update sourmash.h

sourmash-bio · Jan 7, 2021 · ef5c62f · ef5c62f
1 parent f28fab5
commit ef5c62f
Show file tree

Hide file tree

Showing 3 changed files with 17 additions and 15 deletions.
diff --git a/include/sourmash.h b/include/sourmash.h
@@ -211,13 +211,20 @@ SourmashStr searchresult_filename(const SourmashSearchResult *ptr);
 
 SourmashSignature *searchresult_signature(const SourmashSearchResult *ptr);
 
-SourmashRevIndex *revindex_new(const SourmashStr *const *search_sigs_ptr,
-                               uintptr_t insigs,
-                               const SourmashKmerMinHash *template_ptr,
-                               uintptr_t threshold,
-                               const SourmashKmerMinHash *const *queries_ptr,
-                               uintptr_t inqueries,
-                               bool keep_sigs);
+SourmashRevIndex *revindex_new_with_paths(const SourmashStr *const *search_sigs_ptr,
+                                          uintptr_t insigs,
+                                          const SourmashKmerMinHash *template_ptr,
+                                          uintptr_t threshold,
+                                          const SourmashKmerMinHash *const *queries_ptr,
+                                          uintptr_t inqueries,
+                                          bool keep_sigs);
+
+SourmashRevIndex *revindex_new_with_sigs(const SourmashSignature *const *search_sigs_ptr,
+                                         uintptr_t insigs,
+                                         const SourmashKmerMinHash *template_ptr,
+                                         uintptr_t threshold,
+                                         const SourmashKmerMinHash *const *queries_ptr,
+                                         uintptr_t inqueries);
 
 void revindex_free(SourmashRevIndex *ptr);
 

diff --git a/src/core/src/encodings.rs b/src/core/src/encodings.rs
@@ -439,7 +439,6 @@ impl Colors {
                     old_idxs.1 += 1;
                 })
                 .or_insert_with(|| (idxs.0, 1));
-            //self.colors.insert(new_color, idxs);
             Ok(new_color)
         }
     }

diff --git a/src/core/src/index/greyhound.rs b/src/core/src/index/greyhound.rs
@@ -363,6 +363,9 @@ impl RevIndex {
             large_hashes
                 .entry(hash)
                 .and_modify(|entry| {
+                    // Hash is already present.
+                    // Update the current color by adding the indices from
+                    // small_colors.
                     let ids = small_colors.indices(&color);
                     let new_color = large_colors.update(Some(*entry), ids).unwrap();
                     *entry = new_color;
@@ -378,13 +381,6 @@ impl RevIndex {
                 });
         });
 
-        // Doing this outside reduce (at the end) uses more memory (since it
-        // accumulates unused colors), but doesn't iterate over all
-        // hashes/colors so frequently. For now keeping it here to
-        // save memory
-        //let used_colors: HashSet<_> = large_hashes.values().collect();
-        //large_colors.retain(|color, _| used_colors.contains(color));
-
         (large_hashes, large_colors)
     }