Fix PAF corruption: flush after each pairwise alignment write

Without flushing after each write_all(), buffered writes could be
incomplete or corrupted if the process was interrupted or the buffer
wasn't full. Now we flush after each pairwise alignment completes
to ensure data integrity.

Author: ekg

src/main.rs

@@ -1217,6 +1217,7 @@ fn align_multiple_fastas(
             // Append to merged output
             let paf_content = std::fs::read_to_string(temp_paf.path())?;
             merged_output.write_all(paf_content.as_bytes())?;
+            merged_output.flush()?; // Flush after each alignment to prevent corruption
 
             let alignment_count = paf_content.lines().count();
             total_alignments += alignment_count;
@@ -1237,13 +1238,15 @@ fn align_multiple_fastas(
 
             let paf_content = std::fs::read_to_string(temp_paf.path())?;
             merged_output.write_all(paf_content.as_bytes())?;
+            merged_output.flush()?; // Flush after each alignment to prevent corruption
 
             let alignment_count = paf_content.lines().count();
             total_alignments += alignment_count;
             total_pairs += 1;
         }
     }
 
+    // Final flush (redundant but safe)
     merged_output.flush()?;
 
     if !quiet {