optionally force global biwfa alignment of mappings

src/align/include/align_parameters.hpp

@@ -25,6 +25,8 @@ struct Parameters {
     //wflambda
     uint16_t wflambda_segment_length;             //segment length for wflambda
 
+    bool force_biwfa_alignment;				   //force biwfa alignment
+
     int wfa_mismatch_score;
     int wfa_gap_opening_score;
     int wfa_gap_extension_score;

src/align/include/computeAlignments.hpp

@@ -496,6 +496,7 @@ namespace align
         wflign::wavefront::WFlign* wflign = new wflign::wavefront::WFlign(
                 param.wflambda_segment_length,
                 param.min_identity,
+                param.force_biwfa_alignment,
                 param.wfa_mismatch_score,
                 param.wfa_gap_opening_score,
                 param.wfa_gap_extension_score,

src/common/wflign/src/wflign.cpp

@@ -42,6 +42,7 @@ void clean_up_sketches(std::vector<std::vector<rkmh::hash_t>*> &sketches) {
 WFlign::WFlign(
     const uint16_t segment_length,
     const float min_identity,
+    const bool force_biwfa_alignment,
     const int wfa_mismatch_score,
     const int wfa_gap_opening_score,
     const int wfa_gap_extension_score,
@@ -66,6 +67,8 @@ WFlign::WFlign(
     this->segment_length = segment_length;
     this->min_identity = min_identity;
 
+    this->force_biwfa_alignment = force_biwfa_alignment;
+
     this->wfa_mismatch_score = wfa_mismatch_score;
     this->wfa_gap_opening_score = wfa_gap_opening_score;
     this->wfa_gap_extension_score = wfa_gap_extension_score;
@@ -436,7 +439,7 @@ void WFlign::wflign_affine_wavefront(
 #ifdef WFA_PNG_TSV_TIMING
     const auto start_time = std::chrono::steady_clock::now();
 #endif
-    if (
+    if (force_biwfa_alignment ||
             (query_length <= segment_length * 8 || target_length <= segment_length * 8) ||
             (mashmap_estimated_identity >= 0.99
              && query_length <= MAX_LEN_FOR_STANDARD_WFA && target_length <= MAX_LEN_FOR_STANDARD_WFA)

src/common/wflign/src/wflign.hpp

@@ -91,10 +91,12 @@ namespace wflign {
             bool emit_md_tag;
             bool paf_format_else_sam;
             bool no_seq_in_sam;
+            bool force_biwfa_alignment;
             // Setup
             WFlign(
                     const uint16_t segment_length,
                     const float min_identity,
+                    const bool force_biwfa_alignment,
                     const int wfa_mismatch_score,
                     const int wfa_gap_opening_score,
                     const int wfa_gap_extension_score,

src/interface/parse_args.hpp

@@ -102,6 +102,7 @@ void parse_args(int argc,
 
     args::Group alignment_opts(parser, "[ Alignment Options ]");
     args::ValueFlag<std::string> align_input_paf(alignment_opts, "FILE", "derive precise alignments for this input PAF", {'i', "input-paf"});
+    args::Flag force_biwfa_alignment(alignment_opts, "force-biwfa", "force alignment with biWFA for all sequence pairs", {'I', "force-biwfa"});
     args::Flag invert_filtering(alignment_opts, "A", "if an input PAF is specified, remove alignments with gap-compressed identity below --map-pct-id x 0.8, else keep all alignments "
 								"[default: if an input PAF is specified, keep all alignments, else remove alignments with gap-compressed identity below --map-pct-id x 0.8]",
                                 {'O', "invert-filtering"});
@@ -365,6 +366,7 @@ void parse_args(int argc,
     align_parameters.emit_md_tag = args::get(emit_md_tag);
     align_parameters.sam_format = args::get(sam_format);
     align_parameters.no_seq_in_sam = args::get(no_seq_in_sam);
+    align_parameters.force_biwfa_alignment = args::get(force_biwfa_alignment);
     map_parameters.split = !args::get(no_split);
     map_parameters.dropRand = false;//ToFix: !args::get(keep_ties);
     align_parameters.split = !args::get(no_split);