libkhmer untraceable abort

gaaah.cc

#include "hashbits.hh"
#include "subset.hh"

#include <string>
#include <exception>

using namespace khmer;
using namespace std;

bool file_exists (const string& name) {
  ifstream f(name.c_str());
  if (f.good()) {
    // f.close();
    return true;
  } else {
    // f.close();
    return false;
  }
}

int main(void) {

  vector<HashIntoType> sizes =
    {static_cast<HashIntoType>(4e9+7), static_cast<HashIntoType>(4e9+9)};
  int k = 19;

  Hashbits htable(k, sizes);
  SubsetPartition part(&htable);

  string left = "example_data/left.fq";
  string right = "example_data/right.fq";
  string pmap_out = "out.part";

  if (file_exists(pmap_out)) {

    // load existing pmap

    cout << "Loading partition map from existing file" << endl;

    try {
      part.load_partitionmap(pmap_out);
    } catch (exception &e) {
      cerr << "ERROR loading partition map" << endl << e.what() << endl;
      exit(1);
    }

  } else  {

    // do fresh partitioning

    unsigned long long n_consumed = 0;
    unsigned int total_reads = 0;
    htable.consume_fasta_and_tag(left, total_reads, n_consumed);
    htable.consume_fasta_and_tag(right, total_reads, n_consumed);
    part.do_partition(0, 0, true, true);
    part.save_partitionmap(pmap_out);

  }

}

this was eventually resolved to being a problem caused by -static-libgcc