Merge remote-tracking branch 'upstream/no-tail-surject' into limit-su…

…rject-tails

src/multipath_alignment_graph.hpp

@@ -194,10 +194,11 @@ namespace vg {
         /// order, even if this MultipathAlignmentGraph is. You MUST sort it
         /// with topologically_order_subpaths() before trying to run DP on it.
         void align(const Alignment& alignment, const HandleGraph& align_graph, const GSSWAligner* aligner, bool score_anchors_as_matches,
-                   size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies,
-                   size_t unmergeable_len, size_t band_padding, multipath_alignment_t& multipath_aln_out, SnarlManager* cutting_snarls = nullptr,
-                   SnarlDistanceIndex* dist_index = nullptr, const function<pair<id_t, bool>(id_t)>* project = nullptr,
-                   bool allow_negative_scores = false, unordered_map<handle_t, bool>* left_align_strand = nullptr);
+                   size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length,
+                   bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t& multipath_aln_out,
+                   SnarlManager* cutting_snarls = nullptr, SnarlDistanceIndex* dist_index = nullptr,
+                   const function<pair<id_t, bool>(id_t)>* project = nullptr, bool allow_negative_scores = false,
+                   unordered_map<handle_t, bool>* left_align_strand = nullptr);
 
         /// Do intervening and tail alignments between the anchoring paths and
         /// store the result in a multipath_alignment_t. Reachability edges must
@@ -212,8 +213,8 @@ namespace vg {
         /// order, even if this MultipathAlignmentGraph is. You MUST sort it
         /// with topologically_order_subpaths() before trying to run DP on it.
         void align(const Alignment& alignment, const HandleGraph& align_graph, const GSSWAligner* aligner, bool score_anchors_as_matches,
-                   size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies,
-                   size_t unmergeable_len, function<size_t(const Alignment&,const HandleGraph&)> band_padding_function,
+                   size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length,
+                   bool simplify_topologies, size_t unmergeable_len, function<size_t(const Alignment&,const HandleGraph&)> band_padding_function,
                    multipath_alignment_t& multipath_aln_out, SnarlManager* cutting_snarls = nullptr, SnarlDistanceIndex* dist_index = nullptr,
                    const function<pair<id_t, bool>(id_t)>* project = nullptr, bool allow_negative_scores = false,
                    unordered_map<handle_t, bool>* left_align_strand = nullptr);
@@ -312,12 +313,16 @@ namespace vg {
         /// Alignments of the tail off of that subpath. Also computes the
         /// source subpaths and adds their numbers to the given set if not
         /// null.
+        ///
+        /// If a tail is longer than max_tail_length, produces an alignment
+        /// softclipping it.
+        ///
         /// If dynamic alignment count is also selected, can indicate a minimum number
         /// of paths that must be in the extending graph in order to do an alignment
         unordered_map<bool, unordered_map<size_t, vector<Alignment>>>
         align_tails(const Alignment& alignment, const HandleGraph& align_graph, const GSSWAligner* aligner,
                     size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier,
-                    size_t min_paths, unordered_set<size_t>* sources = nullptr);
+                    size_t min_paths, size_t max_tail_length, unordered_set<size_t>* sources = nullptr);
 
         /// Removes alignments that follow the same path through the graph, retaining only the
         /// highest scoring ones. If deduplicating leftward, then also removes paths that take a

src/multipath_mapper.cpp

@@ -6256,9 +6256,9 @@ namespace vg {
 
             // do the connecting alignments and fill out the multipath_alignment_t object
             multi_aln_graph.align(alignment, *align_dag, aligner, true, num_alt_alns, dynamic_max_alt_alns, max_alignment_gap,
-                                  use_pessimistic_tail_alignment ? pessimistic_gap_multiplier : 0.0, simplify_topologies,
-                                  max_tail_merge_supress_length, choose_band_padding, multipath_aln_out, snarl_manager,
-                                  distance_index, &translator);
+                                  use_pessimistic_tail_alignment ? pessimistic_gap_multiplier : 0.0, std::numeric_limits<size_t>::max(),
+                                  simplify_topologies, max_tail_merge_supress_length, choose_band_padding, multipath_aln_out,
+                                  snarl_manager, distance_index, &translator);
 
             // Note that we do NOT topologically order the multipath_alignment_t. The
             // caller has to do that, after it is finished breaking it up into
@@ -6313,8 +6313,8 @@ namespace vg {
 
         // do the connecting alignments and fill out the multipath_alignment_t object
         multi_aln_graph.align(alignment, subgraph, aligner, false, num_alt_alns, dynamic_max_alt_alns, max_alignment_gap,
-                              use_pessimistic_tail_alignment ? pessimistic_gap_multiplier : 0.0, simplify_topologies,
-                              max_tail_merge_supress_length, choose_band_padding, multipath_aln_out);
+                              use_pessimistic_tail_alignment ? pessimistic_gap_multiplier : 0.0, std::numeric_limits<size_t>::max(),
+                              simplify_topologies, max_tail_merge_supress_length, choose_band_padding, multipath_aln_out);
 
         for (size_t j = 0; j < multipath_aln_out.subpath_size(); j++) {
             translate_oriented_node_ids(*multipath_aln_out.mutable_subpath(j)->mutable_path(), translator);

src/subcommand/surject_main.cpp

@@ -47,6 +47,7 @@ void help_surject(char** argv) {
          << "  -b, --bam-output         write BAM to stdout" << endl
          << "  -s, --sam-output         write SAM to stdout" << endl
          << "  -l, --subpath-local      let the multipath mapping surjection produce local (rather than global) alignments" << endl
+         << "  -T, --max-tail-len N     do not align read tails longer than N" << 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
          << "  -S, --spliced            interpret long deletions against paths as spliced alignments" << endl
@@ -96,6 +97,7 @@ int main_surject(int argc, char** argv) {
     int min_splice_length = 20;
     size_t watchdog_timeout = 10;
     bool subpath_global = true; // force full length alignments in mpmap resolution
+    size_t max_tail_len = std::numeric_limits<size_t>::max();
     bool qual_adj = false;
     bool prune_anchors = false;
     size_t max_anchors = 200;
@@ -114,7 +116,8 @@ int main_surject(int argc, char** argv) {
             {"into-path", required_argument, 0, 'p'},
             {"into-paths", required_argument, 0, 'F'},
             {"ref-paths", required_argument, 0, 'F'}, // Now an alias for --into-paths
-            {"subpath-local", required_argument, 0, 'l'},
+            {"subpath-local", no_argument, 0, 'l'},
+            {"max-tail-len", required_argument, 0, 'T'},
             {"interleaved", no_argument, 0, 'i'},
             {"multimap", no_argument, 0, 'M'},
             {"gaf-input", no_argument, 0, 'G'},
@@ -137,7 +140,7 @@ int main_surject(int argc, char** argv) {
         };
 
         int option_index = 0;
-        c = getopt_long (argc, argv, "hx:p:F:liGmcbsN:R:f:C:t:SPa:ALMVw:",
+        c = getopt_long (argc, argv, "hx:p:F:lT:iGmcbsN:R:f:C:t:SPa:ALMVw:",
                 long_options, &option_index);
 
         // Detect the end of the options.
@@ -163,6 +166,10 @@ int main_surject(int argc, char** argv) {
             subpath_global = false;
             break;
 
+        case 'T':
+            max_tail_len = parse<size_t>(optarg);
+            break;
+
         case 'i':
             interleaved = true;
             break;
@@ -303,8 +310,9 @@ int main_surject(int argc, char** argv) {
     else {
         surjector.min_splice_length = numeric_limits<int64_t>::max();
     }
+    surjector.max_tail_length = max_tail_len;
     surjector.annotate_with_all_path_scores = annotate_with_all_path_scores;
-    
+
     // Count our threads
     int thread_count = vg::get_thread_count();
 

src/surjector.cpp

@@ -3095,6 +3095,7 @@ using namespace std;
                                false,                                    // dynamic alt alns
                                numeric_limits<int64_t>::max(),           // max gap
                                0.0,                                      // pessimistic tail gap multiplier
+                               max_tail_length,                          // max length of tail to align
                                false,                                    // simplify topologies
                                0,                                        // unmergeable len
                                1,                                        // band padding

src/surjector.hpp

@@ -108,6 +108,9 @@ using namespace std;
 
         /// the minimum length apparent intron that we will try to repair
         int64_t min_splice_repair_length = 250;
+
+        /// the maximum length of a tail that we will try to align
+        size_t max_tail_length = std::numeric_limits<size_t>::max();
 
         /// How big of a graph in bp should we ever try to align against for realigning surjection?
         size_t max_subgraph_bases = 100 * 1024;

src/unittest/multipath_alignment_graph.cpp

@@ -110,7 +110,7 @@ TEST_CASE( "MultipathAlignmentGraph::align handles tails correctly", "[multipath
             mpg.resect_snarls_from_paths(&snarl_manager, identity, 5);
             
             // Make it align, with alignments per gap/tail
-            mpg.align(query, vg, &aligner, true, 2, false, 100, 0.0, 5, out);
+            mpg.align(query, vg, &aligner, true, 2, false, 100, 0.0, std::numeric_limits<size_t>::max(), false, 5, out);
             
             // Make sure to topologically sort the resulting alignment. TODO: Should
             // the MultipathAlignmentGraph guarantee this for us by construction?
@@ -148,7 +148,7 @@ TEST_CASE( "MultipathAlignmentGraph::align handles tails correctly", "[multipath
         SECTION("Handles tails when anchors for them are not generated") {
         
             // Make it align, with alignments per gap/tail
-            mpg.align(query, vg, &aligner, true, 2, false, 100, 0.0, 5, out);
+            mpg.align(query, vg, &aligner, true, 2, false, 100, 0.0, std::numeric_limits<size_t>::max(), false, 5, out);
             
             // Make sure to topologically sort the resulting alignment. TODO: Should
             // the MultipathAlignmentGraph guarantee this for us by construction?
@@ -208,7 +208,7 @@ TEST_CASE( "MultipathAlignmentGraph::align handles tails correctly", "[multipath
                                          MultipathAlignmentGraph::create_projector(identity), 5);
 
             // Make it align, with alignments per gap/tail
-            mpg.align(query, vg, &aligner, true, 2, false, 100, 0.0, false, 0, 5, out);
+            mpg.align(query, vg, &aligner, true, 2, false, 100, 0.0, std::numeric_limits<size_t>::max(), false, 0, 5, out);
 
             // Make sure to topologically sort the resulting alignment. TODO: Should
             // the MultipathAlignmentGraph guarantee this for us by construction?
@@ -244,7 +244,7 @@ TEST_CASE( "MultipathAlignmentGraph::align handles tails correctly", "[multipath
 
         SECTION("Handles tails when anchors for them are not generated") {
             // Make it align, with alignments per gap/tail
-            mpg.align(query, vg, &aligner, true, 2, false, 100, 0.0, false, 0, 5, out);
+            mpg.align(query, vg, &aligner, true, 2, false, 100, 0.0, std::numeric_limits<size_t>::max(), false, 0, 5, out);
 
             // Make sure to topologically sort the resulting alignment. TODO: Should
             // the MultipathAlignmentGraph guarantee this for us by construction?
@@ -301,7 +301,7 @@ TEST_CASE( "MultipathAlignmentGraph::align handles tails correctly", "[multipath
                                          MultipathAlignmentGraph::create_projector(identity), 5);
 
             // Make it align, with alignments per gap/tail
-            mpg.align(query, vg, &aligner, true, 2, false, 100, 0.0, false, 0, 5, out);
+            mpg.align(query, vg, &aligner, true, 2, false, 100, 0.0, std::numeric_limits<size_t>::max(), false, 0, 5, out);
 
             // Make sure to topologically sort the resulting alignment. TODO: Should
             // the MultipathAlignmentGraph guarantee this for us by construction?
@@ -338,7 +338,7 @@ TEST_CASE( "MultipathAlignmentGraph::align handles tails correctly", "[multipath
 
         SECTION("Handles tails when anchors for them are not generated") {
             // Make it align, with alignments per gap/tail
-            mpg.align(query, vg, &aligner, true, 2, false, 100, 0.0, false, 0, 5, out);
+            mpg.align(query, vg, &aligner, true, 2, false, 100, 0.0, std::numeric_limits<size_t>::max(), false, 0, 5, out);
 
             // Make sure to topologically sort the resulting alignment. TODO: Should
             // the MultipathAlignmentGraph guarantee this for us by construction?