critical section

libradicl/src/collate.rs

@@ -88,6 +88,11 @@ pub fn collate(
         total_to_collate += record.1;
     }
 
+    // sort this so that we deal with largest cells (by # of reads) first
+    // sort in _descending_ order by count.
+    quickersort::sort_by_key(&mut tsv_map[..], |&a : &(u64, u64)| std::cmp::Reverse(a.1) );
+    //println!("{:?}", tsv_map);
+
     // get the correction map
     let cmfile = std::fs::File::open(parent.join("permit_map.bin")).unwrap();
     let correct_map: HashMap<u64, u64> = bincode::deserialize_from(&cmfile).unwrap();

libradicl/src/pugutils.rs

@@ -247,7 +247,9 @@ pub(super) fn get_num_molecules_cell_ranger_like(
                     // count for this UMI
                     unresolvable = true;
                 }
-                Ordering::Less => {}
+                Ordering::Less => { 
+                    // we do nothing 
+                }
             }
         }
 

libradicl/src/quant.rs

@@ -481,23 +481,25 @@ pub fn quantify(
                     // update the matrix
                     for (i, v) in counts.into_iter().enumerate() {
                         if v > 0.0 {
-                            omat.add_triplet(i, cell_num, v);
+                            omat.add_triplet(i, 0, v);
                         }
                     }
 
                     {
                         let bc_mer: BitKmer = (bc, bclen as u8);
 
                         // writing the files
+                        let omat_csr = &omat.to_csr(); 
                         let writer = &mut *bcout.lock().unwrap();
-                        sce::eds::append_writer(&mut writer.1, &omat.to_csr())
+                        sce::eds::append_writer(&mut writer.1, &omat_csr)
                             .expect("can't write matrix");
 
                         // write to barcode file
                         writeln!(&mut writer.0, "{}\t{}", cell_num, unsafe {
                             std::str::from_utf8_unchecked(&bitmer_to_bytes(bc_mer)[..])
                         })
                         .expect("can't write to barcode file.");
+
                     }
 
                     cells_remaining.fetch_sub(1, Ordering::SeqCst);