fixed macos segfault (due to stack overflow?)

voutcn · Jul 13, 2019 · 533a602 · 533a602
1 parent 02475be
commit 533a602
Showing 1 changed file with 42 additions and 25 deletions.
diff --git a/src/main_iterate.cpp b/src/main_iterate.cpp
@@ -1,7 +1,6 @@
 /*
  *  MEGAHIT
- *  Copyright (C) 2014 - 2015 The University of Hong Kong & L3 Bioinformatics
- * Limited
+ *  Copyright (C) 2014 - 2015 The University of Hong Kong & L3 Bioinformatics Limited
  *
  *  This program is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
@@ -19,15 +18,18 @@
 
 /* contact: Dinghua Li <dhli@cs.hku.hk> */
 
+#include <assert.h>
 #include <omp.h>
-#include <cassert>
+#include <stdio.h>
 
 #include <algorithm>
 #include <iostream>
 #include <sstream>
 #include <stdexcept>
 #include <string>
 #include <vector>
+#include <list>
+#include <functional>
 
 #include "definitions.h"
 #include "iterate/contig_flank_index.h"
@@ -59,10 +61,9 @@ static void ParseIterOptions(int argc, char *argv[]) {
   desc.AddOption("num_cpu_threads", "t", opt.num_cpu_threads, "number of cpu threads, at least 2. 0 for auto detect.");
   desc.AddOption("kmer_k", "k", opt.kmer_k, "(*) current kmer size.");
   desc.AddOption("step", "s", opt.step,
-                 "(*) step for iteration (<= 29). i.e. this iteration is from "
-                 "kmer_k to (kmer_k + step)");
+                 "(*) step for iteration (<= 28). i.e. this iteration is from kmer_k to (kmer_k + step)");
   desc.AddOption("output_prefix", "o", opt.output_prefix,
-                 "(*) output_prefix.edges.0 and output_prefix.rr.pb will be created.");
+                 "(*) output_prefix.edges.0 will be created.");
 
   try {
     desc.Parse(argc, argv);
@@ -110,19 +111,18 @@ static bool ReadReadsAndProcessKernel(const Option &opt, const IndexType &index)
     return false;
   }
   xinfo("Selected kmer type size for next k: {}\n", sizeof(KmerType));
-  BinaryReader binary_reader(opt.read_file);
-  AsyncSequenceReader reader(&binary_reader);
+  AsyncReadReader reader(opt.read_file);
   KmerCollector<KmerType> collector(opt.kmer_k + opt.step + 1, opt.output_prefix);
   int64_t num_aligned_reads = 0;
   int64_t num_total_reads = 0;
 
   while (true) {
     const auto &read_pkg = reader.Next();
-    if (read_pkg.seq_count() == 0) {
+    if (read_pkg.SeqCount() == 0) {
       break;
     }
     num_aligned_reads += index.FindNextKmersFromReads(read_pkg, &collector);
-    num_total_reads += read_pkg.seq_count();
+    num_total_reads += read_pkg.SeqCount();
     xinfo("Processed: {}, aligned: {}. Iterative edges: {}\n", num_total_reads, num_aligned_reads,
           collector.collection().size());
   }
@@ -152,39 +152,56 @@ static void ReadContigsAndBuildIndex(const Option &opt, const std::string &file_
     auto &pkg = reader.Next();
     auto &contig_pkg = pkg.first;
     auto &mul = pkg.second;
-    if (contig_pkg.seq_count() == 0) {
+    if (contig_pkg.SeqCount() == 0) {
       break;
     }
-    xinfo("Read {} contigs\n", contig_pkg.seq_count());
+    xinfo("Read {} contigs\n", contig_pkg.SeqCount());
     index->FeedBatchContigs(contig_pkg, mul);
     xinfo("Number of flank kmers: {}\n", index->size());
   }
 }
 
+struct BaseRunner {
+  virtual void Run(const Option &opt) = 0;
+  virtual uint32_t max_k() const = 0;
+};
+
 template <class KmerType>
-bool KmerTypeSelectAndRun(const Option &opt) {
-  if (KmerType::max_size() >= static_cast<unsigned>(opt.kmer_k + 1)) {
+struct Runner : public BaseRunner {
+  void Run(const Option &opt) override {
     xinfo("Selected kmer type size for k: {}\n", sizeof(KmerType));
     ContigFlankIndex<KmerType> index(opt.kmer_k, opt.step);
     ReadContigsAndBuildIndex(opt, opt.contig_file, &index);
     ReadContigsAndBuildIndex(opt, opt.bubble_file, &index);
     ReadReadsAndProcess(opt, index);
-    return true;
   }
-  return false;
-}
+  uint32_t max_k() const override {
+    return KmerType::max_size();
+  }
+};
+
 
 int main_iterate(int argc, char *argv[]) {
   AutoMaxRssRecorder recorder;
   ParseIterOptions(argc, argv);
 
-  if (KmerTypeSelectAndRun<Kmer<1, uint64_t>>(opt)) return 0;
-  if (KmerTypeSelectAndRun<Kmer<3, uint32_t>>(opt)) return 0;
-  if (KmerTypeSelectAndRun<Kmer<2, uint64_t>>(opt)) return 0;
-  if (KmerTypeSelectAndRun<Kmer<5, uint32_t>>(opt)) return 0;
-  if (KmerTypeSelectAndRun<Kmer<3, uint64_t>>(opt)) return 0;
-  if (KmerTypeSelectAndRun<Kmer<7, uint32_t>>(opt)) return 0;
-  if (KmerTypeSelectAndRun<Kmer<4, uint64_t>>(opt)) return 0;
-  if (KmerTypeSelectAndRun<Kmer<kUint32PerKmerMaxK, uint32_t>>(opt)) return 0;
+  std::list<std::unique_ptr<BaseRunner>> runners;
+  runners.emplace_back(new Runner<Kmer<1, uint64_t>>());
+  runners.emplace_back(new Runner<Kmer<3, uint32_t>>());
+  runners.emplace_back(new Runner<Kmer<2, uint64_t>>());
+  runners.emplace_back(new Runner<Kmer<5, uint32_t>>());
+  runners.emplace_back(new Runner<Kmer<3, uint64_t>>());
+  runners.emplace_back(new Runner<Kmer<7, uint32_t>>());
+  runners.emplace_back(new Runner<Kmer<4, uint64_t>>());
+  runners.emplace_back(new Runner<Kmer<kUint32PerKmerMaxK, uint32_t>>());
+
+  for (auto &runner: runners) {
+    if (runner->max_k() >= static_cast<uint32_t>(opt.kmer_k + 1)) {
+      runner->Run(opt);
+      return 0;
+    }
+  }
+
   xfatal("k is too large!\n");
+  return 1;
 }