@gmod/gbz-base 1.0.0 → 2.0.0

package/dist/query.js

@@ -1,37 +1,43 @@
-import { GENERIC_SAMPLE } from "./db.js";
+import { pathNameFor } from "./pathName.js";
 import { Subgraph } from "./subgraph.js";
-function pathName(query, fragment) {
-    return {
-        sample: query.sample ?? GENERIC_SAMPLE,
-        contig: query.contig,
-        haplotype: query.haplotype ?? 0,
-        fragment,
-    };
-}
 export async function subgraphAtOffset(db, query, offset, opts = {}) {
-    const subgraph = new Subgraph(db);
-    subgraph.limit = opts.limit;
-    const reference = await subgraph.pathPosition(pathName(query, offset));
+    const subgraph = new Subgraph(db, opts);
+    const reference = await subgraph.pathPosition(pathNameFor(query, offset));
     await subgraph.aroundPosition(reference.position.handle, reference.position.nodeOffset, opts.context ?? 100);
+    await subgraph.extractSnarls(opts.snarls ?? 'none');
     subgraph.extractPaths(reference, opts.haplotypes ?? 'all');
     return subgraph;
 }
 export async function subgraphInInterval(db, query, start, end, opts = {}) {
-    const subgraph = new Subgraph(db);
-    subgraph.limit = opts.limit;
-    const reference = await subgraph.pathPosition(pathName(query, start));
+    const subgraph = new Subgraph(db, opts);
+    const reference = await subgraph.pathPosition(pathNameFor(query, start));
     await subgraph.aroundInterval(reference.position, end - start, opts.context ?? 100);
+    await subgraph.extractSnarls(opts.snarls ?? 'none');
     subgraph.extractPaths(reference, opts.haplotypes ?? 'all');
     return subgraph;
 }
 export async function subgraphAroundNodes(db, nodes, opts = {}) {
     const haplotypes = opts.haplotypes ?? 'all';
+    const snarls = opts.snarls ?? 'none';
     if (haplotypes === 'reference-only') {
         throw new Error('Cannot output a reference path in a node-based query');
     }
-    const subgraph = new Subgraph(db);
-    subgraph.limit = opts.limit;
+    if (snarls === 'overlapping' && nodes.length > 1) {
+        throw new Error('Overlapping snarls cannot be extracted for a node-based query with multiple nodes');
+    }
+    const subgraph = new Subgraph(db, opts);
     await subgraph.aroundNodes(nodes, opts.context ?? 100);
+    await subgraph.extractSnarls(snarls);
+    subgraph.extractPaths(undefined, haplotypes);
+    return subgraph;
+}
+export async function subgraphBetween(db, start, end, opts = {}) {
+    const haplotypes = opts.haplotypes ?? 'all';
+    if (haplotypes === 'reference-only') {
+        throw new Error('Cannot output a reference path in a node-based query');
+    }
+    const subgraph = new Subgraph(db, opts);
+    await subgraph.betweenNodes(start, end);
     subgraph.extractPaths(undefined, haplotypes);
     return subgraph;
 }

package/dist/query.js.map

@@ -1 +1 @@
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+{"version":3,"file":"query.js","sourceRoot":"","sources":["../src/query.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAA;AAC3C,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAgBxC,MAAM,CAAC,KAAK,UAAU,gBAAgB,CACpC,EAAW,EACX,KAAgB,EAChB,MAAc,EACd,OAAqB,EAAE;IAEvB,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;IACvC,MAAM,SAAS,GAAG,MAAM,QAAQ,CAAC,YAAY,CAAC,WAAW,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAA;IACzE,MAAM,QAAQ,CAAC,cAAc,CAC3B,SAAS,CAAC,QAAQ,CAAC,MAAM,EACzB,SAAS,CAAC,QAAQ,CAAC,UAAU,EAC7B,IAAI,CAAC,OAAO,IAAI,GAAG,CACpB,CAAA;IACD,MAAM,QAAQ,CAAC,aAAa,CAAC,IAAI,CAAC,MAAM,IAAI,MAAM,CAAC,CAAA;IACnD,QAAQ,CAAC,YAAY,CAAC,SAAS,EAAE,IAAI,CAAC,UAAU,IAAI,KAAK,CAAC,CAAA;IAC1D,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CACtC,EAAW,EACX,KAAgB,EAChB,KAAa,EACb,GAAW,EACX,OAAqB,EAAE;IAEvB,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;IACvC,MAAM,SAAS,GAAG,MAAM,QAAQ,CAAC,YAAY,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC,CAAA;IACxE,MAAM,QAAQ,CAAC,cAAc,CAC3B,SAAS,CAAC,QAAQ,EAClB,GAAG,GAAG,KAAK,EACX,IAAI,CAAC,OAAO,IAAI,GAAG,CACpB,CAAA;IACD,MAAM,QAAQ,CAAC,aAAa,CAAC,IAAI,CAAC,MAAM,IAAI,MAAM,CAAC,CAAA;IACnD,QAAQ,CAAC,YAAY,CAAC,SAAS,EAAE,IAAI,CAAC,UAAU,IAAI,KAAK,CAAC,CAAA;IAC1D,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,EAAW,EACX,KAAe,EACf,OAAqB,EAAE;IAEvB,MAAM,UAAU,GAAG,IAAI,CAAC,UAAU,IAAI,KAAK,CAAA;IAC3C,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,IAAI,MAAM,CAAA;IACpC,IAAI,UAAU,KAAK,gBAAgB,EAAE,CAAC;QACpC,MAAM,IAAI,KAAK,CAAC,sDAAsD,CAAC,CAAA;IACzE,CAAC;IACD,IAAI,MAAM,KAAK,aAAa,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACjD,MAAM,IAAI,KAAK,CACb,mFAAmF,CACpF,CAAA;IACH,CAAC;IACD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;IACvC,MAAM,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,IAAI,CAAC,OAAO,IAAI,GAAG,CAAC,CAAA;IACtD,MAAM,QAAQ,CAAC,aAAa,CAAC,MAAM,CAAC,CAAA;IACpC,QAAQ,CAAC,YAAY,CAAC,SAAS,EAAE,UAAU,CAAC,CAAA;IAC5C,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,eAAe,CACnC,EAAW,EACX,KAAa,EACb,GAAW,EACX,OAA8D,EAAE;IAEhE,MAAM,UAAU,GAAG,IAAI,CAAC,UAAU,IAAI,KAAK,CAAA;IAC3C,IAAI,UAAU,KAAK,gBAAgB,EAAE,CAAC;QACpC,MAAM,IAAI,KAAK,CAAC,sDAAsD,CAAC,CAAA;IACzE,CAAC;IACD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;IACvC,MAAM,QAAQ,CAAC,YAAY,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IACvC,QAAQ,CAAC,YAAY,CAAC,SAAS,EAAE,UAAU,CAAC,CAAA;IAC5C,OAAO,QAAQ,CAAA;AACjB,CAAC"}

package/dist/sqlite/btree.d.ts

@@ -3,6 +3,7 @@ import type { SqlValue } from './record.ts';
 export declare class BTree {
     private readonly usable;
     private pager;
+    private decodedIndexPages;
     constructor(pager: Pager, reservedBytes: number);
     private localPayloadSize;
     private payload;
@@ -12,6 +13,7 @@ export declare class BTree {
         rowid: number;
         values: SqlValue[];
     }>;
+    private decodedCells;
     private indexCell;
     indexScanFrom(root: number, low: number[]): AsyncGenerator<SqlValue[]>;
     indexSeekLE(root: number, key: number[]): Promise<SqlValue[] | undefined>;

package/dist/sqlite/btree.js

@@ -3,8 +3,16 @@ const INTERIOR_INDEX = 0x02;
 const INTERIOR_TABLE = 0x05;
 const LEAF_INDEX = 0x0a;
 const LEAF_TABLE = 0x0d;
+function readUint16(page, offset) {
+    return page[offset] * 256 + page[offset + 1];
+}
+function readUint32(page, offset) {
+    return (page[offset] * 16777216 +
+        page[offset + 1] * 65536 +
+        page[offset + 2] * 256 +
+        page[offset + 3]);
+}
 function readHeader(page, start) {
-    const view = new DataView(page.buffer, page.byteOffset, page.byteLength);
     const type = page[start];
     if (type !== INTERIOR_INDEX &&
         type !== INTERIOR_TABLE &&
@@ -15,22 +23,19 @@ function readHeader(page, start) {
     const interior = type === INTERIOR_INDEX || type === INTERIOR_TABLE;
     return {
         type,
-        cellCount: view.getUint16(start + 3),
-        rightChild: interior ? view.getUint32(start + 8) : 0,
+        cellCount: readUint16(page, start + 3),
+        rightChild: interior ? readUint32(page, start + 8) : 0,
         cellPointers: start + (interior ? 12 : 8),
     };
 }
 function cellOffset(page, header, index) {
-    const view = new DataView(page.buffer, page.byteOffset, page.byteLength);
-    return view.getUint16(header.cellPointers + 2 * index);
-}
-function readUint32(page, offset) {
-    const view = new DataView(page.buffer, page.byteOffset, page.byteLength);
-    return view.getUint32(offset);
+    return readUint16(page, header.cellPointers + 2 * index);
 }
+const MAX_DECODED_INDEX_PAGES = 4096;
 export class BTree {
     usable;
     pager;
+    decodedIndexPages = new Map();
     constructor(pager, reservedBytes) {
         this.pager = pager;
         this.usable = pager.pageSize - reservedBytes;
@@ -132,18 +137,48 @@ export class BTree {
             }
         }
         else {
+            const children = [];
             for (let i = 0; i < header.cellCount; i++) {
-                yield* this.tableScan(readUint32(page, cellOffset(page, header, i)));
+                children.push(readUint32(page, cellOffset(page, header, i)));
+            }
+            children.push(header.rightChild);
+            this.pager.prefetch(children);
+            for (const child of children) {
+                yield* this.tableScan(child);
             }
-            yield* this.tableScan(header.rightChild);
         }
     }
-    async indexCell(page, header, index) {
-        const offset = cellOffset(page, header, index);
-        const interior = header.type === INTERIOR_INDEX;
-        const [size, afterSize] = readVarint(page, interior ? offset + 4 : offset);
-        const values = decodeRecord(await this.payload(page, afterSize, size, true));
-        return { values, leftChild: interior ? readUint32(page, offset) : 0 };
+    decodedCells(pageNumber, header) {
+        let cells = this.decodedIndexPages.get(pageNumber);
+        if (cells) {
+            this.decodedIndexPages.delete(pageNumber);
+        }
+        else {
+            cells = new Array(header.cellCount);
+            if (this.decodedIndexPages.size >= MAX_DECODED_INDEX_PAGES) {
+                const oldest = this.decodedIndexPages.keys().next().value;
+                if (oldest !== undefined) {
+                    this.decodedIndexPages.delete(oldest);
+                }
+            }
+        }
+        this.decodedIndexPages.set(pageNumber, cells);
+        return cells;
+    }
+    async indexCell(pageNumber, page, header, index) {
+        const cells = this.decodedCells(pageNumber, header);
+        let cell = cells[index];
+        if (!cell) {
+            const offset = cellOffset(page, header, index);
+            const interior = header.type === INTERIOR_INDEX;
+            const [size, afterSize] = readVarint(page, interior ? offset + 4 : offset);
+            cell = {
+                values: decodeRecord(await this.payload(page, afterSize, size, true)),
+                leftChild: interior ? readUint32(page, offset) : 0,
+            };
+            cells[index] = cell;
+        }
+        return cell;
     }
     async *indexScanFrom(root, low) {
         const { page, header } = await this.pageAt(root);
@@ -151,7 +186,7 @@ export class BTree {
         let high = header.cellCount;
         while (first < high) {
             const mid = (first + high) >> 1;
-            const cell = await this.indexCell(page, header, mid);
+            const cell = await this.indexCell(root, page, header, mid);
             if (compareKey(cell.values, low) < 0) {
                 first = mid + 1;
             }
@@ -160,7 +195,7 @@ export class BTree {
             }
         }
         for (let i = first; i < header.cellCount; i++) {
-            const cell = await this.indexCell(page, header, i);
+            const cell = await this.indexCell(root, page, header, i);
             if (header.type === INTERIOR_INDEX) {
                 yield* this.indexScanFrom(cell.leftChild, low);
             }
@@ -180,7 +215,7 @@ export class BTree {
             let child = 0;
             while (low < high) {
                 const mid = (low + high) >> 1;
-                const cell = await this.indexCell(page, header, mid);
+                const cell = await this.indexCell(pageNumber, page, header, mid);
                 if (compareKey(cell.values, key) <= 0) {
                     best = cell.values;
                     low = mid + 1;

package/dist/sqlite/btree.js.map

@@ -1 +1 @@
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package/dist/sqlite/pager.d.ts

@@ -13,7 +13,12 @@ export declare class Pager {
     readonly pageSize: number;
     private fileSize;
     constructor(source: ByteSource, pageSize: number, fileSize: number, opts?: PagerOptions);
+    private read;
     seed(index: number, bytes: Uint8Array): void;
     private block;
+    prefetch(pageNumbers: number[]): void;
+    private fetchRun;
+    private forgetOnFailure;
+    private evict;
     page(pageNumber: number): Promise<Uint8Array<ArrayBufferLike>>;
 }

package/dist/sqlite/pager.js

@@ -15,6 +15,23 @@ 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)) {
@@ -30,19 +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;

package/dist/sqlite/pager.js.map

@@ -1 +1 @@
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+{"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/subgraph.d.ts

@@ -1,7 +1,9 @@
-import type { GBZBase, PathName } from './db.ts';
+import type { GBZBase } from './db.ts';
 import type { Orientation } from './gbwt/node.ts';
 import type { Pos } from './gbwt/record.ts';
+import type { PathName } from './pathName.ts';
 export type HaplotypeOutput = 'all' | 'distinct' | 'reference-only' | 'none';
+export type SnarlOutput = 'none' | 'contained' | 'overlapping';
 export interface PathPosition {
     seqOffset: number;
     handle: number;
@@ -42,12 +44,8 @@ export interface SubgraphJson {
     }[];
     paths: SubgraphPath[];
 }
-export interface HaplotypeAlignment {
-    pathHandle: number | undefined;
-    name: PathName | undefined;
+export interface AlignmentSpan {
     strand: '+' | '-';
-    hapStart: number | undefined;
-    hapEnd: number | undefined;
     refStart: number;
     refEnd: number;
     cigar: string;
@@ -55,8 +53,23 @@ export interface HaplotypeAlignment {
     path: number[];
     start: Pos;
 }
-export interface ToJsonOptions {
-    names?: 'anonymous' | 'resolved';
+export type HaplotypeAlignment = AlignmentSpan & ({
+    resolved: true;
+    name: PathName;
+    label: string;
+    pathHandle: number;
+    hapStart: number;
+    hapEnd: number;
+} | {
+    resolved: false;
+});
+export interface SubgraphOutputOptions {
+    cigar?: boolean | undefined;
+    names?: 'anonymous' | 'resolved' | undefined;
+}
+export interface SubgraphOptions {
+    limit?: number | undefined;
+    signal?: AbortSignal | undefined;
 }
 export declare class Subgraph {
     private records;
@@ -67,7 +80,6 @@ export declare class Subgraph {
     private refInterval;
     private refIndexCache;
     private refPrefixCache;
-    limit: number | undefined;
     readonly stats: {
         orderedAlignments: number;
         lcsAlignments: number;
@@ -75,7 +87,9 @@ export declare class Subgraph {
         identificationFetches: number;
     };
     private db;
-    constructor(db: GBZBase);
+    private readonly limit;
+    private readonly signal;
+    constructor(db: GBZBase, opts?: SubgraphOptions);
     get nodeCount(): number;
     get pathCount(): number;
     get referenceInterval(): {
@@ -105,6 +119,12 @@ 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 +138,8 @@ export declare class Subgraph {
     private edits;
     alignToRef(pathIndex: number): string | undefined;
     alignments(): HaplotypeAlignment[];
-    toJSON(cigar: boolean, opts?: ToJsonOptions): SubgraphJson;
+    private canonicalEdges;
+    stableName(): Promise<string>;
+    toGFA(opts?: SubgraphOutputOptions): Promise<string>;
+    toSubgraphJson(opts?: SubgraphOutputOptions): SubgraphJson;
 }