@gmod/gbz-base 2.1.0 → 2.3.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +48 -21
- package/dist/cli.js +34 -1
- package/dist/cli.js.map +1 -1
- package/dist/db.d.ts +7 -3
- package/dist/db.js +10 -14
- package/dist/db.js.map +1 -1
- package/dist/gbwt/node.d.ts +1 -0
- package/dist/gbwt/node.js +3 -2
- package/dist/gbwt/node.js.map +1 -1
- package/dist/index.d.ts +3 -3
- package/dist/index.js +1 -1
- package/dist/index.js.map +1 -1
- package/dist/query.js +16 -5
- package/dist/query.js.map +1 -1
- package/dist/sqlite/btree.d.ts +4 -0
- package/dist/sqlite/btree.js +66 -0
- package/dist/sqlite/btree.js.map +1 -1
- package/dist/sqlite/database.d.ts +1 -0
- package/dist/sqlite/database.js +3 -0
- package/dist/sqlite/database.js.map +1 -1
- package/dist/subgraph.d.ts +45 -6
- package/dist/subgraph.js +407 -120
- package/dist/subgraph.js.map +1 -1
- package/package.json +1 -1
- package/src/cli.ts +43 -1
- package/src/db.ts +26 -22
- package/src/gbwt/node.ts +7 -2
- package/src/index.ts +5 -1
- package/src/query.ts +19 -9
- package/src/sqlite/btree.ts +72 -0
- package/src/sqlite/database.ts +4 -0
- package/src/subgraph.ts +511 -135
package/dist/sqlite/btree.js.map
CHANGED
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-
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|
|
@@ -19,6 +19,7 @@ export declare class SqliteDatabase {
|
|
|
19
19
|
rootPage(name: string): number;
|
|
20
20
|
indexOn(tableName: string): number;
|
|
21
21
|
byRowid(table: string, rowid: number): Promise<SqlValue[] | undefined>;
|
|
22
|
+
prefetchRows(table: string, lo: number, hi: number): Promise<void>;
|
|
22
23
|
scan(table: string): AsyncGenerator<{
|
|
23
24
|
rowid: number;
|
|
24
25
|
values: SqlValue[];
|
package/dist/sqlite/database.js
CHANGED
|
@@ -65,6 +65,9 @@ export class SqliteDatabase {
|
|
|
65
65
|
byRowid(table, rowid) {
|
|
66
66
|
return this.btree.tableRowid(this.rootPage(table), rowid);
|
|
67
67
|
}
|
|
68
|
+
prefetchRows(table, lo, hi) {
|
|
69
|
+
return this.btree.prefetchRowidRange(this.rootPage(table), lo, hi);
|
|
70
|
+
}
|
|
68
71
|
scan(table) {
|
|
69
72
|
return this.btree.tableScan(this.rootPage(table));
|
|
70
73
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/dist/subgraph.d.ts
CHANGED
|
@@ -71,21 +71,56 @@ export interface SubgraphOptions {
|
|
|
71
71
|
limit?: number | undefined;
|
|
72
72
|
signal?: AbortSignal | undefined;
|
|
73
73
|
}
|
|
74
|
+
export declare class SubgraphLimitError extends Error {
|
|
75
|
+
name: string;
|
|
76
|
+
readonly limit: number;
|
|
77
|
+
readonly windowBp: number | undefined;
|
|
78
|
+
readonly walkedBp: number | undefined;
|
|
79
|
+
constructor(limit: number, walk?: {
|
|
80
|
+
windowBp: number;
|
|
81
|
+
walkedBp: number;
|
|
82
|
+
});
|
|
83
|
+
}
|
|
84
|
+
export type ChainEnd = 'in-fragment sample' | 'identified sibling' | 'out-of-window sample' | 'bound' | 'endmarker' | 'cycle';
|
|
85
|
+
export interface ChainRecord {
|
|
86
|
+
fragments: number;
|
|
87
|
+
steps: number;
|
|
88
|
+
seeks: number;
|
|
89
|
+
reentries: number;
|
|
90
|
+
twinLandings: number;
|
|
91
|
+
end: ChainEnd;
|
|
92
|
+
pathHandle: number | undefined;
|
|
93
|
+
}
|
|
94
|
+
export interface IdentificationStats {
|
|
95
|
+
interval: number;
|
|
96
|
+
scans: [number, number][];
|
|
97
|
+
windowSamples: number;
|
|
98
|
+
fragmentLengths: number[];
|
|
99
|
+
companionSeeks: number;
|
|
100
|
+
companionMisses: number;
|
|
101
|
+
graphLookups: number;
|
|
102
|
+
graphFetches: number;
|
|
103
|
+
chains: ChainRecord[];
|
|
104
|
+
}
|
|
105
|
+
interface SubgraphStats {
|
|
106
|
+
orderedAlignments: number;
|
|
107
|
+
lcsAlignments: number;
|
|
108
|
+
identificationSteps: number;
|
|
109
|
+
identificationFetches: number;
|
|
110
|
+
identification: IdentificationStats;
|
|
111
|
+
}
|
|
74
112
|
export declare class Subgraph {
|
|
75
113
|
private records;
|
|
76
114
|
private paths;
|
|
115
|
+
private twinStarts;
|
|
77
116
|
private refId;
|
|
78
117
|
private refPath;
|
|
79
118
|
private refHandle;
|
|
80
119
|
private refInterval;
|
|
81
120
|
private refIndexCache;
|
|
82
121
|
private refPrefixCache;
|
|
83
|
-
|
|
84
|
-
|
|
85
|
-
lcsAlignments: number;
|
|
86
|
-
identificationSteps: number;
|
|
87
|
-
identificationFetches: number;
|
|
88
|
-
};
|
|
122
|
+
private walkedBp;
|
|
123
|
+
readonly stats: SubgraphStats;
|
|
89
124
|
private db;
|
|
90
125
|
private readonly limit;
|
|
91
126
|
private readonly signal;
|
|
@@ -110,10 +145,13 @@ export declare class Subgraph {
|
|
|
110
145
|
inserted: number;
|
|
111
146
|
removed: number;
|
|
112
147
|
}>;
|
|
148
|
+
prefetchReferenceWalk(reference: ReferencePath, len: number): Promise<void>;
|
|
113
149
|
aroundInterval(start: PathPosition, len: number, context: number): Promise<{
|
|
114
150
|
inserted: number;
|
|
115
151
|
removed: number;
|
|
116
152
|
}>;
|
|
153
|
+
get referenceWalkedBp(): number | undefined;
|
|
154
|
+
private walkInterval;
|
|
117
155
|
aroundNodes(nodes: Iterable<number>, context: number): Promise<{
|
|
118
156
|
inserted: number;
|
|
119
157
|
removed: number;
|
|
@@ -145,3 +183,4 @@ export declare class Subgraph {
|
|
|
145
183
|
toGFA(opts?: SubgraphOutputOptions): Promise<string>;
|
|
146
184
|
toSubgraphJson(opts?: SubgraphOutputOptions): SubgraphJson;
|
|
147
185
|
}
|
|
186
|
+
export {};
|