WIP: support RocksDB databases in sourmash proper through FFI

Makefile

@@ -32,11 +32,12 @@ include/sourmash.h: src/core/src/lib.rs \
                     src/core/src/ffi/nodegraph.rs \
                     src/core/src/ffi/index/mod.rs \
                     src/core/src/ffi/index/revindex.rs \
+                    src/core/src/ffi/index/disk_revindex.rs \
                     src/core/src/ffi/storage.rs \
                     src/core/src/errors.rs \
                     src/core/cbindgen.toml
 	cd src/core && \
-	RUSTC_BOOTSTRAP=1 cbindgen -c cbindgen.toml . -o ../../$@
+	RUSTC_BOOTSTRAP=1 cbindgen -c cbindgen.toml . -o ../../$@ -v
 
 coverage: all
 	tox -e coverage

include/sourmash.h

@@ -60,6 +60,8 @@ typedef uint32_t SourmashErrorCode;
 
 typedef struct SourmashComputeParameters SourmashComputeParameters;
 
+typedef struct SourmashDiskRevIndex SourmashDiskRevIndex;
+
 typedef struct SourmashHyperLogLog SourmashHyperLogLog;
 
 typedef struct SourmashKmerMinHash SourmashKmerMinHash;
@@ -138,6 +140,37 @@ void computeparams_set_track_abundance(SourmashComputeParameters *ptr, bool v);
 
 bool computeparams_track_abundance(const SourmashComputeParameters *ptr);
 
+SourmashSignature *disk_revindex_best_containment(const SourmashDiskRevIndex *db_ptr,
+                                                  const SourmashSignature *query_ptr,
+                                                  uint16_t threshold_bp);
+
+void disk_revindex_free(SourmashDiskRevIndex *ptr);
+
+uint64_t disk_revindex_ksize(const SourmashDiskRevIndex *ptr);
+
+uint64_t disk_revindex_len(const SourmashDiskRevIndex *ptr);
+
+const char *disk_revindex_moltype(const SourmashDiskRevIndex *ptr);
+
+SourmashDiskRevIndex *disk_revindex_new_from_rocksdb(const char *path_ptr);
+
+SourmashSignature *disk_revindex_peek(const SourmashDiskRevIndex *db_ptr,
+                                      const SourmashKmerMinHash *query_ptr);
+
+const SourmashSearchResult *const *disk_revindex_prefetch(const SourmashDiskRevIndex *db_ptr,
+                                                          const SourmashSignature *query_ptr,
+                                                          uint64_t threshold_bp,
+                                                          uintptr_t *return_size);
+
+uint32_t disk_revindex_scaled(const SourmashDiskRevIndex *ptr);
+
+const SourmashSearchResult *const *disk_revindex_search_jaccard(const SourmashDiskRevIndex *db_ptr,
+                                                                const SourmashSignature *query_ptr,
+                                                                double threshold,
+                                                                uintptr_t *return_size);
+
+SourmashSignature **disk_revindex_signatures(const SourmashDiskRevIndex *ptr, uintptr_t *size);
+
 uint64_t hash_murmur(const char *kmer, uint64_t seed);
 
 void hll_add_hash(SourmashHyperLogLog *ptr, uint64_t hash);