Merge pull request #2 from pangenome/copy-aln-records

Add method to copy alignment records with trace data

Author: AndreaGuarracino

Cargo.lock

@@ -17,7 +17,7 @@ libc = "0.2"
 num_cpus = "1.16"
 nix = { version = "0.27", features = ["fs", "process"] }
 which = "6.0"
-onecode = { git = "https://github.com/pangenome/onecode-rs.git", rev = "2811715" }
+onecode = { git = "https://github.com/pangenome/onecode-rs.git", rev = "3ac229e39d72b0ac724c688e91fb2525e08922f7" }
 
 [build-dependencies]
 cc = "1.0"

Cargo.toml

@@ -68,7 +68,7 @@ pub struct AlnRecord {
 
 /// Reader for .1aln files
 pub struct AlnReader {
-    file: OneFile,
+    pub file: OneFile,
     num_alignments: i64,
     contig_offsets: std::collections::HashMap<i64, (i64, i64)>, // contig_id → (sbeg, clen)
 }
@@ -508,6 +508,103 @@ impl AlnWriter {
         Ok(())
     }
 
+    /// Copy an alignment record directly from input to output, preserving all data including trace points
+    ///
+    /// This method copies the raw alignment record from the input file positioned at an 'A' record,
+    /// including all associated data lines ('R', 'L', 'M', 'D', 'Q', 'T', 'X', etc.).
+    /// This is the preferred method for filtering, as it preserves trace data that ALNtoPAF needs.
+    ///
+    /// # Safety
+    /// The input_file must be positioned at an 'A' record when this method is called.
+    pub fn copy_alignment_record_from_file(&mut self, input_file: &mut OneFile) -> Result<()> {
+        // Verify we're at an 'A' record
+        if input_file.line_type() != 'A' {
+            anyhow::bail!("Input file not positioned at 'A' record");
+        }
+
+        // Copy 'A' record (alignment coordinates)
+        for i in 0..6 {
+            self.file.set_int(i, input_file.int(i));
+        }
+        self.file.write_line('A', 0, None);
+
+        // Copy all associated records until we hit 'T' (trace) or next 'A'
+        loop {
+            let next_type = input_file.read_line();
+
+            if next_type == '\0' {
+                break; // EOF
+            }
+
+            match next_type {
+                'T' => {
+                    // Copy T record (trace point positions - INT_LIST)
+                    if let Some(t_values) = input_file.int_list() {
+                        let len = t_values.len() as i64;
+                        let ptr = t_values.as_ptr() as *mut std::ffi::c_void;
+                        self.file.write_line('T', len, Some(ptr));
+                    } else {
+                        // Empty T record
+                        self.file.write_line('T', 0, None);
+                    }
+
+                    // Next should be X record (trace point diffs)
+                    let x_type = input_file.read_line();
+                    if x_type == 'X' {
+                        // Copy X record (INT_LIST of differences at each trace point)
+                        if let Some(x_values) = input_file.int_list() {
+                            let len = x_values.len() as i64;
+                            let ptr = x_values.as_ptr() as *mut std::ffi::c_void;
+                            self.file.write_line('X', len, Some(ptr));
+                        } else {
+                            // Empty X record
+                            self.file.write_line('X', 0, None);
+                        }
+                    }
+                    break; // Done with this alignment
+                }
+                'R' => {
+                    // Reverse complement flag
+                    self.file.write_line('R', 0, None);
+                }
+                'L' => {
+                    // Sequence lengths
+                    self.file.set_int(0, input_file.int(0));
+                    self.file.set_int(1, input_file.int(1));
+                    self.file.write_line('L', 0, None);
+                }
+                'M' => {
+                    // Matches
+                    self.file.set_int(0, input_file.int(0));
+                    self.file.write_line('M', 0, None);
+                }
+                'D' => {
+                    // Differences
+                    self.file.set_int(0, input_file.int(0));
+                    self.file.write_line('D', 0, None);
+                }
+                'Q' => {
+                    // Quality
+                    self.file.set_int(0, input_file.int(0));
+                    self.file.write_line('Q', 0, None);
+                }
+                'A' => {
+                    // Hit next alignment without seeing 'T' - this alignment had no trace data
+                    // Write empty trace records
+                    self.file.write_line('T', 0, None);
+                    self.file.write_line('X', 0, None);
+                    break;
+                }
+                _ => {
+                    // Skip unknown records
+                    continue;
+                }
+            }
+        }
+
+        Ok(())
+    }
+
     /// Write an alignment to the file
     pub fn write_alignment(&mut self, aln: &Alignment) -> Result<()> {
         // Parse sequence IDs from names (they should be numeric contig IDs)