From 9e54402cadfd31b5fd97f5650dcf80ba320fd169 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Mon, 11 May 2020 10:23:21 -0700
Subject: [PATCH] Go back to Cactus snarl finder for release

---
 src/subcommand/call_main.cpp   | 4 ++--
 src/subcommand/snarls_main.cpp | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/subcommand/call_main.cpp b/src/subcommand/call_main.cpp
index 423f1c5c7e1..795631200e4 100644
--- a/src/subcommand/call_main.cpp
+++ b/src/subcommand/call_main.cpp
@@ -13,7 +13,7 @@
 #include "subcommand.hpp"
 #include "../path.hpp"
 #include "../graph_caller.hpp"
-#include "../integrated_snarl_finder.hpp"
+#include "../cactus_snarl_finder.hpp"
 #include "../xg.hpp"
 #include <vg/io/stream.hpp>
 #include <vg/io/vpkg.hpp>
@@ -295,7 +295,7 @@ int main_call(int argc, char** argv) {
         }
         snarl_manager = vg::io::VPKG::load_one<SnarlManager>(snarl_file);
     } else {
-        IntegratedSnarlFinder finder(*graph);
+        CactusSnarlFinder finder(*graph);
         snarl_manager = unique_ptr<SnarlManager>(new SnarlManager(std::move(finder.find_snarls_parallel())));
     }
     
diff --git a/src/subcommand/snarls_main.cpp b/src/subcommand/snarls_main.cpp
index 4a075dac4b6..3411fe2257b 100644
--- a/src/subcommand/snarls_main.cpp
+++ b/src/subcommand/snarls_main.cpp
@@ -28,7 +28,7 @@ void help_snarl(char** argv) {
     cerr << "usage: " << argv[0] << " snarls [options] graph > snarls.pb" << endl
          << "       By default, a list of protobuf Snarls is written" << endl
          << "options:" << endl
-         << "    -A, --algorithm NAME   compute snarls using 'cactus' or 'integrated' algorithms (default: integrated)" << endl
+         << "    -A, --algorithm NAME   compute snarls using 'cactus' or 'integrated' algorithms (default: cactus)" << endl
          << "    -p, --pathnames        output variant paths as SnarlTraversals to STDOUT" << endl
          << "    -r, --traversals FILE  output SnarlTraversals for ultrabubbles." << endl
          << "    -l, --leaf-only        restrict traversals to leaf ultrabubbles." << endl
@@ -52,7 +52,7 @@ int main_snarl(int argc, char** argv) {
 
     static const int buffer_size = 100;
     
-    string algorithm = "integrated";
+    string algorithm = "cactus";
     string traversal_file;
     bool leaf_only = false;
     bool top_level_only = false;