From 984aee9d2d0649cc73d0151de3c268ade2988958 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Wed, 28 Sep 2022 22:02:21 +0200
Subject: [PATCH] fix the interface and the doc; cleaning

---
 docs/rst/commands/odgi_flip.rst  | 2 +-
 docs/rst/commands/odgi_paths.rst | 3 +++
 src/algorithms/path_keep.cpp     | 3 +--
 src/subcommand/paths_main.cpp    | 2 +-
 4 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/docs/rst/commands/odgi_flip.rst b/docs/rst/commands/odgi_flip.rst
index ebd362f9..b7a7c409 100644
--- a/docs/rst/commands/odgi_flip.rst
+++ b/docs/rst/commands/odgi_flip.rst
@@ -26,7 +26,7 @@ MANDATORY OPTIONS
 | Load the succinct variation graph in ODGI format from this *FILE*. The file name usually ends with *.og*. It also accepts GFAv1, but the on-the-fly conversion to the ODGI format requires additional time!
 
 | **-o, --out**\ =\ *FILE*
-| Write the graph with fliped paths to *.og*.
+| Write the graph with flipped paths to *.og*.
 
 Threading
 ---------
diff --git a/docs/rst/commands/odgi_paths.rst b/docs/rst/commands/odgi_paths.rst
index 9f96441a..f53d2bbb 100644
--- a/docs/rst/commands/odgi_paths.rst
+++ b/docs/rst/commands/odgi_paths.rst
@@ -72,6 +72,9 @@ Path Modification Options
 | **-X, --drop-paths**\ =\ *[FILE]*
 | Drop paths listed (by line) in *FILE*.
 
+| **-o, --out**\ =\ *FILE*
+| Write the dynamic succinct variation graph to this file (e.g. *.og*)
+
 Threading
 ---------
 
diff --git a/src/algorithms/path_keep.cpp b/src/algorithms/path_keep.cpp
index a8ff44c1..c3d5843f 100644
--- a/src/algorithms/path_keep.cpp
+++ b/src/algorithms/path_keep.cpp
@@ -4,7 +4,6 @@ namespace odgi {
 namespace algorithms {
 
 void keep_paths(const graph_t& graph, graph_t& into, const ska::flat_hash_set<path_handle_t>& to_keep) {
-    // for each path, find its average orientation
     graph.for_each_handle([&](const handle_t& h) {
         into.create_handle(graph.get_sequence(h), graph.get_id(h));
     });
@@ -27,7 +26,7 @@ void keep_paths(const graph_t& graph, graph_t& into, const ska::flat_hash_set<pa
             into.create_path_handle(graph.get_path_name(path));
         }
     }
-    // then add the steps in parallel
+    // add the steps in parallel
 #pragma omp parallel for
     for (auto& path : paths) {
         if (to_keep.count(path)) {
diff --git a/src/subcommand/paths_main.cpp b/src/subcommand/paths_main.cpp
index 09d7c790..73e1f652 100644
--- a/src/subcommand/paths_main.cpp
+++ b/src/subcommand/paths_main.cpp
@@ -33,7 +33,6 @@ int main_paths(int argc, char** argv) {
     args::ArgumentParser parser("Interrogate the embedded paths of a graph. Does not print anything to stdout by default!");
     args::Group mandatory_opts(parser, "[ MANDATORY ARGUMENTS ]");
     args::ValueFlag<std::string> dg_in_file(mandatory_opts, "FILE", "Load the succinct variation graph in ODGI format from this *FILE*. The file name usually ends with *.og*. It also accepts GFAv1, but the on-the-fly conversion to the ODGI format requires additional time!", {'i', "idx"});
-    args::ValueFlag<std::string> dg_out_file(mandatory_opts, "FILE", "Write the sorted dynamic succinct variation graph to this file (e.g. *.og*).", {'o', "out"});
     args::Group path_investigation_opts(parser, "[ Path Investigation Options ]");
     args::ValueFlag<std::string> overlaps_file(path_investigation_opts, "FILE", "Read in the path grouping *FILE* to generate the overlap statistics"
                                                                " from. The file must be tab-delimited. The first column lists a"
@@ -59,6 +58,7 @@ int main_paths(int argc, char** argv) {
     args::Group path_modification_opts(parser, "[ Path Modification Options ]");
     args::ValueFlag<std::string> keep_paths_file(path_modification_opts, "FILE", "Keep paths listed (by line) in *FILE*.", {'K', "keep-paths"});
     args::ValueFlag<std::string> drop_paths_file(path_modification_opts, "FILE", "Drop paths listed (by line) in *FILE*.", {'X', "drop-paths"});
+    args::ValueFlag<std::string> dg_out_file(path_modification_opts, "FILE", "Write the dynamic succinct variation graph to this file (e.g. *.og*).", {'o', "out"});
     args::Group threading_opts(parser, "[ Threading ]");
     args::ValueFlag<uint64_t> threads(threading_opts, "N", "Number of threads to use for parallel operations.", {'t', "threads"});
 	args::Group processing_info_opts(parser, "[ Processing Information ]");