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> let abs = abs_float</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> let inv = ucheck (fun x -> 1. /. x)</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/pplacer_src/guppy_squash.ml</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/pplacer_src/guppy_squash.ml 2020-06-13 17:04:45.732114513 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/pplacer_src/guppy_squash.ml 2020-06-13 17:04:45.728116096 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> module NPreBlob =</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> struct</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> type t = int list * Mass_map.Pre.t</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- let compare = Pervasives.compare</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ let compare = Stdlib.compare</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> let merge (l1, p1) (l2, p2) = (l1 @ l2, p1 @ p2)</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> end</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/pplacer_src/newick_bark.ml</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/pplacer_src/newick_bark.ml 2020-06-13 17:04:45.732114513 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/pplacer_src/newick_bark.ml 2020-06-13 17:04:45.728116096 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -119,7 +119,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> let floato_approx_compare epsilon a b =</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> match (a, b) with</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> | (Some x, Some y) -> float_approx_compare epsilon x y</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- | (a, b) -> Pervasives.compare a b</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ | (a, b) -> Stdlib.compare a b</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> let compare ?epsilon:(epsilon=0.) ?cmp_edge_label:(cmp_edge_label=true) b1 b2 =</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> let fc = floato_approx_compare epsilon in</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/pplacer_src/squashfunc.ml</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/pplacer_src/squashfunc.ml 2020-06-13 17:04:45.732114513 +0200</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/pplacer_src/squashfunc.ml 2020-06-13 17:04:45.728116096 +0200</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="p">@@ -54,7 +54,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> let compare_cble a b =</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> let cdist = compare a.dist b.dist in</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> if cdist <> 0 then cdist</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else Pervasives.compare a b</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else Stdlib.compare a b</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> </span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> let replace_blob distf oldb newb c =</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> if c.small = oldb then cble_of_blobs distf c.big newb</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/pplacer_src/tax_id.ml</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/pplacer_src/tax_id.ml 2020-06-13 17:04:45.732114513 +0200</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/pplacer_src/tax_id.ml 2020-06-13 17:04:45.728116096 +0200</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> (* The taxonomic id type</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> *</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * note use of Pervasives.compare should be redone if speed needed.</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * note use of Stdlib.compare should be redone if speed needed.</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> *)</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> open Ppatteries</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="p">@@ -67,7 +67,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> (* *** Maps and Sets *** *)</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> module OrderedTaxId = struct</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> type t = tax_id</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- let compare = Pervasives.compare</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ let compare = Stdlib.compare</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> end</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> module PprTaxId = struct</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/pplacer_src/guppy_round.ml</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/pplacer_src/guppy_round.ml 2020-06-13 17:04:23.481803484 +0200</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/pplacer_src/guppy_round.ml 2020-06-13 17:05:31.011799071 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="p">@@ -48,7 +48,7 @@</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> Map.Make</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> (struct</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> type t = rounded_pquery</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- let compare = Pervasives.compare</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ let compare = Stdlib.compare</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> end)</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> </span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> let add_listly k v m =</span></pre>
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<a href="https://salsa.debian.org/med-team/pplacer/-/compare/8f6f9aac2953129d004aef65a21c864c88a7a72b...b35a959570d746cf009b164a5d9723e98eddf90c#ac9a0fb7ed09d8775c7899149574abe3381357dd"><strong>debian/patches/ocamlbuild</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/myocamlbuild.ml</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/myocamlbuild.ml 2020-0<span class="idiff left right">5-23 19:56:32.503243020</span> +0200</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/myocamlbuild.ml 2020-0<span class="idiff left right">5-23 19:56:52.42336436</span>4 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer.orig/myocamlbuild.ml 2020-0<span class="idiff left right">6-13 17:31:13.250164814</span> +0200</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer/myocamlbuild.ml 2020-0<span class="idiff left right">6-13 17:31:13.25016481</span>4 +0200</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">@@ -19,10 +19,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> module OCamlFind =</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> struct</span>
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<a href="https://salsa.debian.org/med-team/pplacer/-/compare/8f6f9aac2953129d004aef65a21c864c88a7a72b...b35a959570d746cf009b164a5d9723e98eddf90c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">ocamlbuild</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_makefile.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">ocaml_stdlib</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">ocaml_bytes</span></pre>
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