Merge pull request #119 from pangenome/more-pafs

Support more alignment files in input

Author: AndreaGuarracino

src/impg.rs

@@ -89,7 +89,7 @@ pub struct QueryMetadata {
     target_end: i32,
     query_start: i32,
     query_end: i32,
-    paf_file_index: u16,
+    paf_file_index: u32,
     strand_and_cigar_offset: u64, // Track strand and cigar offset
     cigar_bytes: usize,
 }
@@ -308,7 +308,7 @@ impl Impg {
                             target_end: record.target_end as i32,
                             query_start: record.query_start as i32,
                             query_end: record.query_end as i32,
-                            paf_file_index: file_index as u16,
+                            paf_file_index: file_index as u32,
                             strand_and_cigar_offset: record.strand_and_cigar_offset, // Already includes strand bit
                             cigar_bytes: record.cigar_bytes,
                         };

src/main.rs

@@ -1702,14 +1702,14 @@ fn resolve_paf_files(paf: &PafOpts) -> io::Result<Vec<String>> {
         ));
     };
 
-    // Check if the number of PAF files exceeds u16::MAX
-    if paf_files.len() > u16::MAX as usize {
+    // Check if the number of PAF files exceeds u32::MAX
+    if paf_files.len() > u32::MAX as usize {
         return Err(io::Error::new(
             io::ErrorKind::InvalidInput,
             format!(
                 "Too many PAF files specified: {} (maximum allowed: {})",
                 paf_files.len(),
-                u16::MAX
+                u32::MAX
             ),
         ));
     }