npm - @gmod/gbz-base - Versions diffs - 2.1.0 → 2.2.0 - Mend

@gmod/gbz-base 2.1.0 → 2.2.0

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Files changed (9) hide show

package/README.md CHANGED Viewed

@@ -40,10 +40,18 @@ The path is a PanSN `sample#haplotype#contig` string, or a bare contig for a
 graph whose reference paths have no sample. `{ sample, haplotype, contig }`
 works too, and `parsePathName` is the parser if you want it separately.
-Both take `{ context, haplotypes, snarls, limit, signal }` and both resolve
-haplotype names when the database can. `signal` is an `AbortSignal`; a query
-checks it between range requests, so an abort stops the next fetch rather than
-the one in flight.
+Both take `{ context, haplotypes, limit, signal }`, and `getSubgraphForRange`
+also `snarls`; both resolve haplotype names when the database can. For
+alignments `haplotypes` is `all` or `distinct`, the two outputs that leave
+something to align against the reference.
+`context` is the graph context in bp to extend past the window, 100 by default,
+and it shapes the answer rather than padding it: a haplotype's walk ends where
+it leaves the subgraph, so at `context: 0` every bubble cuts a walk into pieces
+and the same window returns several times as many records as it does at 100.
+`limit` caps the subgraph at that many nodes, per fragment. `signal` is an
+`AbortSignal`; a query checks it between range requests, so an abort stops the
+next fetch rather than the one in flight.
 ### One returns records, the other a query object
@@ -53,11 +61,12 @@ coordinate-correct because a record's `refStart`/`refEnd` are absolute.
 `getSubgraphForRange` hands back the `Subgraph` itself, because two disjoint
 fragments do not merge into one graph. It answers for the first fragment
-overlapping the window, clamped to it, and `subgraph.referenceInterval` says
-which interval that was. It is `undefined` when the path is unknown, when no
-fragment overlaps the window, or when the clamped window is empty. Use
-`pathFragmentsForRange` to see the fragments yourself, and `hasPath` to ask
-about a path alone.
+overlapping the window, clamped to it, and is `undefined` when the path is
+unknown or no fragment overlaps the window. `subgraph.referenceInterval` is the
+reference walk the subgraph holds, which runs to node boundaries and through
+`context`, so it is wider than the clamped window on both sides. Use
+`pathFragmentsForRange` to see the fragment bounds themselves, and `hasPath` to
+ask about a path alone.
 A path that exists but was never indexed for random access throws rather than
 returning nothing — that is a database that needs rebuilding, not an empty

package/dist/db.d.ts CHANGED Viewed

@@ -6,13 +6,16 @@ import type { GraphName } from './graphName.ts';
 import type { PathName, PathRef } from './pathName.ts';
 import type { QueryOptions } from './query.ts';
 import type { PagerOptions } from './sqlite/pager.ts';
-import type { HaplotypeAlignment, Subgraph } from './subgraph.ts';
+import type { HaplotypeAlignment } from './subgraph.ts';
 export declare const SCHEMA_VERSION = "GBZ-base version 4";
 export interface PathFragment {
     path: GbzPath;
     start: number;
     end: number;
 }
+export interface AlignmentOptions extends Pick<QueryOptions, 'context' | 'limit' | 'signal'> {
+    haplotypes?: 'all' | 'distinct' | undefined;
+}
 export declare class SchemaVersionError extends Error {
     name: string;
     readonly found: string | undefined;
@@ -72,8 +75,8 @@ export declare class GBZBase {
     private walkPathLength;
     pathFragmentsForRange(ref: PathRef, start: number, end: number): Promise<PathFragment[]>;
     private subgraphForFragment;
-    getSubgraphForRange(ref: PathRef, start: number, end: number, opts?: QueryOptions): Promise<Subgraph | undefined>;
-    getAlignmentsForRange(ref: PathRef, start: number, end: number, opts?: QueryOptions): Promise<HaplotypeAlignment[]>;
+    getSubgraphForRange(ref: PathRef, start: number, end: number, opts?: QueryOptions): Promise<import("./subgraph.ts").Subgraph | undefined>;
+    getAlignmentsForRange(ref: PathRef, start: number, end: number, opts?: AlignmentOptions): Promise<HaplotypeAlignment[]>;
     graphName(): Promise<GraphName>;
     hasChainLinks(): Promise<boolean>;
     get hasHaplotypeIndex(): boolean;

package/dist/db.js CHANGED Viewed

@@ -241,17 +241,12 @@ export class GBZBase {
         return fragments.filter(f => start < f.end);
     }
     async subgraphForFragment(fragment, start, end, opts) {
-        const lo = Math.max(start, fragment.start);
-        const hi = Math.min(end, fragment.end);
-        let subgraph;
-        if (hi > lo) {
-            const { sample, contig, haplotype } = fragment.path.name;
-            subgraph = await subgraphInInterval(this, { sample, contig, haplotype }, lo, hi, opts);
-            const haplotypes = opts.haplotypes ?? 'all';
-            const named = haplotypes === 'all' || haplotypes === 'distinct';
-            if (this.hasHaplotypeIndex && named) {
-                await subgraph.identifyPaths();
-            }
+        const { sample, contig, haplotype } = fragment.path.name;
+        const subgraph = await subgraphInInterval(this, { sample, contig, haplotype }, Math.max(start, fragment.start), Math.min(end, fragment.end), opts);
+        const haplotypes = opts.haplotypes ?? 'all';
+        const named = haplotypes === 'all' || haplotypes === 'distinct';
+        if (this.hasHaplotypeIndex && named) {
+            await subgraph.identifyPaths();
         }
         return subgraph;
     }
@@ -265,9 +260,7 @@ export class GBZBase {
         const result = [];
         for (const fragment of await this.pathFragmentsForRange(ref, start, end)) {
             const subgraph = await this.subgraphForFragment(fragment, start, end, opts);
-            if (subgraph) {
-                result.push(...subgraph.alignments());
-            }
+            result.push(...subgraph.alignments());
         }
         return result;
     }

package/dist/db.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/index.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 export { GBZBase, GbzRecord, SCHEMA_VERSION, SchemaVersionError } from './db.ts';
-export type { GbzPath, HaplotypeSample, OpenOptions, PathFragment, } from './db.ts';
+export type { AlignmentOptions, GbzPath, HaplotypeSample, OpenOptions, PathFragment, } from './db.ts';
 export { GENERIC_SAMPLE, formatPathName, parsePathName } from './pathName.ts';
 export type { PathName, PathQuery, PathRef } from './pathName.ts';
 export type { ByteSource } from './filehandle.ts';

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,SAAS,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,SAAS,CAAA;~~AAOhF~~,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAI7E,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAcxC,OAAO,EACL,mBAAmB,EACnB,gBAAgB,EAChB,eAAe,EACf,kBAAkB,GACnB,MAAM,YAAY,CAAA;AAEnB,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAA;AAErD,OAAO,EAAE,WAAW,EAAE,MAAM,UAAU,CAAA;AACtC,OAAO,KAAK,KAAK,MAAM,gBAAgB,CAAA"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,SAAS,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,SAAS,CAAA;AAQhF,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAI7E,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAcxC,OAAO,EACL,mBAAmB,EACnB,gBAAgB,EAChB,eAAe,EACf,kBAAkB,GACnB,MAAM,YAAY,CAAA;AAEnB,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAA;AAErD,OAAO,EAAE,WAAW,EAAE,MAAM,UAAU,CAAA;AACtC,OAAO,KAAK,KAAK,MAAM,gBAAgB,CAAA"}

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/gbz-base",
-  "version": "2.1.0",
+  "version": "2.2.0",
   "description": "Pure TypeScript reader for gbz-base pangenome databases (.gbz.db) with random access over HTTP range requests",
   "license": "MIT",
   "packageManager": "pnpm@11.15.1",

package/src/db.ts CHANGED Viewed

@@ -13,7 +13,7 @@ import type { PathName, PathRef } from './pathName.ts'
 import type { QueryOptions } from './query.ts'
 import type { PagerOptions } from './sqlite/pager.ts'
 import type { SqlValue } from './sqlite/record.ts'
-import type { HaplotypeAlignment, Subgraph } from './subgraph.ts'
+import type { HaplotypeAlignment } from './subgraph.ts'
 export const SCHEMA_VERSION = 'GBZ-base version 4'
@@ -23,6 +23,13 @@ export interface PathFragment {
   end: number
 }
+export interface AlignmentOptions extends Pick<
+  QueryOptions,
+  'context' | 'limit' | 'signal'
+> {
+  haplotypes?: 'all' | 'distinct' | undefined
+}
 export class SchemaVersionError extends Error {
   override name = 'SchemaVersionError'
@@ -349,23 +356,18 @@ export class GBZBase {
     end: number,
     opts: QueryOptions,
   ) {
-    const lo = Math.max(start, fragment.start)
-    const hi = Math.min(end, fragment.end)
-    let subgraph: Subgraph | undefined
-    if (hi > lo) {
-      const { sample, contig, haplotype } = fragment.path.name
-      subgraph = await subgraphInInterval(
-        this,
-        { sample, contig, haplotype },
-        lo,
-        hi,
-        opts,
-      )
-      const haplotypes = opts.haplotypes ?? 'all'
-      const named = haplotypes === 'all' || haplotypes === 'distinct'
-      if (this.hasHaplotypeIndex && named) {
-        await subgraph.identifyPaths()
-      }
+    const { sample, contig, haplotype } = fragment.path.name
+    const subgraph = await subgraphInInterval(
+      this,
+      { sample, contig, haplotype },
+      Math.max(start, fragment.start),
+      Math.min(end, fragment.end),
+      opts,
+    )
+    const haplotypes = opts.haplotypes ?? 'all'
+    const named = haplotypes === 'all' || haplotypes === 'distinct'
+    if (this.hasHaplotypeIndex && named) {
+      await subgraph.identifyPaths()
     }
     return subgraph
   }
@@ -386,7 +388,7 @@ export class GBZBase {
     ref: PathRef,
     start: number,
     end: number,
-    opts: QueryOptions = {},
+    opts: AlignmentOptions = {},
   ) {
     const result: HaplotypeAlignment[] = []
     for (const fragment of await this.pathFragmentsForRange(ref, start, end)) {
@@ -396,9 +398,7 @@ export class GBZBase {
         end,
         opts,
       )
-      if (subgraph) {
-        result.push(...subgraph.alignments())
-      }
+      result.push(...subgraph.alignments())
     }
     return result
   }

package/src/index.ts CHANGED Viewed

@@ -1,5 +1,6 @@
 export { GBZBase, GbzRecord, SCHEMA_VERSION, SchemaVersionError } from './db.ts'
 export type {
+  AlignmentOptions,
   GbzPath,
   HaplotypeSample,
   OpenOptions,