fix state, end flag

include/kmtricks/cmd.hpp

@@ -88,6 +88,9 @@ struct main_all
     scheduler.execute();
 
     state::get().write();
+    {
+      std::ofstream endf(opt->end_flag, std::ios::out);
+    }
   }
 };
 

include/kmtricks/cmd/all.hpp

@@ -66,6 +66,7 @@ struct all_options : km_options
   double focus {1.0};
 
   std::string from;
+  std::string end_flag;
 
   MODE mode;
   FORMAT format;

include/kmtricks/signals.hpp

@@ -67,6 +67,7 @@ inline std::string signal_to_string(int signal)
 }
 
 static std::mutex SigLock;
+static bool sig_done = false;
 
 class SignalHandler
 {
@@ -80,11 +81,11 @@ class SignalHandler
   template <typename Callback = void (*)(int)>
   void init(Callback c = nullptr)
   {
-    std::signal(SIGABRT, c ? c : default_callback);
-    std::signal(SIGFPE, c ? c : default_callback);
-    std::signal(SIGILL, c ? c : default_callback);
-    std::signal(SIGSEGV, c ? c : default_callback);
-    std::signal(SIGTERM, c ? c : default_callback);
+    //std::signal(SIGABRT, c ? c : default_callback);
+    //std::signal(SIGFPE, c ? c : default_callback);
+    //std::signal(SIGILL, c ? c : default_callback);
+    //std::signal(SIGSEGV, c ? c : default_callback);
+    //std::signal(SIGTERM, c ? c : default_callback);
 
     std::signal(SIGINT, c ? c : state_callback);
   }
@@ -99,9 +100,15 @@ class SignalHandler
   {
     std::unique_lock<std::mutex> _(SigLock);
 
+    if (!sig_done)
+    {
+
     state::get().write(
       fmt::format(
         "Killed after {}. The run can be resumed by running the same command again.", signal_to_string(signal)));
+
+      sig_done = true;
+    }
   }
 
   static void default_callback(int signal)

include/kmtricks/state.hpp

@@ -29,12 +29,14 @@ namespace km {
         m_superk.resize(f, 0);
         m_count.resize(f * p, 0);
         m_merge.resize(p, 0);
+
       }
 
       void init_f(const std::string& f, std::size_t n, std::size_t p)
       {
         m_nb = n;
         m_part = p;
+        m_path = f;
         std::ifstream inf(f, std::ios::in | std::ios::binary);
 
         m_superk.resize(m_nb, 0);
@@ -46,20 +48,22 @@ namespace km {
         inf.read(reinterpret_cast<char*>(m_superk.data()), sizeof(std::uint8_t) * n);
         inf.read(reinterpret_cast<char*>(m_count.data()), sizeof(std::uint8_t) * (n*p));
         inf.read(reinterpret_cast<char*>(m_merge.data()), sizeof(std::uint8_t) * p);
+
       }
 
       void write(const std::string& msg = "")
       {
         std::unique_lock<spinlock> _1(m_lock_1);
         std::unique_lock<spinlock> _2(m_lock_2);
-        std::ofstream inf(m_path, std::ios::out | std::ios::binary);
-
-        inf.write(reinterpret_cast<char*>(&m_config), sizeof(m_config));
-        inf.write(reinterpret_cast<char*>(&m_repart), sizeof(m_repart));
-        inf.write(reinterpret_cast<char*>(m_superk.data()), sizeof(std::uint8_t) * m_nb);
-        inf.write(reinterpret_cast<char*>(m_count.data()), sizeof(std::uint8_t) * (m_nb*m_part));
-        inf.write(reinterpret_cast<char*>(m_merge.data()), sizeof(std::uint8_t) * m_part);
 
+        {
+          std::ofstream inf(m_path, std::ios::out | std::ios::binary);
+          inf.write(reinterpret_cast<char*>(&m_config), sizeof(m_config));
+          inf.write(reinterpret_cast<char*>(&m_repart), sizeof(m_repart));
+          inf.write(reinterpret_cast<char*>(m_superk.data()), sizeof(std::uint8_t) * m_nb);
+          inf.write(reinterpret_cast<char*>(m_count.data()), sizeof(std::uint8_t) * (m_nb*m_part));
+          inf.write(reinterpret_cast<char*>(m_merge.data()), sizeof(std::uint8_t) * m_part);
+        }
         if (!msg.empty())
         {
           spdlog::info(msg);

include/kmtricks/task.hpp

@@ -742,6 +742,8 @@ class HashMergeTask : public ITask
   void preprocess() {}
   void postprocess()
   {
+    state::get().merge_done(m_part_id);
+
     if (this->m_clear)
     {
       for (auto& f : KmDir::get().get_files_to_merge(m_part_id, m_lz4, KM_FILE::HASH))
@@ -750,7 +752,6 @@ class HashMergeTask : public ITask
       }
     }
     this->m_finish = true;
-    state::get().merge_done(m_part_id);
     this->exec_callback();
   }
 

scripts/clear_run.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+echo $1
+
+rm -rf $1/fpr \
+       $1/filters \
+       $1/howde_index \
+       $1/merge_infos \
+       $1/counts \
+       $1/histograms \
+       $1/partition_infos \
+       $1/superkmers \
+       $1/minimizers

src/cli.cpp

@@ -238,6 +238,10 @@ km_options_t all_cli(std::shared_ptr<bc::Parser<1>> cli, all_options_t options)
 
   all_cmd->add_group("merge options", "");
 
+  all_cmd->add_param("--end-flag", "write an empty file at the end of the run.")
+         ->meta("STR")
+         ->setter(options->end_flag);
+
   auto a_min_setter = [options](const std::string& v) {
     auto [f, _] = bc::check::is_file("", v);
     if (f)