@gmod/gbz-base 2.2.0 → 2.4.0

package/dist/sqlite/database.d.ts

@@ -19,6 +19,7 @@ export declare class SqliteDatabase {
     rootPage(name: string): number;
     indexOn(tableName: string): number;
     byRowid(table: string, rowid: number): Promise<SqlValue[] | undefined>;
+    prefetchRows(table: string, lo: number, hi: number): Promise<void>;
     scan(table: string): AsyncGenerator<{
         rowid: number;
         values: SqlValue[];

package/dist/sqlite/database.js

@@ -65,6 +65,9 @@ export class SqliteDatabase {
     byRowid(table, rowid) {
         return this.btree.tableRowid(this.rootPage(table), rowid);
     }
+    prefetchRows(table, lo, hi) {
+        return this.btree.prefetchRowidRange(this.rootPage(table), lo, hi);
+    }
     scan(table) {
         return this.btree.tableScan(this.rootPage(table));
     }

package/dist/sqlite/database.js.map

@@ -1 +1 @@
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package/dist/subgraph.d.ts

@@ -71,21 +71,56 @@ export interface SubgraphOptions {
     limit?: number | undefined;
     signal?: AbortSignal | undefined;
 }
+export declare class SubgraphLimitError extends Error {
+    name: string;
+    readonly limit: number;
+    readonly windowBp: number | undefined;
+    readonly walkedBp: number | undefined;
+    constructor(limit: number, walk?: {
+        windowBp: number;
+        walkedBp: number;
+    });
+}
+export type ChainEnd = 'in-fragment sample' | 'identified sibling' | 'out-of-window sample' | 'bound' | 'endmarker' | 'cycle';
+export interface ChainRecord {
+    fragments: number;
+    steps: number;
+    seeks: number;
+    reentries: number;
+    twinLandings: number;
+    end: ChainEnd;
+    pathHandle: number | undefined;
+}
+export interface IdentificationStats {
+    interval: number;
+    scans: [number, number][];
+    windowSamples: number;
+    fragmentLengths: number[];
+    companionSeeks: number;
+    companionMisses: number;
+    graphLookups: number;
+    graphFetches: number;
+    chains: ChainRecord[];
+}
+interface SubgraphStats {
+    orderedAlignments: number;
+    lcsAlignments: number;
+    identificationSteps: number;
+    identificationFetches: number;
+    identification: IdentificationStats;
+}
 export declare class Subgraph {
     private records;
     private paths;
+    private twinStarts;
     private refId;
     private refPath;
     private refHandle;
     private refInterval;
     private refIndexCache;
     private refPrefixCache;
-    readonly stats: {
-        orderedAlignments: number;
-        lcsAlignments: number;
-        identificationSteps: number;
-        identificationFetches: number;
-    };
+    private walkedBp;
+    readonly stats: SubgraphStats;
     private db;
     private readonly limit;
     private readonly signal;
@@ -110,10 +145,13 @@ export declare class Subgraph {
         inserted: number;
         removed: number;
     }>;
+    prefetchReferenceWalk(reference: ReferencePath, len: number): Promise<void>;
     aroundInterval(start: PathPosition, len: number, context: number): Promise<{
         inserted: number;
         removed: number;
     }>;
+    get referenceWalkedBp(): number | undefined;
+    private walkInterval;
     aroundNodes(nodes: Iterable<number>, context: number): Promise<{
         inserted: number;
         removed: number;
@@ -127,6 +165,7 @@ export declare class Subgraph {
     private findCoveringSnarl;
     extractPaths(reference: ReferencePath | undefined, output: HaplotypeOutput): void;
     private distinctPaths;
+    keepHaplotypes(wanted: (name: PathName) => boolean): void;
     identifyPaths(): Promise<void>;
     private refIndex;
     private refPrefix;
@@ -145,3 +184,4 @@ export declare class Subgraph {
     toGFA(opts?: SubgraphOutputOptions): Promise<string>;
     toSubgraphJson(opts?: SubgraphOutputOptions): SubgraphJson;
 }
+export {};