Skip to content

Commit

Permalink
Stop lying about whether we are going to try rescue
Browse files Browse the repository at this point in the history
  • Loading branch information
adamnovak committed Jul 29, 2024
1 parent 62bb596 commit b1c2731
Showing 1 changed file with 9 additions and 1 deletion.
10 changes: 9 additions & 1 deletion src/minimizer_mapper.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -2072,7 +2072,7 @@ pair<vector<Alignment>, vector<Alignment>> MinimizerMapper::map_paired(Alignment
if (show_work) {
#pragma omp critical (cerr)
{
cerr << log_name() << "Found no pairs and we aren't doing rescue: return best alignment for each read" << endl;
cerr << log_name() << "Found no pairs" << endl;
}
}
std::array<alignment_index_t, 2> best_index {NO_INDEX, NO_INDEX};
Expand All @@ -2088,6 +2088,14 @@ pair<vector<Alignment>, vector<Alignment>> MinimizerMapper::map_paired(Alignment
}
if (max_rescue_attempts == 0 ) {
// If we aren't attempting rescue, just return the best alignment from each end.

if (show_work) {
#pragma omp critical (cerr)
{
cerr << log_name() << "Not attempting rescue; return best alignment for each read" << endl;
}
}

// By default, use argument alignments for scratch.
std::array<Alignment*, 2> best_aln {alns[0], alns[1]};

Expand Down

1 comment on commit b1c2731

@adamnovak
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

vg CI tests complete for branch no-rescue-lies. View the full report here.

16 tests passed, 0 tests failed and 0 tests skipped in 17297 seconds

Please sign in to comment.