@gmod/gbz-base 0.0.1 → 1.1.0

package/dist/sqlite/pager.js

@@ -1,12 +1,12 @@
 export class Pager {
-    source;
-    pageSize;
-    fileSize;
     blocks = new Map();
     blockSize;
     maxBlocks;
     bytesFetched = 0;
     fetches = 0;
+    source;
+    pageSize;
+    fileSize;
     constructor(source, pageSize, fileSize, opts = {}) {
         this.source = source;
         this.pageSize = pageSize;
@@ -15,8 +15,26 @@ export class Pager {
         this.blockSize = Math.max(pageSize, Math.ceil(requested / pageSize) * pageSize);
         this.maxBlocks = opts.maxBlocks ?? 256;
     }
+    async read(length, start) {
+        let attempt = 0;
+        for (;;) {
+            try {
+                const bytes = await this.source.read(length, start);
+                this.bytesFetched += bytes.length;
+                return bytes;
+            }
+            catch (error) {
+                attempt += 1;
+                if (attempt >= 3) {
+                    throw error;
+                }
+                await new Promise(resolve => setTimeout(resolve, 200 * attempt));
+            }
+        }
+    }
     seed(index, bytes) {
-        if (bytes.length === Math.min(this.blockSize, this.fileSize - index * this.blockSize)) {
+        if (bytes.length ===
+            Math.min(this.blockSize, this.fileSize - index * this.blockSize)) {
             this.blocks.set(index, Promise.resolve(bytes));
         }
     }
@@ -29,19 +47,59 @@ export class Pager {
         }
         const start = index * this.blockSize;
         const length = Math.min(this.blockSize, this.fileSize - start);
-        const pending = this.source.read(length, start).then(bytes => {
-            this.bytesFetched += bytes.length;
-            return bytes;
-        });
+        const pending = this.read(length, start);
         this.fetches += 1;
         this.blocks.set(index, pending);
-        if (this.blocks.size > this.maxBlocks) {
+        this.forgetOnFailure(pending, [index]);
+        this.evict();
+        return pending;
+    }
+    prefetch(pageNumbers) {
+        const wanted = [
+            ...new Set(pageNumbers.map(pageNumber => Math.floor(((pageNumber - 1) * this.pageSize) / this.blockSize))),
+        ]
+            .filter(index => !this.blocks.has(index))
+            .sort((a, b) => a - b);
+        let runStart = 0;
+        while (runStart < wanted.length) {
+            let runEnd = runStart + 1;
+            while (runEnd < wanted.length &&
+                wanted[runEnd] === wanted[runEnd - 1] + 1) {
+                runEnd += 1;
+            }
+            this.fetchRun(wanted[runStart], runEnd - runStart);
+            runStart = runEnd;
+        }
+    }
+    fetchRun(firstIndex, count) {
+        const start = firstIndex * this.blockSize;
+        const length = Math.min(count * this.blockSize, this.fileSize - start);
+        const pending = this.read(length, start);
+        this.fetches += 1;
+        const indexes = [];
+        for (let i = 0; i < count; i++) {
+            const within = i * this.blockSize;
+            indexes.push(firstIndex + i);
+            this.blocks.set(firstIndex + i, pending.then(bytes => bytes.subarray(within, within + this.blockSize)));
+        }
+        this.forgetOnFailure(pending, indexes);
+        this.evict();
+    }
+    forgetOnFailure(pending, indexes) {
+        pending.catch(() => {
+            for (const index of indexes) {
+                this.blocks.delete(index);
+            }
+        });
+    }
+    evict() {
+        while (this.blocks.size > this.maxBlocks) {
             const oldest = this.blocks.keys().next().value;
-            if (oldest !== undefined) {
-                this.blocks.delete(oldest);
+            if (oldest === undefined) {
+                break;
             }
+            this.blocks.delete(oldest);
         }
-        return pending;
     }
     async page(pageNumber) {
         const offset = (pageNumber - 1) * this.pageSize;
@@ -53,3 +111,4 @@ export class Pager {
         return bytes.subarray(within, within + this.pageSize);
     }
 }
+//# sourceMappingURL=pager.js.map

package/dist/sqlite/pager.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pager.js","sourceRoot":"","sources":["../../src/sqlite/pager.ts"],"names":[],"mappings":"AAOA,MAAM,OAAO,KAAK;IACR,MAAM,GAAG,IAAI,GAAG,EAA+B,CAAA;IACtC,SAAS,CAAQ;IACjB,SAAS,CAAQ;IAClC,YAAY,GAAG,CAAC,CAAA;IAChB,OAAO,GAAG,CAAC,CAAA;IAEH,MAAM,CAAY;IACjB,QAAQ,CAAQ;IACjB,QAAQ,CAAQ;IAExB,YACE,MAAkB,EAClB,QAAgB,EAChB,QAAgB,EAChB,OAAqB,EAAE;QAEvB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;QACpB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;QACxB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;QACxB,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,IAAI,KAAK,CAAA;QACzC,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,GAAG,CACvB,QAAQ,EACR,IAAI,CAAC,IAAI,CAAC,SAAS,GAAG,QAAQ,CAAC,GAAG,QAAQ,CAC3C,CAAA;QACD,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,SAAS,IAAI,GAAG,CAAA;IACxC,CAAC;IAEO,KAAK,CAAC,IAAI,CAAC,MAAc,EAAE,KAAa;QAC9C,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,SAAS,CAAC;YACR,IAAI,CAAC;gBACH,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,EAAE,KAAK,CAAC,CAAA;gBACnD,IAAI,CAAC,YAAY,IAAI,KAAK,CAAC,MAAM,CAAA;gBACjC,OAAO,KAAK,CAAA;YACd,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,OAAO,IAAI,CAAC,CAAA;gBACZ,IAAI,OAAO,IAAI,CAAC,EAAE,CAAC;oBACjB,MAAM,KAAK,CAAA;gBACb,CAAC;gBACD,MAAM,IAAI,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,GAAG,GAAG,OAAO,CAAC,CAAC,CAAA;YAClE,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,CAAC,KAAa,EAAE,KAAiB;QACnC,IACE,KAAK,CAAC,MAAM;YACZ,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,QAAQ,GAAG,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC,EAChE,CAAC;YACD,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,EAAE,OAAO,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAA;QAChD,CAAC;IACH,CAAC;IAEO,KAAK,CAAC,KAAa;QACzB,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QACrC,IAAI,MAAM,EAAE,CAAC;YACX,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;YAC9B,OAAO,MAAM,CAAA;QACf,CAAC;QACD,MAAM,KAAK,GAAG,KAAK,GAAG,IAAI,CAAC,SAAS,CAAA;QACpC,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,CAAA;QAC9D,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,KAAK,CAAC,CAAA;QACxC,IAAI,CAAC,OAAO,IAAI,CAAC,CAAA;QACjB,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,EAAE,OAAO,CAAC,CAAA;QAC/B,IAAI,CAAC,eAAe,CAAC,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;QACtC,IAAI,CAAC,KAAK,EAAE,CAAA;QACZ,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,QAAQ,CAAC,WAAqB;QAC5B,MAAM,MAAM,GAAG;YACb,GAAG,IAAI,GAAG,CACR,WAAW,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE,CAC3B,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,UAAU,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,IAAI,CAAC,SAAS,CAAC,CAChE,CACF;SACF;aACE,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;aACxC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;QACxB,IAAI,QAAQ,GAAG,CAAC,CAAA;QAChB,OAAO,QAAQ,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC;YAChC,IAAI,MAAM,GAAG,QAAQ,GAAG,CAAC,CAAA;YACzB,OACE,MAAM,GAAG,MAAM,CAAC,MAAM;gBACtB,MAAM,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,CAAC,EAC1C,CAAC;gBACD,MAAM,IAAI,CAAC,CAAA;YACb,CAAC;YACD,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAE,EAAE,MAAM,GAAG,QAAQ,CAAC,CAAA;YACnD,QAAQ,GAAG,MAAM,CAAA;QACnB,CAAC;IACH,CAAC;IAEO,QAAQ,CAAC,UAAkB,EAAE,KAAa;QAChD,MAAM,KAAK,GAAG,UAAU,GAAG,IAAI,CAAC,SAAS,CAAA;QACzC,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,CAAA;QACtE,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,KAAK,CAAC,CAAA;QACxC,IAAI,CAAC,OAAO,IAAI,CAAC,CAAA;QACjB,MAAM,OAAO,GAAa,EAAE,CAAA;QAC5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC;YAC/B,MAAM,MAAM,GAAG,CAAC,GAAG,IAAI,CAAC,SAAS,CAAA;YACjC,OAAO,CAAC,IAAI,CAAC,UAAU,GAAG,CAAC,CAAC,CAAA;YAC5B,IAAI,CAAC,MAAM,CAAC,GAAG,CACb,UAAU,GAAG,CAAC,EACd,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CACvE,CAAA;QACH,CAAC;QACD,IAAI,CAAC,eAAe,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QACtC,IAAI,CAAC,KAAK,EAAE,CAAA;IACd,CAAC;IAEO,eAAe,CAAC,OAA4B,EAAE,OAAiB;QACrE,OAAO,CAAC,KAAK,CAAC,GAAG,EAAE;YACjB,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;gBAC5B,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YAC3B,CAAC;QACH,CAAC,CAAC,CAAA;IACJ,CAAC;IAEO,KAAK;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC,SAAS,EAAE,CAAC;YACzC,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;YAC9C,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;gBACzB,MAAK;YACP,CAAC;YACD,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5B,CAAC;IACH,CAAC;IAED,KAAK,CAAC,IAAI,CAAC,UAAkB;QAC3B,MAAM,MAAM,GAAG,CAAC,UAAU,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAA;QAC/C,IAAI,UAAU,GAAG,CAAC,IAAI,MAAM,GAAG,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC;YAC7D,MAAM,IAAI,KAAK,CAAC,eAAe,UAAU,sBAAsB,CAAC,CAAA;QAClE,CAAC;QACD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAA;QACnE,MAAM,MAAM,GAAG,MAAM,GAAG,IAAI,CAAC,SAAS,CAAA;QACtC,OAAO,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAA;IACvD,CAAC;CACF"}

package/dist/sqlite/record.js

@@ -34,7 +34,8 @@ function readSignedInt(view, offset, width) {
             return view.getInt16(offset) * 4294967296 + view.getUint32(offset + 2);
         default: {
             const big = view.getBigInt64(offset);
-            if (big > BigInt(Number.MAX_SAFE_INTEGER) || big < BigInt(Number.MIN_SAFE_INTEGER)) {
+            if (big > BigInt(Number.MAX_SAFE_INTEGER) ||
+                big < BigInt(Number.MIN_SAFE_INTEGER)) {
                 throw new Error(`SQLite integer ${big} exceeds the safe integer range`);
             }
             return Number(big);
@@ -83,3 +84,4 @@ export function decodeRecord(payload) {
         throw new Error(`SQLite serial type ${type} is reserved`);
     });
 }
+//# sourceMappingURL=record.js.map

package/dist/sqlite/record.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"record.js","sourceRoot":"","sources":["../../src/sqlite/record.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,UAAU,CACxB,KAAiB,EACjB,MAAc;IAEd,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3B,MAAM,IAAI,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QAC9B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;YACvB,MAAM,IAAI,KAAK,CAAC,+CAA+C,CAAC,CAAA;QAClE,CAAC;QACD,KAAK,GAAG,KAAK,GAAG,GAAG,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,CAAA;QACnC,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;YACxB,OAAO,CAAC,KAAK,EAAE,MAAM,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;QAChC,CAAC;IACH,CAAC;IACD,MAAM,IAAI,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;IAC9B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,+CAA+C,CAAC,CAAA;IAClE,CAAC;IACD,KAAK,GAAG,KAAK,GAAG,GAAG,GAAG,IAAI,CAAA;IAC1B,IAAI,CAAC,MAAM,CAAC,aAAa,CAAC,KAAK,CAAC,EAAE,CAAC;QACjC,MAAM,IAAI,KAAK,CAAC,8CAA8C,CAAC,CAAA;IACjE,CAAC;IACD,OAAO,CAAC,KAAK,EAAE,MAAM,GAAG,CAAC,CAAC,CAAA;AAC5B,CAAC;AAED,SAAS,aAAa,CAAC,IAAc,EAAE,MAAc,EAAE,KAAa;IAClE,QAAQ,KAAK,EAAE,CAAC;QACd,KAAK,CAAC;YACJ,OAAO,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;QAC7B,KAAK,CAAC;YACJ,OAAO,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QAC9B,KAAK,CAAC;YACJ,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QAClE,KAAK,CAAC;YACJ,OAAO,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QAC9B,KAAK,CAAC;YACJ,OAAO,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,GAAG,UAAU,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACxE,OAAO,CAAC,CAAC,CAAC;YACR,MAAM,GAAG,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;YACpC,IACE,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,gBAAgB,CAAC;gBACrC,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACrC,CAAC;gBACD,MAAM,IAAI,KAAK,CAAC,kBAAkB,GAAG,iCAAiC,CAAC,CAAA;YACzE,CAAC;YACD,OAAO,MAAM,CAAC,GAAG,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;AAEjC,MAAM,UAAU,YAAY,CAAC,OAAmB;IAC9C,MAAM,CAAC,UAAU,EAAE,SAAS,CAAC,GAAG,UAAU,CAAC,OAAO,EAAE,CAAC,CAAC,CAAA;IACtD,MAAM,KAAK,GAAa,EAAE,CAAA;IAC1B,IAAI,MAAM,GAAG,SAAS,CAAA;IACtB,OAAO,MAAM,GAAG,UAAU,EAAE,CAAC;QAC3B,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,GAAG,UAAU,CAAC,OAAO,EAAE,MAAM,CAAC,CAAA;QAChD,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAChB,MAAM,GAAG,IAAI,CAAA;IACf,CAAC;IACD,MAAM,IAAI,GAAG,IAAI,QAAQ,CACvB,OAAO,CAAC,MAAM,EACd,OAAO,CAAC,UAAU,EAClB,OAAO,CAAC,UAAU,CACnB,CAAA;IACD,IAAI,IAAI,GAAG,UAAU,CAAA;IACrB,OAAO,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;QACtB,IAAI,IAAI,KAAK,CAAC,EAAE,CAAC;YACf,OAAO,IAAI,CAAA;QACb,CAAC;QACD,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YACnD,MAAM,KAAK,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,EAAE,KAAK,CAAC,CAAA;YAC9C,IAAI,IAAI,KAAK,CAAA;YACb,OAAO,KAAK,CAAA;QACd,CAAC;QACD,IAAI,IAAI,KAAK,CAAC,EAAE,CAAC;YACf,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;YACnC,IAAI,IAAI,CAAC,CAAA;YACT,OAAO,KAAK,CAAA;QACd,CAAC;QACD,IAAI,IAAI,KAAK,CAAC,EAAE,CAAC;YACf,OAAO,CAAC,CAAA;QACV,CAAC;QACD,IAAI,IAAI,KAAK,CAAC,EAAE,CAAC;YACf,OAAO,CAAC,CAAA;QACV,CAAC;QACD,IAAI,IAAI,IAAI,EAAE,EAAE,CAAC;YACf,MAAM,MAAM,GAAG,CAAC,IAAI,GAAG,EAAE,CAAC,IAAI,CAAC,CAAA;YAC/B,MAAM,KAAK,GAAG,OAAO,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,GAAG,MAAM,CAAC,CAAA;YACnD,IAAI,IAAI,MAAM,CAAA;YACd,OAAO,IAAI,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;QACvD,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,sBAAsB,IAAI,cAAc,CAAC,CAAA;IAC3D,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/subgraph.d.ts

@@ -1,7 +1,8 @@
 import type { GBZBase, PathName } from './db.ts';
-import type { Pos } from './gbwt/record.ts';
 import type { Orientation } from './gbwt/node.ts';
+import type { Pos } from './gbwt/record.ts';
 export type HaplotypeOutput = 'all' | 'distinct' | 'reference-only' | 'none';
+export type SnarlOutput = 'none' | 'contained' | 'overlapping';
 export interface PathPosition {
     seqOffset: number;
     handle: number;
@@ -59,7 +60,6 @@ export interface ToJsonOptions {
     names?: 'anonymous' | 'resolved';
 }
 export declare class Subgraph {
-    private db;
     private records;
     private paths;
     private refId;
@@ -75,6 +75,7 @@ export declare class Subgraph {
         identificationSteps: number;
         identificationFetches: number;
     };
+    private db;
     constructor(db: GBZBase);
     get nodeCount(): number;
     get pathCount(): number;
@@ -105,6 +106,12 @@ export declare class Subgraph {
         removed: number;
     }>;
     private insertContext;
+    betweenNodes(start: number, end: number): Promise<number>;
+    extractSnarls(snarls: SnarlOutput): Promise<number>;
+    private overlappingSnarls;
+    private isSnarlEntryInSubgraph;
+    private recordReader;
+    private findCoveringSnarl;
     extractPaths(reference: ReferencePath | undefined, output: HaplotypeOutput): void;
     private distinctPaths;
     identifyPaths(): Promise<void>;
@@ -118,5 +125,8 @@ export declare class Subgraph {
     private edits;
     alignToRef(pathIndex: number): string | undefined;
     alignments(): HaplotypeAlignment[];
+    private canonicalEdges;
+    stableName(): Promise<string>;
+    toGFA(cigar: boolean, opts?: ToJsonOptions): Promise<string>;
     toJSON(cigar: boolean, opts?: ToJsonOptions): SubgraphJson;
 }