Merge pull request #271 from waveygang/fix-query-end

Fix query end position

.github/workflows/test_on_push.yml

@@ -46,3 +46,22 @@ jobs:
         run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/reference.fa.gz data/reads.500bps.fa.gz -s 0.5k -N -a > reads.500bps.sam && samtools view reads.500bps.sam -bS | samtools sort > reads.500bps.bam && samtools index reads.500bps.bam && samtools view reads.500bps.bam | head
       - name: Test mapping+alignment with short reads (255bps) (PAF output)
         run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/reads.255bps.fa.gz -w 16 -s 100 -L > reads.255bps.paf && head reads.255bps.paf
+      - name: Install Rust and Cargo
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+      - name: Install wgatools
+        run: cargo install --git https://github.com/wjwei-handsome/wgatools.git
+      - name: Run wfmash and generate PAF
+        run: build/bin/wfmash -t 8 -n 1 -k 19 -s 5000 -p 90 -c 30k -P 50k -T SGDref -Q S288C -Y '#' data/scerevisiae8.fa.gz data/scerevisiae8.fa.gz > test.paf
+      - name: Convert PAF to MAF using wgatools
+        run: wgatools paf2maf --target data/scerevisiae8.fa.gz --query data/scerevisiae8.fa.gz test.paf > test.maf
+      - name: Check if MAF file is not empty
+        run: |
+          if [ -s test.maf ]; then
+            echo "MAF file is not empty. Test passed."
+          else
+            echo "MAF file is empty. Test failed."
+            exit 1
+          fi

.gitignore

@@ -35,3 +35,4 @@ test/
 .idea/
 cmake-build-debug/
 result
+.aider*

src/common/wflign/src/wflign_patch.cpp

@@ -939,7 +939,8 @@ void write_merged_alignment(
                          &max_dist_threshold, &wf_aligner,
                          &multi_patch_alns,
                          &convex_penalties,
-                         &chain_gap, &max_patching_score, &min_inversion_length, &erode_k
+                         &chain_gap, &max_patching_score, &min_inversion_length, &erode_k,
+                         &query_total_length  // Add this line to capture query_total_length
 #ifdef WFA_PNG_TSV_TIMING
                          ,&emit_patching_tsv,
                          &out_patching_tsv
@@ -1396,8 +1397,17 @@ void write_merged_alignment(
                     query_pos = query_length;
                     target_pos = target_length;
 
-                    // Adjust target_length if we used additional sequence
-                    target_end += tail_aln.target_length;
+                    // Add safety checks first
+                    uint64_t new_query_end = query_offset + query_length;
+                    uint64_t new_target_end = target_offset + target_length + actual_extension;
+
+                    if (new_query_end > query_total_length || new_target_end > target_total_length) {
+                        std::cerr << "[wfmash::patch] Warning: Alignment extends beyond sequence bounds. Truncating." << std::endl;
+                    }
+
+                    // Adjust query_end and target_end, ensuring we don't exceed the total lengths
+                    query_end = std::min(new_query_end, query_total_length);
+                    target_end = std::min(new_target_end, target_total_length);
                 }
             }