@gmod/gbz-base 0.0.1 → 1.0.0

package/README.md

@@ -62,9 +62,9 @@ cd tools/haplotype-index && cargo build --release
 ./target/release/gbz-haplotype-index --interval 4096 --from-db graph.gbz.db
 ```
 
-The second form walks the paths through the database's own node records, so
-a database whose GBZ is no longer at hand can still be augmented; the two
-forms write identical tables.
+The second form walks the paths through the database's own node records, so a
+database whose GBZ is no longer at hand can still be augmented; the two forms
+write identical tables.
 
 `HaplotypeSamples` holds one GBWT position every `--interval` bp along every
 path in both orientations, with the path handle and the forward coordinate of

package/bin/query.js

@@ -2,6 +2,8 @@
 import { main } from '../dist/cli.js'
 
 main(process.argv.slice(2)).catch(error => {
-  process.stderr.write(`${error instanceof Error ? error.message : String(error)}\n`)
+  process.stderr.write(
+    `${error instanceof Error ? error.message : String(error)}\n`,
+  )
   process.exit(1)
 })

package/dist/cli.js

@@ -1,6 +1,6 @@
 import { LocalFile, RemoteFile } from 'generic-filehandle2';
 import { GBZBase, formatPathName } from "./db.js";
-import { subgraphAroundNodes, subgraphAtOffset, subgraphInInterval } from "./query.js";
+import { subgraphAroundNodes, subgraphAtOffset, subgraphInInterval, } from "./query.js";
 const USAGE = `Usage: gbz-base-query [options] graph.gbz.db
 
   --sample STR         sample name (default: generic path)
@@ -111,10 +111,20 @@ function parseArgs(argv) {
 }
 export async function main(argv) {
     const args = parseArgs(argv);
-    const source = /^https?:\/\//.test(args.file) ? new RemoteFile(args.file) : new LocalFile(args.file);
+    const source = /^https?:\/\//.test(args.file)
+        ? new RemoteFile(args.file)
+        : new LocalFile(args.file);
     const db = await GBZBase.open(source, { blockSize: args.blockSize });
-    const opts = { context: args.context, haplotypes: args.haplotypes, ...(args.limit === undefined ? {} : { limit: args.limit }) };
-    const query = { contig: args.contig ?? '', haplotype: args.haplotype, ...(args.sample === undefined ? {} : { sample: args.sample }) };
+    const opts = {
+        context: args.context,
+        haplotypes: args.haplotypes,
+        ...(args.limit === undefined ? {} : { limit: args.limit }),
+    };
+    const query = {
+        contig: args.contig ?? '',
+        haplotype: args.haplotype,
+        ...(args.sample === undefined ? {} : { sample: args.sample }),
+    };
     const subgraph = args.nodes.length > 0
         ? await subgraphAroundNodes(db, args.nodes, opts)
         : args.interval
@@ -129,12 +139,21 @@ export async function main(argv) {
         await subgraph.identifyPaths();
     }
     const output = args.alignments
-        ? subgraph.alignments().map(a => ({ ...a, name: a.name ? formatPathName(a.name, a.name.fragment) : undefined, start: undefined }))
-        : subgraph.toJSON(args.cigar, { names: args.resolve ? 'resolved' : 'anonymous' });
+        ? subgraph.alignments().map(a => ({
+            ...a,
+            name: a.name && a.hapStart !== undefined && a.hapEnd !== undefined
+                ? formatPathName({ ...a.name, fragment: a.hapStart }, a.hapEnd)
+                : undefined,
+            start: undefined,
+        }))
+        : subgraph.toJSON(args.cigar, {
+            names: args.resolve ? 'resolved' : 'anonymous',
+        });
     process.stdout.write(`${JSON.stringify(output)}\n`);
     if (args.stats) {
         const { fetches, bytesFetched } = db.sqlite.pager;
-        const { orderedAlignments, lcsAlignments, identificationSteps, identificationFetches } = subgraph.stats;
+        const { orderedAlignments, lcsAlignments, identificationSteps, identificationFetches, } = subgraph.stats;
         process.stderr.write(`Subgraph contains ${subgraph.nodeCount} nodes and ${subgraph.pathCount} paths; ${fetches} fetches, ${bytesFetched} bytes; ${orderedAlignments} ordered + ${lcsAlignments} lcs alignments; identification ${identificationSteps} steps, ${identificationFetches} lookups\n`);
     }
 }
+//# sourceMappingURL=cli.js.map

package/dist/cli.js.map

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package/dist/db.d.ts

@@ -1,7 +1,7 @@
-import type { ByteSource } from './filehandle.ts';
 import { GbwtRecord } from './gbwt/record.ts';
-import type { Pos } from './gbwt/record.ts';
 import { SqliteDatabase } from './sqlite/database.ts';
+import type { ByteSource } from './filehandle.ts';
+import type { Pos } from './gbwt/record.ts';
 import type { PagerOptions } from './sqlite/pager.ts';
 export interface PathName {
     sample: string;
@@ -12,8 +12,8 @@ export interface PathName {
 export declare const GENERIC_SAMPLE = "_gbwt_ref";
 export declare const SCHEMA_VERSION = "GBZ-base version 4";
 export declare class SchemaVersionError extends Error {
-    readonly found: string | undefined;
     name: string;
+    readonly found: string | undefined;
     constructor(found: string | undefined);
 }
 export declare function formatPathName(name: PathName, end: number): string;
@@ -32,12 +32,12 @@ export interface GbzPath {
     isIndexed: boolean;
 }
 export declare class GbzRecord {
+    readonly sequenceLen: number;
     readonly handle: number;
     readonly edges: Pos[];
     readonly bwt: Uint8Array;
     readonly encodedSequence: Uint8Array;
     readonly next: number | undefined;
-    readonly sequenceLen: number;
     private decoded;
     constructor(handle: number, edges: Pos[], bwt: Uint8Array, encodedSequence: Uint8Array, next: number | undefined);
     get id(): number;
@@ -47,9 +47,9 @@ export declare class GbzRecord {
     gbwt(): GbwtRecord;
 }
 export declare class GBZBase {
-    readonly sqlite: SqliteDatabase;
     private tagCache;
     private pathCache;
+    readonly sqlite: SqliteDatabase;
     private constructor();
     static open(source: ByteSource, opts?: PagerOptions): Promise<GBZBase>;
     tags(): Promise<Map<string, string>>;

package/dist/db.js

@@ -1,12 +1,12 @@
-import { GbwtRecord, decompressEdges } from "./gbwt/record.js";
 import { ENDMARKER, nodeId, nodeOrientation } from "./gbwt/node.js";
+import { GbwtRecord, decompressEdges } from "./gbwt/record.js";
 import { decodeSequence, encodedSequenceLength } from "./gbwt/sequence.js";
 import { SqliteDatabase } from "./sqlite/database.js";
 export const GENERIC_SAMPLE = '_gbwt_ref';
 export const SCHEMA_VERSION = 'GBZ-base version 4';
 export class SchemaVersionError extends Error {
-    found;
     name = 'SchemaVersionError';
+    found;
     constructor(found) {
         super(found === undefined
             ? `not a gbz-base database: its Tags table has no version`
@@ -18,12 +18,12 @@ export function formatPathName(name, end) {
     return `${name.sample}#${name.haplotype}#${name.contig}[${name.fragment}-${end}]`;
 }
 export class GbzRecord {
+    sequenceLen;
     handle;
     edges;
     bwt;
     encodedSequence;
     next;
-    sequenceLen;
     decoded;
     constructor(handle, edges, bwt, encodedSequence, next) {
         this.handle = handle;
@@ -74,8 +74,14 @@ function blob(value, what) {
 function rowToPath(rowid, values) {
     return {
         handle: rowid,
-        fwStart: { node: num(values[1], 'Paths.fw_node'), offset: num(values[2], 'Paths.fw_offset') },
-        revStart: { node: num(values[3], 'Paths.rev_node'), offset: num(values[4], 'Paths.rev_offset') },
+        fwStart: {
+            node: num(values[1], 'Paths.fw_node'),
+            offset: num(values[2], 'Paths.fw_offset'),
+        },
+        revStart: {
+            node: num(values[3], 'Paths.rev_node'),
+            offset: num(values[4], 'Paths.rev_offset'),
+        },
         name: {
             sample: str(values[5], 'Paths.sample'),
             contig: str(values[6], 'Paths.contig'),
@@ -86,9 +92,9 @@ function rowToPath(rowid, values) {
     };
 }
 export class GBZBase {
-    sqlite;
     tagCache;
     pathCache;
+    sqlite;
     constructor(sqlite) {
         this.sqlite = sqlite;
     }
@@ -150,7 +156,7 @@ export class GBZBase {
         return (await this.paths()).filter(p => p.name.sample === sample);
     }
     get hasHaplotypeIndex() {
-        return this.sqlite.has('HaplotypeSamples') && this.sqlite.has('HaplotypeLengths');
+        return (this.sqlite.has('HaplotypeSamples') && this.sqlite.has('HaplotypeLengths'));
     }
     async haplotypeSampleInterval() {
         const value = await this.tag('haplotype_index_interval');
@@ -161,13 +167,18 @@ export class GBZBase {
             node: num(values[0], 'HaplotypeSamples.node_handle'),
             offset: num(values[1], 'HaplotypeSamples.node_offset'),
             pathHandle: num(values[2], 'HaplotypeSamples.path_handle'),
-            orientation: num(values[3], 'HaplotypeSamples.orientation') === 0 ? 'forward' : 'reverse',
+            orientation: num(values[3], 'HaplotypeSamples.orientation') === 0
+                ? 'forward'
+                : 'reverse',
             pathOffset: num(values[4], 'HaplotypeSamples.path_offset'),
         };
     }
     async haplotypeSamplesInRange(minHandle, maxHandle) {
         const samples = [];
-        for await (const key of this.sqlite.indexScanFrom('HaplotypeSamples', [minHandle, 0])) {
+        for await (const key of this.sqlite.indexScanFrom('HaplotypeSamples', [
+            minHandle,
+            0,
+        ])) {
             const node = num(key[0], 'HaplotypeSamples.node_handle');
             if (node > maxHandle) {
                 break;
@@ -180,8 +191,11 @@ export class GBZBase {
         return samples;
     }
     async haplotypeSampleAt(node, offset) {
-        const key = await this.sqlite.indexSeekLE('HaplotypeSamples', [node, offset]);
-        if (!key || key[0] !== node || key[1] !== offset) {
+        const key = await this.sqlite.indexSeekLE('HaplotypeSamples', [
+            node,
+            offset,
+        ]);
+        if (key?.[0] !== node || key[1] !== offset) {
             return undefined;
         }
         const row = await this.sqlite.byRowid('HaplotypeSamples', num(key[2], 'HaplotypeSamples rowid'));
@@ -192,8 +206,11 @@ export class GBZBase {
         return row ? num(row[1], 'HaplotypeLengths.length') : undefined;
     }
     async indexedPosition(pathHandle, pathOffset) {
-        const key = await this.sqlite.indexSeekLE('ReferenceIndex', [pathHandle, pathOffset]);
-        if (!key || key[0] !== pathHandle) {
+        const key = await this.sqlite.indexSeekLE('ReferenceIndex', [
+            pathHandle,
+            pathOffset,
+        ]);
+        if (key?.[0] !== pathHandle) {
             return undefined;
         }
         const row = await this.sqlite.byRowid('ReferenceIndex', num(key[2], 'ReferenceIndex rowid'));
@@ -202,7 +219,11 @@ export class GBZBase {
         }
         return {
             pathOffset: num(row[1], 'ReferenceIndex.path_offset'),
-            pos: { node: num(row[2], 'ReferenceIndex.node_handle'), offset: num(row[3], 'ReferenceIndex.node_offset') },
+            pos: {
+                node: num(row[2], 'ReferenceIndex.node_handle'),
+                offset: num(row[3], 'ReferenceIndex.node_offset'),
+            },
         };
     }
 }
+//# sourceMappingURL=db.js.map

package/dist/db.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"db.js","sourceRoot":"","sources":["../src/db.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,EAAE,eAAe,EAAE,MAAM,gBAAgB,CAAA;AACnE,OAAO,EAAE,UAAU,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAC9D,OAAO,EAAE,cAAc,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAA;AAC1E,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAA;AAcrD,MAAM,CAAC,MAAM,cAAc,GAAG,WAAW,CAAA;AACzC,MAAM,CAAC,MAAM,cAAc,GAAG,oBAAoB,CAAA;AAElD,MAAM,OAAO,kBAAmB,SAAQ,KAAK;IAClC,IAAI,GAAG,oBAAoB,CAAA;IAE3B,KAAK,CAAoB;IAElC,YAAY,KAAyB;QACnC,KAAK,CACH,KAAK,KAAK,SAAS;YACjB,CAAC,CAAC,wDAAwD;YAC1D,CAAC,CAAC,gCAAgC,KAAK,+BAA+B,cAAc,GAAG,CAC1F,CAAA;QACD,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;IACpB,CAAC;CACF;AAED,MAAM,UAAU,cAAc,CAAC,IAAc,EAAE,GAAW;IACxD,OAAO,GAAG,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,SAAS,IAAI,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,QAAQ,IAAI,GAAG,GAAG,CAAA;AACnF,CAAC;AAkBD,MAAM,OAAO,SAAS;IACX,WAAW,CAAQ;IACnB,MAAM,CAAQ;IACd,KAAK,CAAO;IACZ,GAAG,CAAY;IACf,eAAe,CAAY;IAC3B,IAAI,CAAoB;IACzB,OAAO,CAAoB;IAEnC,YACE,MAAc,EACd,KAAY,EACZ,GAAe,EACf,eAA2B,EAC3B,IAAwB;QAExB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;QACpB,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;QAClB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,eAAe,GAAG,eAAe,CAAA;QACtC,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,WAAW,GAAG,qBAAqB,CAAC,eAAe,CAAC,CAAA;IAC3D,CAAC;IAED,IAAI,EAAE;QACJ,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IAC5B,CAAC;IAED,IAAI,WAAW;QACb,OAAO,eAAe,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IACrC,CAAC;IAED,IAAI,QAAQ;QACV,IAAI,CAAC,OAAO,KAAK,cAAc,CAAC,IAAI,CAAC,eAAe,CAAC,CAAA;QACrD,OAAO,IAAI,CAAC,OAAO,CAAA;IACrB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IACtE,CAAC;IAED,IAAI;QACF,IAAI,IAAI,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC5B,MAAM,IAAI,KAAK,CAAC,0BAA0B,IAAI,CAAC,MAAM,WAAW,CAAC,CAAA;QACnE,CAAC;QACD,OAAO,IAAI,UAAU,CAAC,IAAI,CAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAA;IAC7C,CAAC;CACF;AAED,SAAS,GAAG,CAAC,KAA2B,EAAE,IAAY;IACpD,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QAC9B,MAAM,IAAI,KAAK,CAAC,GAAG,IAAI,kCAAkC,CAAC,CAAA;IAC5D,CAAC;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAED,SAAS,GAAG,CAAC,KAA2B,EAAE,IAAY;IACpD,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QAC9B,MAAM,IAAI,KAAK,CAAC,GAAG,IAAI,8BAA8B,CAAC,CAAA;IACxD,CAAC;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAED,SAAS,IAAI,CAAC,KAA2B,EAAE,IAAY;IACrD,IAAI,CAAC,CAAC,KAAK,YAAY,UAAU,CAAC,EAAE,CAAC;QACnC,MAAM,IAAI,KAAK,CAAC,GAAG,IAAI,gCAAgC,CAAC,CAAA;IAC1D,CAAC;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAED,SAAS,SAAS,CAAC,KAAa,EAAE,MAAkB;IAClD,OAAO;QACL,MAAM,EAAE,KAAK;QACb,OAAO,EAAE;YACP,IAAI,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,eAAe,CAAC;YACrC,MAAM,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,iBAAiB,CAAC;SAC1C;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,gBAAgB,CAAC;YACtC,MAAM,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,kBAAkB,CAAC;SAC3C;QACD,IAAI,EAAE;YACJ,MAAM,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,cAAc,CAAC;YACtC,MAAM,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,cAAc,CAAC;YACtC,SAAS,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,iBAAiB,CAAC;YAC5C,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,gBAAgB,CAAC;SAC3C;QACD,SAAS,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,kBAAkB,CAAC,KAAK,CAAC;KACpD,CAAA;AACH,CAAC;AAED,MAAM,OAAO,OAAO;IACV,QAAQ,CAA0C;IAClD,SAAS,CAAgC;IAExC,MAAM,CAAgB;IAE/B,YAAoB,MAAsB;QACxC,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;IACtB,CAAC;IAED,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,MAAkB,EAAE,OAAqB,EAAE;QAC3D,MAAM,MAAM,GAAG,MAAM,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACtD,KAAK,MAAM,KAAK,IAAI,CAAC,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,gBAAgB,CAAC,EAAE,CAAC;YACjE,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAA;QACxB,CAAC;QACD,MAAM,EAAE,GAAG,IAAI,OAAO,CAAC,MAAM,CAAC,CAAA;QAC9B,MAAM,OAAO,GAAG,MAAM,EAAE,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;QACvC,IAAI,OAAO,KAAK,cAAc,EAAE,CAAC;YAC/B,MAAM,IAAI,kBAAkB,CAAC,OAAO,CAAC,CAAA;QACvC,CAAC;QACD,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI;QACF,IAAI,CAAC,QAAQ,KAAK,CAAC,KAAK,IAAI,EAAE;YAC5B,MAAM,IAAI,GAAG,IAAI,GAAG,EAAkB,CAAA;YACtC,IAAI,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC;gBACxD,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,UAAU,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,YAAY,CAAC,CAAC,CAAA;YACpE,CAAC;YACD,OAAO,IAAI,CAAA;QACb,CAAC,CAAC,EAAE,CAAA;QACJ,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED,KAAK,CAAC,GAAG,CAAC,GAAW;QACnB,OAAO,CAAC,MAAM,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;IACrC,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,MAAc;QAC5B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,OAAO,CAAC,OAAO,EAAE,MAAM,CAAC,CAAA;QACtD,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,IAAI,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;QACnB,OAAO,IAAI,SAAS,CAClB,MAAM,EACN,eAAe,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,aAAa,CAAC,CAAC,EAC5C,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,WAAW,CAAC,EACzB,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,gBAAgB,CAAC,EAC9B,OAAO,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,SAAS,CAC5C,CAAA;IACH,CAAC;IAED,KAAK;QACH,IAAI,CAAC,SAAS,KAAK,CAAC,KAAK,IAAI,EAAE;YAC7B,MAAM,KAAK,GAAc,EAAE,CAAA;YAC3B,IAAI,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,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package/dist/filehandle.js

@@ -1 +1,2 @@
 export {};
+//# sourceMappingURL=filehandle.js.map

package/dist/filehandle.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"filehandle.js","sourceRoot":"","sources":["../src/filehandle.ts"],"names":[],"mappings":""}

package/dist/gbwt/bytecode.d.ts

@@ -1,6 +1,6 @@
 export declare class ByteCodeReader {
-    private bytes;
     offset: number;
+    private bytes;
     constructor(bytes: Uint8Array);
     get done(): boolean;
     byte(): number | undefined;

package/dist/gbwt/bytecode.js

@@ -1,6 +1,6 @@
 export class ByteCodeReader {
-    bytes;
     offset = 0;
+    bytes;
     constructor(bytes) {
         this.bytes = bytes;
     }
@@ -39,13 +39,16 @@ export class RunReader {
     constructor(bytes, sigma) {
         this.source = new ByteCodeReader(bytes);
         this.sigma = sigma === 0 ? Number.MAX_SAFE_INTEGER : sigma;
-        this.threshold = this.sigma < RLE_THRESHOLD ? Math.floor(RLE_UNIVERSE / this.sigma) : 0;
+        this.threshold =
+            this.sigma < RLE_THRESHOLD ? Math.floor(RLE_UNIVERSE / this.sigma) : 0;
     }
     next() {
         if (this.sigma >= RLE_THRESHOLD) {
             const value = this.source.int();
             const len = this.source.int();
-            return value === undefined || len === undefined ? undefined : { value, len: len + 1 };
+            return value === undefined || len === undefined
+                ? undefined
+                : { value, len: len + 1 };
         }
         const byte = this.source.byte();
         if (byte === undefined) {
@@ -68,3 +71,4 @@ export class RunReader {
         }
     }
 }
+//# sourceMappingURL=bytecode.js.map

package/dist/gbwt/bytecode.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"bytecode.js","sourceRoot":"","sources":["../../src/gbwt/bytecode.ts"],"names":[],"mappings":"AAAA,MAAM,OAAO,cAAc;IACzB,MAAM,GAAG,CAAC,CAAA;IACF,KAAK,CAAY;IAEzB,YAAY,KAAiB;QAC3B,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;IACpB,CAAC;IAED,IAAI,IAAI;QACN,OAAO,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,KAAK,CAAC,MAAM,CAAA;IACzC,CAAC;IAED,IAAI;QACF,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACrC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,IAAI,CAAC,MAAM,IAAI,CAAC,CAAA;QAChB,OAAO,KAAK,CAAA;IACd,CAAC;IAED,GAAG;QACD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,IAAI,MAAM,GAAG,CAAC,CAAA;QACd,OAAO,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;YACvC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAE,CAAA;YACtC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAA;YAChB,MAAM,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,KAAK,CAAA;YAChC,KAAK,IAAI,GAAG,CAAA;YACZ,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;gBACzB,OAAO,MAAM,CAAA;YACf,CAAC;QACH,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;CACF;AAOD,MAAM,aAAa,GAAG,GAAG,CAAA;AACzB,MAAM,YAAY,GAAG,GAAG,CAAA;AAExB,MAAM,OAAO,SAAS;IACZ,MAAM,CAAgB;IACtB,KAAK,CAAQ;IACb,SAAS,CAAQ;IAEzB,YAAY,KAAiB,EAAE,KAAa;QAC1C,IAAI,CAAC,MAAM,GAAG,IAAI,cAAc,CAAC,KAAK,CAAC,CAAA;QACvC,IAAI,CAAC,KAAK,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,gBAAgB,CAAC,CAAC,CAAC,KAAK,CAAA;QAC1D,IAAI,CAAC,SAAS;YACZ,IAAI,CAAC,KAAK,GAAG,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,YAAY,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC1E,CAAC;IAED,IAAI;QACF,IAAI,IAAI,CAAC,KAAK,IAAI,aAAa,EAAE,CAAC;YAChC,MAAM,KAAK,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,EAAE,CAAA;YAC/B,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,EAAE,CAAA;YAC7B,OAAO,KAAK,KAAK,SAAS,IAAI,GAAG,KAAK,SAAS;gBAC7C,CAAC,CAAC,SAAS;gBACX,CAAC,CAAC,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,GAAG,CAAC,EAAE,CAAA;QAC7B,CAAC;QACD,MAAM,IAAI,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,CAAA;QAC/B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;YACvB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,KAAK,GAAG,IAAI,GAAG,IAAI,CAAC,KAAK,CAAA;QAC/B,IAAI,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC3C,IAAI,GAAG,KAAK,IAAI,CAAC,SAAS,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,EAAE,CAAA;YAC/B,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,GAAG,IAAI,KAAK,CAAA;QACd,CAAC;QACD,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,CAAA;IACvB,CAAC;IAED,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC;QAChB,KAAK,IAAI,GAAG,GAAG,IAAI,CAAC,IAAI,EAAE,EAAE,GAAG,KAAK,SAAS,EAAE,GAAG,GAAG,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC;YACjE,MAAM,GAAG,CAAA;QACX,CAAC;IACH,CAAC;CACF"}

package/dist/gbwt/node.js

@@ -32,7 +32,9 @@ export function exitOrientation(side) {
 export function edgeIsCanonical(from, to) {
     const fromId = nodeId(from);
     const toId = nodeId(to);
-    return isReverse(from) ? toId > fromId || (toId === fromId && !isReverse(to)) : toId >= fromId;
+    return isReverse(from)
+        ? toId > fromId || (toId === fromId && !isReverse(to))
+        : toId >= fromId;
 }
 export function pathIsCanonical(path) {
     const first = path[0];
@@ -40,5 +42,8 @@ export function pathIsCanonical(path) {
     if (first === undefined || last === undefined) {
         return true;
     }
-    return isReverse(first) === isReverse(last) ? !isReverse(first) : edgeIsCanonical(first, last);
+    return isReverse(first) === isReverse(last)
+        ? !isReverse(first)
+        : edgeIsCanonical(first, last);
 }
+//# sourceMappingURL=node.js.map

package/dist/gbwt/node.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"node.js","sourceRoot":"","sources":["../../src/gbwt/node.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,SAAS,GAAG,CAAC,CAAA;AAI1B,MAAM,UAAU,UAAU,CAAC,EAAU,EAAE,WAAwB;IAC7D,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,WAAW,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrD,CAAC;AAED,MAAM,UAAU,MAAM,CAAC,MAAc;IACnC,OAAO,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;AAC/B,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,MAAc;IAC5C,OAAO,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;AACjD,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,MAAc;IACtC,OAAO,MAAM,GAAG,CAAC,KAAK,CAAC,CAAA;AACzB,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,MAAc;IACrC,OAAO,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;AACnD,CAAC;AAID,MAAM,UAAU,QAAQ,CAAC,IAAc;IACrC,OAAO,IAAI,KAAK,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;AAC3C,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,WAAwB;IAChD,OAAO,WAAW,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAA;AACrD,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,WAAwB;IAC/C,OAAO,WAAW,KAAK,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;AACrD,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,IAAc;IAC7C,OAAO,IAAI,KAAK,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;AAChD,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,IAAc;IAC5C,OAAO,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;AACjD,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,IAAY,EAAE,EAAU;IACtD,MAAM,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA;IAC3B,MAAM,IAAI,GAAG,MAAM,CAAC,EAAE,CAAC,CAAA;IACvB,OAAO,SAAS,CAAC,IAAI,CAAC;QACpB,CAAC,CAAC,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,KAAK,MAAM,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,CAAC;QACtD,CAAC,CAAC,IAAI,IAAI,MAAM,CAAA;AACpB,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,IAAc;IAC5C,MAAM,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;IACrB,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;IAClC,IAAI,KAAK,KAAK,SAAS,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QAC9C,OAAO,IAAI,CAAA;IACb,CAAC;IACD,OAAO,SAAS,CAAC,KAAK,CAAC,KAAK,SAAS,CAAC,IAAI,CAAC;QACzC,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC;QACnB,CAAC,CAAC,eAAe,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;AAClC,CAAC"}

package/dist/gbwt/record.js

@@ -43,7 +43,9 @@ export class GbwtRecord {
             const edge = this.edge(run.value);
             const soFar = offsets[run.value];
             if (offset + run.len > i) {
-                return edge.node === ENDMARKER ? undefined : { node: edge.node, offset: soFar + (i - offset) };
+                return edge.node === ENDMARKER
+                    ? undefined
+                    : { node: edge.node, offset: soFar + (i - offset) };
             }
             offsets[run.value] = soFar + run.len;
             offset += run.len;
@@ -94,7 +96,10 @@ export class GbwtRecord {
         return undefined;
     }
     predecessorAt(i) {
-        const counts = this.edges.map(e => ({ node: e.node === ENDMARKER ? ENDMARKER : flipNode(e.node), count: 0 }));
+        const counts = this.edges.map(e => ({
+            node: e.node === ENDMARKER ? ENDMARKER : flipNode(e.node),
+            count: 0,
+        }));
         for (const run of this.runs()) {
             const entry = counts[run.value];
             if (entry) {
@@ -131,3 +136,4 @@ export class GbwtRecord {
         return result;
     }
 }
+//# sourceMappingURL=record.js.map

package/dist/gbwt/record.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"record.js","sourceRoot":"","sources":["../../src/gbwt/record.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACzD,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,EAAE,MAAM,WAAW,CAAA;AAOvD,MAAM,UAAU,eAAe,CAAC,KAAiB;IAC/C,MAAM,MAAM,GAAG,IAAI,cAAc,CAAC,KAAK,CAAC,CAAA;IACxC,MAAM,KAAK,GAAG,MAAM,CAAC,GAAG,EAAE,CAAA;IAC1B,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;QACvC,OAAO,EAAE,CAAA;IACX,CAAC;IACD,MAAM,KAAK,GAAU,EAAE,CAAA;IACvB,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC;QAC/B,MAAM,KAAK,GAAG,MAAM,CAAC,GAAG,EAAE,CAAA;QAC1B,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,EAAE,CAAA;QAC3B,IAAI,KAAK,KAAK,SAAS,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YAChD,MAAM,IAAI,KAAK,CAAC,2BAA2B,CAAC,CAAA;QAC9C,CAAC;QACD,IAAI,IAAI,KAAK,CAAA;QACb,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;IACpC,CAAC;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAED,MAAM,OAAO,UAAU;IACZ,KAAK,CAAO;IACZ,GAAG,CAAY;IAExB,YAAY,KAAY,EAAE,GAAe;QACvC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;QAClB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;IAChB,CAAC;IAED,IAAI;QACF,OAAO,IAAI,SAAS,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IACnD,CAAC;IAEO,IAAI,CAAC,IAAY;QACvB,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;YACvB,MAAM,IAAI,KAAK,CACb,gCAAgC,IAAI,OAAO,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAC/D,CAAA;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,EAAE,CAAC,CAAS;QACV,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAA;QAC7C,IAAI,MAAM,GAAG,CAAC,CAAA;QACd,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC;YAC9B,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAE,CAAA;YACjC,IAAI,MAAM,GAAG,GAAG,CAAC,GAAG,GAAG,CAAC,EAAE,CAAC;gBACzB,OAAO,IAAI,CAAC,IAAI,KAAK,SAAS;oBAC5B,CAAC,CAAC,SAAS;oBACX,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,EAAE,CAAA;YACvD,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,KAAK,GAAG,GAAG,CAAC,GAAG,CAAA;YACpC,MAAM,IAAI,GAAG,CAAC,GAAG,CAAA;QACnB,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAEO,MAAM,CAAC,IAAY;QACzB,IAAI,GAAG,GAAG,CAAC,CAAA;QACX,IAAI,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,CAAA;QAC5B,OAAO,GAAG,GAAG,IAAI,EAAE,CAAC;YAClB,MAAM,GAAG,GAAG,CAAC,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAA;YAC7B,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAE,CAAA;YAC7B,IAAI,IAAI,CAAC,IAAI,KAAK,IAAI,EAAE,CAAC;gBACvB,OAAO,GAAG,CAAA;YACZ,CAAC;YACD,IAAI,IAAI,CAAC,IAAI,GAAG,IAAI,EAAE,CAAC;gBACrB,GAAG,GAAG,GAAG,GAAG,CAAC,CAAA;YACf,CAAC;iBAAM,CAAC;gBACN,IAAI,GAAG,GAAG,CAAA;YACZ,CAAC;QACH,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ,CAAC,GAAQ;QACf,IAAI,GAAG,CAAC,IAAI,KAAK,SAAS,EAAE,CAAC;YAC3B,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,IAAI,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;QAClC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;YACvB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,IAAI,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAE,CAAC,MAAM,CAAA;QACvC,IAAI,QAAQ,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;YAC1B,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,IAAI,MAAM,GAAG,CAAC,CAAA;QACd,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC;YAC9B,MAAM,IAAI,GAAG,CAAC,GAAG,CAAA;YACjB,IAAI,GAAG,CAAC,KAAK,KAAK,IAAI,EAAE,CAAC;gBACvB,SAAQ;YACV,CAAC;YACD,QAAQ,IAAI,GAAG,CAAC,GAAG,CAAA;YACnB,IAAI,QAAQ,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;gBAC1B,OAAO,MAAM,GAAG,CAAC,QAAQ,GAAG,GAAG,CAAC,MAAM,CAAC,CAAA;YACzC,CAAC;QACH,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa,CAAC,CAAS;QACrB,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YAClC,IAAI,EAAE,CAAC,CAAC,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC;YACzD,KAAK,EAAE,CAAC;SACT,CAAC,CAAC,CAAA;QACH,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC;YAC9B,MAAM,KAAK,GAAG,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAC/B,IAAI,KAAK,EAAE,CAAC;gBACV,KAAK,CAAC,KAAK,IAAI,GAAG,CAAC,GAAG,CAAA;YACxB,CAAC;QACH,CAAC;QACD,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,MAAM,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE,CAAC;YAChD,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,GAAG,CAAC,CAAoC,CAAA;YAChE,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAoC,CAAA;YAC5D,IAAI,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;gBAC5C,MAAM,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,IAAI,CAAA;gBACvB,MAAM,CAAC,IAAI,CAAC,GAAG,IAAI,CAAA;YACrB,CAAC;QACH,CAAC;QACD,IAAI,MAAM,GAAG,CAAC,CAAA;QACd,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;YAC3B,MAAM,IAAI,KAAK,CAAC,KAAK,CAAA;YACrB,IAAI,MAAM,GAAG,CAAC,EAAE,CAAC;gBACf,OAAO,KAAK,CAAC,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAA;YAC1D,CAAC;QACH,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,UAAU;QACR,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,MAAM,GAAU,EAAE,CAAA;QACxB,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC;YAC9B,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;gBACjC,MAAM,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAE,EAAE,CAAC,CAAA;gBAC7D,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAE,GAAG,CAAC,CAAA;YAC9C,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;CACF"}

package/dist/gbwt/sequence.js

@@ -30,7 +30,13 @@ export function decodeSequence(encoded) {
     }
     return result;
 }
-const COMPLEMENT = { A: 'T', C: 'G', G: 'C', T: 'A', N: 'N' };
+const COMPLEMENT = {
+    A: 'T',
+    C: 'G',
+    G: 'C',
+    T: 'A',
+    N: 'N',
+};
 export function reverseComplement(sequence) {
     let result = '';
     for (let i = sequence.length - 1; i >= 0; i--) {
@@ -38,3 +44,4 @@ export function reverseComplement(sequence) {
     }
     return result;
 }
+//# sourceMappingURL=sequence.js.map

package/dist/gbwt/sequence.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"sequence.js","sourceRoot":"","sources":["../../src/gbwt/sequence.ts"],"names":[],"mappings":"AAAA,MAAM,MAAM,GAAG,CAAC,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;AAE5C,MAAM,UAAU,qBAAqB,CAAC,OAAmB;IACvD,MAAM,IAAI,GAAG,OAAO,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;IACxC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QACvB,OAAO,CAAC,CAAA;IACV,CAAC;IACD,IAAI,KAAK,GAAG,IAAI,CAAA;IAChB,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3B,IAAI,KAAK,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;YACpB,MAAK;QACP,CAAC;QACD,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QAC7B,MAAM,IAAI,CAAC,CAAA;IACb,CAAC;IACD,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,MAAM,CAAA;AAC1C,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,OAAmB;IAChD,IAAI,MAAM,GAAG,EAAE,CAAA;IACf,KAAK,MAAM,IAAI,IAAI,OAAO,EAAE,CAAC;QAC3B,IAAI,KAAK,GAAG,IAAI,CAAA;QAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3B,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,GAAG,CAAC,CAAE,CAAA;YAC/B,IAAI,IAAI,KAAK,EAAE,EAAE,CAAC;gBAChB,OAAO,MAAM,CAAA;YACf,CAAC;YACD,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;YAC7B,MAAM,IAAI,IAAI,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,UAAU,GAA2B;IACzC,CAAC,EAAE,GAAG;IACN,CAAC,EAAE,GAAG;IACN,CAAC,EAAE,GAAG;IACN,CAAC,EAAE,GAAG;IACN,CAAC,EAAE,GAAG;CACP,CAAA;AAED,MAAM,UAAU,iBAAiB,CAAC,QAAgB;IAChD,IAAI,MAAM,GAAG,EAAE,CAAA;IACf,KAAK,IAAI,CAAC,GAAG,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC9C,MAAM,IAAI,UAAU,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,GAAG,CAAA;IAC3C,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC"}

package/dist/index.d.ts

@@ -1,10 +1,10 @@
-export { GBZBase, GbzRecord, SchemaVersionError, formatPathName, GENERIC_SAMPLE, SCHEMA_VERSION } from './db.ts';
+export { GBZBase, GENERIC_SAMPLE, GbzRecord, SCHEMA_VERSION, SchemaVersionError, formatPathName, } from './db.ts';
 export type { GbzPath, HaplotypeSample, PathName } from './db.ts';
 export type { ByteSource } from './filehandle.ts';
 export type { Pos } from './gbwt/record.ts';
 export { Subgraph } from './subgraph.ts';
 export type { HaplotypeAlignment, HaplotypeOutput, PathIdentity, PathPosition, ReferencePath, SubgraphJson, SubgraphPath, ToJsonOptions, } from './subgraph.ts';
-export { subgraphAtOffset, subgraphInInterval, subgraphAroundNodes } from './query.ts';
+export { subgraphAroundNodes, subgraphAtOffset, subgraphInInterval, } from './query.ts';
 export type { PathQuery, QueryOptions } from './query.ts';
 export { SqliteDatabase } from './sqlite/database.ts';
 export { weightedLcs } from './lcs.ts';

package/dist/index.js

@@ -1,6 +1,7 @@
-export { GBZBase, GbzRecord, SchemaVersionError, formatPathName, GENERIC_SAMPLE, SCHEMA_VERSION } from "./db.js";
+export { GBZBase, GENERIC_SAMPLE, GbzRecord, SCHEMA_VERSION, SchemaVersionError, formatPathName, } from "./db.js";
 export { Subgraph } from "./subgraph.js";
-export { subgraphAtOffset, subgraphInInterval, subgraphAroundNodes } from "./query.js";
+export { subgraphAroundNodes, subgraphAtOffset, subgraphInInterval, } from "./query.js";
 export { SqliteDatabase } from "./sqlite/database.js";
 export { weightedLcs } from "./lcs.js";
 export * as nodes from "./gbwt/node.js";
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,OAAO,EACP,cAAc,EACd,SAAS,EACT,cAAc,EACd,kBAAkB,EAClB,cAAc,GACf,MAAM,SAAS,CAAA;AAIhB,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAWxC,OAAO,EACL,mBAAmB,EACnB,gBAAgB,EAChB,kBAAkB,GACnB,MAAM,YAAY,CAAA;AAEnB,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAA;AACrD,OAAO,EAAE,WAAW,EAAE,MAAM,UAAU,CAAA;AACtC,OAAO,KAAK,KAAK,MAAM,gBAAgB,CAAA"}

package/dist/lcs.js

@@ -54,10 +54,10 @@ class MinHeap {
     }
 }
 class Matrix {
-    a;
-    b;
     aSums;
     bSums;
+    a;
+    b;
     points = new Map();
     pendingEdits = new MinHeap();
     constructor(a, b, weight) {
@@ -103,7 +103,9 @@ class Matrix {
                 continue;
             }
             const point = { ...found };
-            while (point.a < this.a.length && point.b < this.b.length && this.a[point.a] === this.b[point.b]) {
+            while (point.a < this.a.length &&
+                point.b < this.b.length &&
+                this.a[point.a] === this.b[point.b]) {
                 point.weight += 2 * this.aWeight(point.a);
                 point.a += 1;
                 point.b += 1;
@@ -117,27 +119,44 @@ class Matrix {
             }
             if (point.a < this.a.length) {
                 const w = this.aWeight(point.a);
-                this.tryInsert(edits + w, diagonal + w, { weight: point.weight, a: point.a + 1, b: point.b, matches: 0 });
+                this.tryInsert(edits + w, diagonal + w, {
+                    weight: point.weight,
+                    a: point.a + 1,
+                    b: point.b,
+                    matches: 0,
+                });
             }
             if (point.b < this.b.length) {
                 const w = this.bWeight(point.b);
-                this.tryInsert(edits + w, diagonal - w, { weight: point.weight, a: point.a, b: point.b + 1, matches: 0 });
+                this.tryInsert(edits + w, diagonal - w, {
+                    weight: point.weight,
+                    a: point.a,
+                    b: point.b + 1,
+                    matches: 0,
+                });
             }
         }
         return undefined;
     }
     nextEdits(edits) {
-        while (this.pendingEdits.peek() !== undefined && this.pendingEdits.peek() <= edits) {
+        while (this.pendingEdits.peek() !== undefined &&
+            this.pendingEdits.peek() <= edits) {
             this.pendingEdits.pop();
         }
         return this.pendingEdits.peek();
     }
     predecessor(a, b, edits) {
         const diagonal = this.aSums[a] - this.bSums[b];
-        const prev = a > 0 && this.aWeight(a - 1) <= edits ? this.get(edits - this.aWeight(a - 1), diagonal - this.aWeight(a - 1)) : undefined;
-        const next = b > 0 && this.bWeight(b - 1) <= edits ? this.get(edits - this.bWeight(b - 1), diagonal + this.bWeight(b - 1)) : undefined;
+        const prev = a > 0 && this.aWeight(a - 1) <= edits
+            ? this.get(edits - this.aWeight(a - 1), diagonal - this.aWeight(a - 1))
+            : undefined;
+        const next = b > 0 && this.bWeight(b - 1) <= edits
+            ? this.get(edits - this.bWeight(b - 1), diagonal + this.bWeight(b - 1))
+            : undefined;
         if (prev && next) {
-            return prev.weight > next.weight ? [prev, edits - this.aWeight(a - 1)] : [next, edits - this.bWeight(b - 1)];
+            return prev.weight > next.weight
+                ? [prev, edits - this.aWeight(a - 1)]
+                : [next, edits - this.bWeight(b - 1)];
         }
         if (prev) {
             return [prev, edits - this.aWeight(a - 1)];
@@ -154,7 +173,9 @@ export function weightedLcs(a, b, weight) {
         prefix += 1;
     }
     let suffix = 0;
-    while (suffix < a.length - prefix && suffix < b.length - prefix && a[a.length - 1 - suffix] === b[b.length - 1 - suffix]) {
+    while (suffix < a.length - prefix &&
+        suffix < b.length - prefix &&
+        a[a.length - 1 - suffix] === b[b.length - 1 - suffix]) {
         suffix += 1;
     }
     const pairs = [];
@@ -212,3 +233,4 @@ function weightedLcsCore(a, b, weight) {
     result.reverse();
     return [result, finalWeight];
 }
+//# sourceMappingURL=lcs.js.map

package/dist/lcs.js.map

@@ -0,0 +1 @@
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package/dist/query.d.ts

@@ -1,5 +1,5 @@
-import type { GBZBase } from './db.ts';
 import { Subgraph } from './subgraph.ts';
+import type { GBZBase } from './db.ts';
 import type { HaplotypeOutput } from './subgraph.ts';
 export interface QueryOptions {
     context?: number;

package/dist/query.js

@@ -35,3 +35,4 @@ export async function subgraphAroundNodes(db, nodes, opts = {}) {
     subgraph.extractPaths(undefined, haplotypes);
     return subgraph;
 }
+//# sourceMappingURL=query.js.map

package/dist/query.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"query.js","sourceRoot":"","sources":["../src/query.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,SAAS,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAiBxC,SAAS,QAAQ,CAAC,KAAgB,EAAE,QAAgB;IAClD,OAAO;QACL,MAAM,EAAE,KAAK,CAAC,MAAM,IAAI,cAAc;QACtC,MAAM,EAAE,KAAK,CAAC,MAAM;QACpB,SAAS,EAAE,KAAK,CAAC,SAAS,IAAI,CAAC;QAC/B,QAAQ;KACT,CAAA;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,gBAAgB,CACpC,EAAW,EACX,KAAgB,EAChB,MAAc,EACd,OAAqB,EAAE;IAEvB,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,CAAC,CAAA;IACjC,QAAQ,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;IAC3B,MAAM,SAAS,GAAG,MAAM,QAAQ,CAAC,YAAY,CAAC,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAA;IACtE,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,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,CAAC,CAAA;IACjC,QAAQ,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;IAC3B,MAAM,SAAS,GAAG,MAAM,QAAQ,CAAC,YAAY,CAAC,QAAQ,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC,CAAA;IACrE,MAAM,QAAQ,CAAC,cAAc,CAC3B,SAAS,CAAC,QAAQ,EAClB,GAAG,GAAG,KAAK,EACX,IAAI,CAAC,OAAO,IAAI,GAAG,CACpB,CAAA;IACD,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,IAAI,UAAU,KAAK,gBAAgB,EAAE,CAAC;QACpC,MAAM,IAAI,KAAK,CAAC,sDAAsD,CAAC,CAAA;IACzE,CAAC;IACD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,CAAC,CAAA;IACjC,QAAQ,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;IAC3B,MAAM,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,IAAI,CAAC,OAAO,IAAI,GAAG,CAAC,CAAA;IACtD,QAAQ,CAAC,YAAY,CAAC,SAAS,EAAE,UAAU,CAAC,CAAA;IAC5C,OAAO,QAAQ,CAAA;AACjB,CAAC"}

package/dist/sqlite/btree.d.ts

@@ -1,8 +1,8 @@
 import type { Pager } from './pager.ts';
 import type { SqlValue } from './record.ts';
 export declare class BTree {
-    private pager;
     private readonly usable;
+    private pager;
     constructor(pager: Pager, reservedBytes: number);
     private localPayloadSize;
     private payload;