optionally force global biwfa alignment of mappings

scripts/make_align_test_case.sh

@@ -0,0 +1,78 @@
+#!/bin/bash
+
+# Function to display usage
+usage() {
+    echo "Usage: $0 -p <paf_file> -f <fasta_file> -o <output_prefix>"
+    echo "  -p, --paf       PAF file"
+    echo "  -f, --fasta     FASTA file"
+    echo "  -o, --output    Output prefix for the new FASTA and adjusted PAF files"
+    exit 1
+}
+
+# Parse command-line arguments
+PARSED_ARGUMENTS=$(getopt -a -n "$0" -o p:f:o: --long paf:,fasta:,output: -- "$@")
+VALID_ARGUMENTS=$?
+if [ "$VALID_ARGUMENTS" != "0" ]; then
+    usage
+fi
+
+eval set -- "$PARSED_ARGUMENTS"
+while :
+do
+    case "$1" in
+        -p | --paf) PAF_FILE="$2" ; shift 2 ;;
+        -f | --fasta) FASTA_FILE="$2" ; shift 2 ;;
+        -o | --output) OUTPUT_PREFIX="$2" ; shift 2 ;;
+        --) shift ; break ;;
+        *) usage ;;
+    esac
+done
+
+# Validate arguments
+if [ -z "$PAF_FILE" ] || [ -z "$FASTA_FILE" ] || [ -z "$OUTPUT_PREFIX" ]; then
+    usage
+fi
+
+OUTPUT_FASTA="${OUTPUT_PREFIX}.fa"
+OUTPUT_PAF="${OUTPUT_PREFIX}.paf"
+
+# Extract the first alignment from the PAF file
+read -r line < "$PAF_FILE"
+
+# Parse the alignment fields
+IFS=$'\t' read -r -a fields <<< "$line"
+
+# Extract query and target information
+query_name="${fields[0]}"
+query_start="${fields[2]}"
+query_end="${fields[3]}"
+target_name="${fields[5]}"
+target_start="${fields[7]}"
+target_end="${fields[8]}"
+
+# Extract sequences using samtools faidx
+samtools faidx "$FASTA_FILE" "$query_name:$query_start-$query_end" > "$OUTPUT_FASTA"
+samtools faidx "$FASTA_FILE" "$target_name:$target_start-$target_end" >> "$OUTPUT_FASTA"
+
+qname=$(grep ^">" "$OUTPUT_FASTA" | head -n 1 | sed 's/^>//')
+tname=$(grep ^">" "$OUTPUT_FASTA" | tail -n 1 | sed 's/^>//')
+
+# Adjust the PAF file
+awk -v qname=$qname \
+    -v tname=$tname \
+    '{
+        if (NF > 0) {
+            query_length = $4 - $3;
+            target_length = $9 - $8;
+            $1 = qname;
+            $6 = tname;
+            $2 = query_length;
+            $3 = 0;
+            $4 = query_length;
+            $7 = target_length;
+            $8 = 0;
+            $9 = target_length;
+            print $0;
+        }
+    }' "$PAF_FILE" | tr ' ' '\t' > "$OUTPUT_PAF"
+

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);