@gmod/gbz-base 0.0.1 → 1.1.0

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.d.ts

@@ -14,5 +14,9 @@ export declare class GbwtRecord {
     private edgeTo;
     offsetTo(pos: Pos): number | undefined;
     predecessorAt(i: number): number | undefined;
+    decompressArrays(): {
+        nodes: Int32Array<ArrayBuffer>;
+        offsets: Int32Array<ArrayBuffer>;
+    };
     decompress(): Pos[];
 }

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) {
@@ -118,6 +123,28 @@ export class GbwtRecord {
         }
         return undefined;
     }
+    decompressArrays() {
+        const offsets = this.edges.map(e => e.offset);
+        let total = 0;
+        for (const run of this.runs()) {
+            total += run.len;
+        }
+        const nodes = new Int32Array(total);
+        const nextOffsets = new Int32Array(total);
+        let i = 0;
+        for (const run of this.runs()) {
+            const edge = this.edge(run.value);
+            let offset = offsets[run.value];
+            for (let k = 0; k < run.len; k++) {
+                nodes[i] = edge.node;
+                nextOffsets[i] = offset;
+                offset += 1;
+                i += 1;
+            }
+            offsets[run.value] = offset;
+        }
+        return { nodes, offsets: nextOffsets };
+    }
     decompress() {
         const offsets = this.edges.map(e => e.offset);
         const result = [];
@@ -131,3 +158,4 @@ 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,gBAAgB;QACd,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAA;QAC7C,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC;YAC9B,KAAK,IAAI,GAAG,CAAC,GAAG,CAAA;QAClB,CAAC;QACD,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,KAAK,CAAC,CAAA;QACnC,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,KAAK,CAAC,CAAA;QACzC,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC;YAC9B,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC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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/graphName.d.ts

@@ -0,0 +1,9 @@
+export interface GraphName {
+    name: string | undefined;
+    subgraph: Map<string, Set<string>>;
+    translation: Map<string, Set<string>>;
+}
+export declare function graphNameFromTags(tags: Map<string, string>): GraphName;
+export declare function subgraphName(name: string, parent: GraphName): GraphName;
+export declare function gfaHeaderLines(graphName: GraphName): string[];
+export declare function sha256Hex(chunks: Uint8Array[]): Promise<string>;

package/dist/graphName.js

@@ -0,0 +1,83 @@
+function parseRelationships(field, what) {
+    const relationships = new Map();
+    if (field !== undefined) {
+        for (const rel of field.split(';')) {
+            const parts = rel.split(',');
+            const [from, to] = parts;
+            if (parts.length !== 2 || !from || !to) {
+                throw new Error(`Invalid ${what} relationship: ${rel}`);
+            }
+            let targets = relationships.get(from);
+            if (!targets) {
+                targets = new Set();
+                relationships.set(from, targets);
+            }
+            targets.add(to);
+        }
+    }
+    return relationships;
+}
+export function graphNameFromTags(tags) {
+    return {
+        name: tags.get('pggname'),
+        subgraph: parseRelationships(tags.get('subgraph'), 'subgraph'),
+        translation: parseRelationships(tags.get('translation'), 'translation'),
+    };
+}
+function merge(into, from) {
+    for (const [key, values] of from) {
+        let targets = into.get(key);
+        if (!targets) {
+            targets = new Set();
+            into.set(key, targets);
+        }
+        for (const value of values) {
+            targets.add(value);
+        }
+    }
+}
+export function subgraphName(name, parent) {
+    const result = {
+        name,
+        subgraph: new Map(),
+        translation: new Map(),
+    };
+    if (parent.name !== undefined) {
+        result.subgraph.set(name, new Set([parent.name]));
+        merge(result.subgraph, parent.subgraph);
+        merge(result.translation, parent.translation);
+    }
+    return result;
+}
+function sortedEntries(relationships) {
+    return [...relationships.entries()]
+        .sort(([a], [b]) => (a < b ? -1 : a > b ? 1 : 0))
+        .flatMap(([from, tos]) => [...tos].sort().map(to => [from, to]));
+}
+export function gfaHeaderLines(graphName) {
+    const lines = [];
+    if (graphName.name !== undefined) {
+        lines.push(`H\tNM:Z:${graphName.name}`);
+    }
+    for (const [subgraph, supergraph] of sortedEntries(graphName.subgraph)) {
+        lines.push(`H\tSG:Z:${subgraph},${supergraph}`);
+    }
+    for (const [from, to] of sortedEntries(graphName.translation)) {
+        lines.push(`H\tTL:Z:${from},${to}`);
+    }
+    return lines;
+}
+export async function sha256Hex(chunks) {
+    const total = chunks.reduce((sum, chunk) => sum + chunk.length, 0);
+    const bytes = new Uint8Array(total);
+    let offset = 0;
+    for (const chunk of chunks) {
+        bytes.set(chunk, offset);
+        offset += chunk.length;
+    }
+    const digest = await globalThis.crypto.subtle.digest('SHA-256', bytes);
+    return [...new Uint8Array(digest)]
+        .map(byte => byte.toString(16).padStart(2, '0'))
+        .join('');
+}
+//# sourceMappingURL=graphName.js.map

package/dist/graphName.js.map

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

@@ -1,11 +1,12 @@
-export { GBZBase, GbzRecord, SchemaVersionError, formatPathName, GENERIC_SAMPLE, SCHEMA_VERSION } from './db.ts';
-export type { GbzPath, HaplotypeSample, PathName } from './db.ts';
+export { GBZBase, GENERIC_SAMPLE, GbzRecord, SCHEMA_VERSION, SchemaVersionError, formatPathName, } from './db.ts';
+export type { GbzPath, HaplotypeSample, OpenOptions, 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 type { HaplotypeAlignment, HaplotypeOutput, PathIdentity, PathPosition, ReferencePath, SnarlOutput, SubgraphJson, SubgraphPath, ToJsonOptions, } from './subgraph.ts';
+export { subgraphAroundNodes, subgraphAtOffset, subgraphBetween, subgraphInInterval, } from './query.ts';
 export type { PathQuery, QueryOptions } from './query.ts';
 export { SqliteDatabase } from './sqlite/database.ts';
+export type { GraphName } from './graphName.ts';
 export { weightedLcs } from './lcs.ts';
 export * as nodes from './gbwt/node.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, subgraphBetween, 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;AAYxC,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/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

@@ -1,9 +1,10 @@
-import type { GBZBase } from './db.ts';
 import { Subgraph } from './subgraph.ts';
-import type { HaplotypeOutput } from './subgraph.ts';
+import type { GBZBase } from './db.ts';
+import type { HaplotypeOutput, SnarlOutput } from './subgraph.ts';
 export interface QueryOptions {
     context?: number;
     haplotypes?: HaplotypeOutput;
+    snarls?: SnarlOutput;
     limit?: number;
 }
 export interface PathQuery {
@@ -14,3 +15,4 @@ export interface PathQuery {
 export declare function subgraphAtOffset(db: GBZBase, query: PathQuery, offset: number, opts?: QueryOptions): Promise<Subgraph>;
 export declare function subgraphInInterval(db: GBZBase, query: PathQuery, start: number, end: number, opts?: QueryOptions): Promise<Subgraph>;
 export declare function subgraphAroundNodes(db: GBZBase, nodes: number[], opts?: QueryOptions): Promise<Subgraph>;
+export declare function subgraphBetween(db: GBZBase, start: number, end: number, opts?: Pick<QueryOptions, 'haplotypes' | 'limit'>): Promise<Subgraph>;

package/dist/query.js

@@ -13,6 +13,7 @@ export async function subgraphAtOffset(db, query, offset, opts = {}) {
     subgraph.limit = opts.limit;
     const reference = await subgraph.pathPosition(pathName(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;
 }
@@ -21,17 +22,35 @@ export async function subgraphInInterval(db, query, start, end, opts = {}) {
     subgraph.limit = opts.limit;
     const reference = await subgraph.pathPosition(pathName(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');
     }
+    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);
     subgraph.limit = opts.limit;
     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);
+    subgraph.limit = opts.limit;
+    await subgraph.betweenNodes(start, end);
     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;AAkBxC,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,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,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,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,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,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,OAAmD,EAAE;IAErD,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,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

@@ -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;

package/dist/sqlite/btree.js

@@ -6,7 +6,10 @@ const LEAF_TABLE = 0x0d;
 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 && type !== LEAF_INDEX && type !== LEAF_TABLE) {
+    if (type !== INTERIOR_INDEX &&
+        type !== INTERIOR_TABLE &&
+        type !== LEAF_INDEX &&
+        type !== LEAF_TABLE) {
         throw new Error(`SQLite page has unknown b-tree type ${type}`);
     }
     const interior = type === INTERIOR_INDEX || type === INTERIOR_TABLE;
@@ -26,15 +29,17 @@ function readUint32(page, offset) {
     return view.getUint32(offset);
 }
 export class BTree {
-    pager;
     usable;
+    pager;
     constructor(pager, reservedBytes) {
         this.pager = pager;
         this.usable = pager.pageSize - reservedBytes;
     }
     localPayloadSize(total, isIndex) {
         const usable = this.usable;
-        const maxLocal = isIndex ? Math.floor(((usable - 12) * 64) / 255) - 23 : usable - 35;
+        const maxLocal = isIndex
+            ? Math.floor(((usable - 12) * 64) / 255) - 23
+            : usable - 35;
         if (total <= maxLocal) {
             return total;
         }
@@ -107,7 +112,10 @@ export class BTree {
                     high = mid;
                 }
             }
-            pageNumber = low === header.cellCount ? header.rightChild : readUint32(page, cellOffset(page, header, low));
+            pageNumber =
+                low === header.cellCount
+                    ? header.rightChild
+                    : readUint32(page, cellOffset(page, header, low));
         }
     }
     async *tableScan(root) {
@@ -117,14 +125,22 @@ export class BTree {
                 const offset = cellOffset(page, header, i);
                 const [size, afterSize] = readVarint(page, offset);
                 const [rowid, afterKey] = readVarint(page, afterSize);
-                yield { rowid, values: decodeRecord(await this.payload(page, afterKey, size, false)) };
+                yield {
+                    rowid,
+                    values: decodeRecord(await this.payload(page, afterKey, size, false)),
+                };
             }
         }
         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) {
@@ -199,3 +215,4 @@ function compareKey(values, key) {
     }
     return 0;
 }
+//# sourceMappingURL=btree.js.map

package/dist/sqlite/btree.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"btree.js","sourceRoot":"","sources":["../../src/sqlite/btree.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AAKtD,MAAM,cAAc,GAAG,IAAI,CAAA;AAC3B,MAAM,cAAc,GAAG,IAAI,CAAA;AAC3B,MAAM,UAAU,GAAG,IAAI,CAAA;AACvB,MAAM,UAAU,GAAG,IAAI,CAAA;AASvB,SAAS,UAAU,CAAC,IAAgB,EAAE,KAAa;IACjD,MAAM,IAAI,GAAG,IAAI,QAAQ,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,UAAU,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;IACxE,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,CAAA;IACxB,IACE,IAAI,KAAK,cAAc;QACvB,IAAI,KAAK,cAAc;QACvB,IAAI,KAAK,UAAU;QACnB,IAAI,KAAK,UAAU,EACnB,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,uCAAuC,IAAI,EAAE,CAAC,CAAA;IAChE,CAAC;IACD,MAAM,QAAQ,GAAG,IAAI,KAAK,cAAc,IAAI,IAAI,KAAK,cAAc,CAAA;IACnE,OAAO;QACL,IAAI;QACJ,SAAS,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,GAAG,CAAC,CAAC;QACpC,UAAU,EAAE,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACpD,YAAY,EAAE,KAAK,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;KAC1C,CAAA;AACH,CAAC;AAED,SAAS,UAAU,CAAC,IAAgB,EAAE,MAAkB,EAAE,KAAa;IACrE,MAAM,IAAI,GAAG,IAAI,QAAQ,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,UAAU,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;IACxE,OAAO,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,YAAY,GAAG,CAAC,GAAG,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,SAAS,UAAU,CAAC,IAAgB,EAAE,MAAc;IAClD,MAAM,IAAI,GAAG,IAAI,QAAQ,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,UAAU,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;IACxE,OAAO,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAA;AAC/B,CAAC;AAED,MAAM,OAAO,KAAK;IACC,MAAM,CAAQ;IACvB,KAAK,CAAO;IAEpB,YAAY,KAAY,EAAE,aAAqB;QAC7C,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;QAClB,IAAI,CAAC,MAAM,GAAG,KAAK,CAAC,QAAQ,GAAG,aAAa,CAAA;IAC9C,CAAC;IAEO,gBAAgB,CAAC,KAAa,EAAE,OAAgB;QACtD,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QAC1B,MAAM,QAAQ,GAAG,OAAO;YACtB,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,GAAG,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,GAAG,CAAC,GAAG,EAAE;YAC7C,CAAC,CAAC,MAAM,GAAG,EAAE,CAAA;QACf,IAAI,KAAK,IAAI,QAAQ,EAAE,CAAC;YACtB,OAAO,KAAK,CAAA;QACd,CAAC;QACD,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,GAAG,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,GAAG,CAAC,GAAG,EAAE,CAAA;QAC5D,MAAM,KAAK,GAAG,QAAQ,GAAG,CAAC,CAAC,KAAK,GAAG,QAAQ,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QAC5D,OAAO,KAAK,IAAI,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;IAC7C,CAAC;IAEO,KAAK,CAAC,OAAO,CACnB,IAAgB,EAChB,MAAc,EACd,KAAa,EACb,OAAgB;QAEhB,MAAM,KAAK,GAAG,IAAI,CAAC,gBAAgB,CAAC,KAAK,EAAE,OAAO,CAAC,CAAA;QACnD,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;YACpB,OAAO,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,MAAM,GAAG,KAAK,CAAC,CAAA;QAC9C,CAAC;QACD,MAAM,MAAM,GAAG,IAAI,UAAU,CAAC,KAAK,CAAC,CAAA;QACpC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,MAAM,GAAG,KAAK,CAAC,EAAE,CAAC,CAAC,CAAA;QACpD,IAAI,MAAM,GAAG,KAAK,CAAA;QAClB,IAAI,IAAI,GAAG,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,KAAK,CAAC,CAAA;QAC3C,OAAO,IAAI,KAAK,CAAC,IAAI,MAAM,GAAG,KAAK,EAAE,CAAC;YACpC,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAC5C,MAAM,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAC7B,CAAC,EACD,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,KAAK,GAAG,MAAM,CAAC,CAC9C,CAAA;YACD,MAAM,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;YACzB,MAAM,IAAI,KAAK,CAAC,MAAM,CAAA;YACtB,IAAI,GAAG,UAAU,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAA;QAChC,CAAC;QACD,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;YACrB,MAAM,IAAI,KAAK,CACb,6DAA6D,CAC9D,CAAA;QACH,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAEO,KAAK,CAAC,MAAM,CAAC,UAAkB;QACrC,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;QAC9C,OAAO,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,IAAI,EAAE,UAAU,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;IACvE,CAAC;IAED,KAAK,CAAC,UAAU,CACd,IAAY,EACZ,KAAa;QAEb,IAAI,UAAU,GAAG,IAAI,CAAA;QACrB,SAAS,CAAC;YACR,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;YACtD,IAAI,MAAM,CAAC,IAAI,KAAK,UAAU,EAAE,CAAC;gBAC/B,IAAI,GAAG,GAAG,CAAC,CAAA;gBACX,IAAI,IAAI,GAAG,MAAM,CAAC,SAAS,CAAA;gBAC3B,OAAO,GAAG,GAAG,IAAI,EAAE,CAAC;oBAClB,MAAM,GAAG,GAAG,CAAC,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAA;oBAC7B,MAAM,MAAM,GAAG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,CAAC,CAAA;oBAC5C,MAAM,CAAC,IAAI,EAAE,SAAS,CAAC,GAAG,UAAU,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;oBAClD,MAAM,CAAC,GAAG,EAAE,QAAQ,CAAC,GAAG,UAAU,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;oBACnD,IAAI,GAAG,KAAK,KAAK,EAAE,CAAC;wBAClB,OAAO,YAAY,CAAC,MAAM,IAAI,CAAC,OAAO,CAAC,IAAI,EAAE,QAAQ,EAAE,IAAI,EAAE,KAAK,CAAC,CAAC,CAAA;oBACtE,CAAC;oBACD,IAAI,GAAG,GAAG,KAAK,EAAE,CAAC;wBAChB,GAAG,GAAG,GAAG,GAAG,CAAC,CAAA;oBACf,CAAC;yBAAM,CAAC;wBACN,IAAI,GAAG,GAAG,CAAA;oBACZ,CAAC;gBACH,CAAC;gBACD,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,IAAI,MAAM,CAAC,IAAI,KAAK,cAAc,EAAE,CAAC;gBACnC,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;YAC/D,CAAC;YACD,IAAI,GAAG,GAAG,CAAC,CAAA;YACX,IAAI,IAAI,GAAG,MAAM,CAAC,SAAS,CAAA;YAC3B,OAAO,GAAG,GAAG,IAAI,EAAE,CAAC;gBAClB,MAAM,GAAG,GAAG,CAAC,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAA;gBAC7B,MAAM,MAAM,GAAG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,CAAC,CAAA;gBAC5C,MAAM,CAAC,GAAG,CAAC,GAAG,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,CAAC,CAAC,CAAA;gBAC1C,IAAI,GAAG,GAAG,KAAK,EAAE,CAAC;oBAChB,GAAG,GAAG,GAAG,GAAG,CAAC,CAAA;gBACf,CAAC;qBAAM,CAAC;oBACN,IAAI,GAAG,GAAG,CAAA;gBACZ,CAAC;YACH,CAAC;YACD,UAAU;gBACR,GAAG,KAAK,MAAM,CAAC,SAAS;oBACtB,CAAC,CAAC,MAAM,CAAC,UAAU;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package/dist/sqlite/database.d.ts

@@ -1,6 +1,6 @@
-import type { ByteSource } from '../filehandle.ts';
 import { BTree } from './btree.ts';
 import { Pager } from './pager.ts';
+import type { ByteSource } from '../filehandle.ts';
 import type { PagerOptions } from './pager.ts';
 import type { SqlValue } from './record.ts';
 export interface SqliteObject {

package/dist/sqlite/database.js

@@ -33,8 +33,17 @@ export class SqliteDatabase {
         const objects = new Map();
         for await (const { values } of btree.tableScan(1)) {
             const [type, name, tableName, rootPage, sql] = values;
-            if (typeof type === 'string' && typeof name === 'string' && typeof tableName === 'string' && typeof rootPage === 'number') {
-                objects.set(name, { type, name, tableName, rootPage, sql: typeof sql === 'string' ? sql : '' });
+            if (typeof type === 'string' &&
+                typeof name === 'string' &&
+                typeof tableName === 'string' &&
+                typeof rootPage === 'number') {
+                objects.set(name, {
+                    type,
+                    name,
+                    tableName,
+                    rootPage,
+                    sql: typeof sql === 'string' ? sql : '',
+                });
             }
         }
         return new SqliteDatabase(pager, btree, objects);
@@ -69,3 +78,4 @@ export class SqliteDatabase {
         return this.objects.has(name);
     }
 }
+//# sourceMappingURL=database.js.map

package/dist/sqlite/database.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"database.js","sourceRoot":"","sources":["../../src/sqlite/database.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAClC,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAclC,MAAM,OAAO,cAAc;IAChB,KAAK,CAAO;IACZ,KAAK,CAAO;IACZ,OAAO,CAA2B;IAE3C,YACE,KAAY,EACZ,KAAY,EACZ,OAAkC;QAElC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;QAClB,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;QAClB,IAAI,CAAC,OAAO,GAAG,OAAO,CAAA;IACxB,CAAC;IAED,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,MAAkB,EAAE,OAAqB,EAAE;QAC3D,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QACpC,MAAM,UAAU,GAAG,MAAM,MAAM,CAAC,IAAI,CAClC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,IAAI,KAAK,EAAE,IAAI,CAAC,EACvC,CAAC,CACF,CAAA;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,QAAQ,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;QAC1C,MAAM,KAAK,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;QAC9D,IAAI,KAAK,KAAK,iBAAiB,EAAE,CAAC;YAChC,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAA;QAC1C,CAAC;QACD,MAAM,IAAI,GAAG,IAAI,QAAQ,CACvB,MAAM,CAAC,MAAM,EACb,MAAM,CAAC,UAAU,EACjB,MAAM,CAAC,UAAU,CAClB,CAAA;QACD,MAAM,WAAW,GAAG,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,CAAA;QACtC,MAAM,QAAQ,GAAG,WAAW,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,WAAW,CAAA;QACxD,MAAM,QAAQ,GAAG,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,CAAA;QAChC,MAAM,QAAQ,GAAG,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,CAAA;QACnC,IAAI,QAAQ,KAAK,CAAC,EAAE,CAAC;YACnB,MAAM,IAAI,KAAK,CAAC,wBAAwB,QAAQ,eAAe,CAAC,CAAA;QAClE,CAAC;QACD,MAAM,KAAK,GAAG,IAAI,KAAK,CAAC,MAAM,EAAE,QAAQ,EAAE,IAAI,EAAE,IAAI,CAAC,CAAA;QACrD,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,UAAU,CAAC,CAAA;QACzB,KAAK,CAAC,OAAO,IAAI,CAAC,CAAA;QAClB,KAAK,CAAC,YAAY,IAAI,UAAU,CAAC,MAAM,CAAA;QACvC,MAAM,KAAK,GAAG,IAAI,KAAK,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAA;QACxC,MAAM,OAAO,GAAG,IAAI,GAAG,EAAwB,CAAA;QAC/C,IAAI,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,IAAI,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC;YAClD,MAAM,CAAC,IAAI,EAAE,IAAI,EAAE,SAAS,EAAE,QAAQ,EAAE,GAAG,CAAC,GAAG,MAAM,CAAA;YACrD,IACE,OAAO,IAAI,KAAK,QAAQ;gBACxB,OAAO,IAAI,KAAK,QAAQ;gBACxB,OAAO,SAAS,KAAK,QAAQ;gBAC7B,OAAO,QAAQ,KAAK,QAAQ,EAC5B,CAAC;gBACD,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE;oBAChB,IAAI;oBACJ,IAAI;oBACJ,SAAS;oBACT,QAAQ;oBACR,GAAG,EAAE,OAAO,GAAG,KAAK,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;iBACxC,CAAC,CAAA;YACJ,CAAC;QACH,CAAC;QACD,OAAO,IAAI,cAAc,CAAC,KAAK,EAAE,KAAK,EAAE,OAAO,CAAC,CAAA;IAClD,CAAC;IAED,QAAQ,CAAC,IAAY;QACnB,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;QACrC,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,uCAAuC,IAAI,EAAE,CAAC,CAAA;QAChE,CAAC;QACD,OAAO,MAAM,CAAC,QAAQ,CAAA;IACxB,CAAC;IAED,OAAO,CAAC,SAAiB;QACvB,MAAM,KAAK,GAAG,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC,IAAI,CAC3C,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,OAAO,IAAI,CAAC,CAAC,SAAS,KAAK,SAAS,CACrD,CAAA;QACD,IAAI,CAAC,KAAK,EAAE,CAAC;YACX,MAAM,IAAI,KAAK,CAAC,gBAAgB,SAAS,eAAe,CAAC,CAAA;QAC3D,CAAC;QACD,OAAO,KAAK,CAAC,QAAQ,CAAA;IACvB,CAAC;IAED,OAAO,CAAC,KAAa,EAAE,KAAa;QAClC,OAAO,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,KAAK,CAAC,CAAA;IAC3D,CAAC;IAED,IAAI,CAAC,KAAa;QAChB,OAAO,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAA;IACnD,CAAC;IAED,WAAW,CAAC,KAAa,EAAE,GAAa;QACtC,OAAO,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,CAAA;IACzD,CAAC;IAED,aAAa,CAAC,KAAa,EAAE,GAAa;QACxC,OAAO,IAAI,CAAC,KAAK,CAAC,aAAa,CAAC,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,CAAA;IAC3D,CAAC;IAED,GAAG,CAAC,IAAY;QACd,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC/B,CAAC;CACF"}

package/dist/sqlite/pager.d.ts

@@ -4,16 +4,21 @@ export interface PagerOptions {
     maxBlocks?: number;
 }
 export declare class Pager {
-    private source;
-    readonly pageSize: number;
-    private fileSize;
     private blocks;
     private readonly blockSize;
     private readonly maxBlocks;
     bytesFetched: number;
     fetches: number;
+    private source;
+    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>>;
 }