Merge remote-tracking branch 'origin/unlimited-anchors' into lr-giraffe

src/subcommand/surject_main.cpp

@@ -28,7 +28,7 @@
 
 using namespace std;
 using namespace vg;
-using namespace vg::subcommand;
+using namespace vg::subcommand; 
 
 void help_surject(char** argv) {
     cerr << "usage: " << argv[0] << " surject [options] <aln.gam> >[proj.cram]" << endl
@@ -50,7 +50,7 @@ void help_surject(char** argv) {
          << "  -T, --max-tail-len N     only align up to N bases of read tails (default: 10000)" << endl
          << "  -g, --max-graph-scale X  make reads unmapped if alignment target subgraph size exceeds read length by a factor of X (default: " << Surjector::DEFAULT_SUBGRAPH_LIMIT << " or " << Surjector::SPLICED_DEFAULT_SUBGRAPH_LIMIT << " with -S)" << endl
          << "  -P, --prune-low-cplx     prune short and low complexity anchors during realignment" << endl
-         << "  -a, --max-anchors N      use no more than N anchors per target path (default: 200)" << endl
+         << "  -a, --max-anchors N      use no more than N anchors per target path (default: unlimited)" << endl
          << "  -S, --spliced            interpret long deletions against paths as spliced alignments" << endl
          << "  -A, --qual-adj           adjust scoring for base qualities, if they are available" << endl
          << "  -N, --sample NAME        set this sample name for all reads" << endl
@@ -103,7 +103,7 @@ int main_surject(int argc, char** argv) {
     std::unique_ptr<double> max_graph_scale;
     bool qual_adj = false;
     bool prune_anchors = false;
-    size_t max_anchors = 200;
+    size_t max_anchors = std::numeric_limits<size_t>::max(); // As close to unlimited as makes no difference
     bool annotate_with_all_path_scores = false;
     bool multimap = false;
     bool validate = true;

src/surjector.hpp

@@ -139,7 +139,7 @@ using namespace std;
         /// How many anchors (per path) will we use when surjecting using
         /// anchors?
         /// Excessive anchors will be pruned away.
-        size_t max_anchors = numeric_limits<size_t>::max();
+        size_t max_anchors = std::numeric_limits<size_t>::max();
 
         bool annotate_with_all_path_scores = false;