@genome-spy/core 0.64.0 → 0.65.0

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.
Files changed (104) hide show
  1. package/dist/bundle/{index-CCJIjehY.js → AbortablePromiseCache-CcuMrnn7.js} +22 -91
  2. package/dist/bundle/browser-txUcLy2H.js +123 -0
  3. package/dist/bundle/index-BQpbYrv4.js +1712 -0
  4. package/dist/bundle/index-BhtHKLUo.js +73 -0
  5. package/dist/bundle/index-C0llXMqm.js +280 -0
  6. package/dist/bundle/index-CCe8rnZz.js +716 -0
  7. package/dist/bundle/index-CD7FLu9x.js +269 -0
  8. package/dist/bundle/{index-C08YCM2T.js → index-D-w7Mmt9.js} +246 -126
  9. package/dist/bundle/index-D74H8TTz.js +508 -0
  10. package/dist/bundle/index-DhcU-Gk-.js +1487 -0
  11. package/dist/bundle/index.es.js +4878 -4680
  12. package/dist/bundle/index.js +151 -167
  13. package/dist/bundle/inflate-DRgHi_KK.js +1050 -0
  14. package/dist/schema.json +9 -1
  15. package/dist/src/data/collector.d.ts +7 -2
  16. package/dist/src/data/collector.d.ts.map +1 -1
  17. package/dist/src/data/collector.js +13 -2
  18. package/dist/src/data/dataFlow.d.ts +20 -42
  19. package/dist/src/data/dataFlow.d.ts.map +1 -1
  20. package/dist/src/data/dataFlow.js +57 -80
  21. package/dist/src/data/dataFlow.test.js +35 -2
  22. package/dist/src/data/flowHandle.d.ts +15 -0
  23. package/dist/src/data/flowHandle.d.ts.map +1 -0
  24. package/dist/src/data/flowHandle.js +13 -0
  25. package/dist/src/data/flowInit.d.ts +85 -0
  26. package/dist/src/data/flowInit.d.ts.map +1 -0
  27. package/dist/src/data/flowInit.js +238 -0
  28. package/dist/src/data/flowInit.test.d.ts +2 -0
  29. package/dist/src/data/flowInit.test.d.ts.map +1 -0
  30. package/dist/src/data/flowInit.test.js +413 -0
  31. package/dist/src/data/flowOptimizer.d.ts +6 -4
  32. package/dist/src/data/flowOptimizer.d.ts.map +1 -1
  33. package/dist/src/data/flowOptimizer.js +29 -14
  34. package/dist/src/data/flowOptimizer.test.js +20 -15
  35. package/dist/src/data/sources/lazy/bamSource.js +1 -1
  36. package/dist/src/data/sources/lazy/bigBedSource.js +1 -1
  37. package/dist/src/data/sources/lazy/bigWigSource.js +1 -1
  38. package/dist/src/data/sources/lazy/gff3Source.d.ts +2 -6
  39. package/dist/src/data/sources/lazy/gff3Source.d.ts.map +1 -1
  40. package/dist/src/data/sources/lazy/gff3Source.js +4 -8
  41. package/dist/src/data/sources/lazy/indexedFastaSource.d.ts.map +1 -1
  42. package/dist/src/data/sources/lazy/indexedFastaSource.js +17 -17
  43. package/dist/src/data/sources/lazy/tabixSource.js +1 -1
  44. package/dist/src/genomeSpy.d.ts +1 -1
  45. package/dist/src/genomeSpy.d.ts.map +1 -1
  46. package/dist/src/genomeSpy.js +18 -61
  47. package/dist/src/marks/mark.d.ts +1 -0
  48. package/dist/src/marks/mark.d.ts.map +1 -1
  49. package/dist/src/marks/mark.js +22 -1
  50. package/dist/src/spec/sampleView.d.ts +3 -2
  51. package/dist/src/types/viewContext.d.ts +1 -1
  52. package/dist/src/view/axisResolution.d.ts +5 -0
  53. package/dist/src/view/axisResolution.d.ts.map +1 -1
  54. package/dist/src/view/axisResolution.js +16 -1
  55. package/dist/src/view/facetView.d.ts.map +1 -1
  56. package/dist/src/view/facetView.js +1 -0
  57. package/dist/src/view/flowBuilder.d.ts +2 -2
  58. package/dist/src/view/flowBuilder.d.ts.map +1 -1
  59. package/dist/src/view/flowBuilder.js +21 -4
  60. package/dist/src/view/gridView/gridView.d.ts.map +1 -1
  61. package/dist/src/view/gridView/gridView.js +13 -0
  62. package/dist/src/view/gridView/selectionRect.d.ts +8 -4
  63. package/dist/src/view/gridView/selectionRect.d.ts.map +1 -1
  64. package/dist/src/view/gridView/selectionRect.js +28 -3
  65. package/dist/src/view/gridView/selectionRect.test.d.ts +2 -0
  66. package/dist/src/view/gridView/selectionRect.test.d.ts.map +1 -0
  67. package/dist/src/view/gridView/selectionRect.test.js +87 -0
  68. package/dist/src/view/paramMediator.d.ts +2 -1
  69. package/dist/src/view/paramMediator.d.ts.map +1 -1
  70. package/dist/src/view/paramMediator.js +13 -1
  71. package/dist/src/view/paramMediator.test.js +22 -0
  72. package/dist/src/view/scaleResolution.d.ts +5 -0
  73. package/dist/src/view/scaleResolution.d.ts.map +1 -1
  74. package/dist/src/view/scaleResolution.js +10 -0
  75. package/dist/src/view/testUtils.d.ts.map +1 -1
  76. package/dist/src/view/testUtils.js +16 -4
  77. package/dist/src/view/unitView.d.ts.map +1 -1
  78. package/dist/src/view/unitView.js +58 -8
  79. package/dist/src/view/view.d.ts +17 -1
  80. package/dist/src/view/view.d.ts.map +1 -1
  81. package/dist/src/view/view.js +57 -1
  82. package/dist/src/view/viewDispose.test.d.ts +2 -0
  83. package/dist/src/view/viewDispose.test.d.ts.map +1 -0
  84. package/dist/src/view/viewDispose.test.js +110 -0
  85. package/dist/src/view/viewUtils.d.ts +4 -4
  86. package/dist/src/view/viewUtils.d.ts.map +1 -1
  87. package/dist/src/view/viewUtils.js +19 -15
  88. package/dist/src/view/viewUtils.test.d.ts +2 -0
  89. package/dist/src/view/viewUtils.test.d.ts.map +1 -0
  90. package/dist/src/view/viewUtils.test.js +87 -0
  91. package/package.json +10 -10
  92. package/dist/bundle/__vite-browser-external-C--ziKoh.js +0 -8
  93. package/dist/bundle/_commonjsHelpers-DjF3Plf2.js +0 -26
  94. package/dist/bundle/index-5ajWdKly.js +0 -1319
  95. package/dist/bundle/index-B03-Om4z.js +0 -274
  96. package/dist/bundle/index-BftNdA0O.js +0 -27
  97. package/dist/bundle/index-Bg7C4Xat.js +0 -2750
  98. package/dist/bundle/index-C3QR8Lv6.js +0 -2131
  99. package/dist/bundle/index-DTcHjAHp.js +0 -505
  100. package/dist/bundle/index-DnIkxb0L.js +0 -1025
  101. package/dist/bundle/index-Ww3TAo6_.js +0 -71
  102. package/dist/bundle/index-g8iXgW0W.js +0 -651
  103. package/dist/bundle/long-B-FASCSo.js +0 -2387
  104. package/dist/bundle/remoteFile-BuaqFGWk.js +0 -94
@@ -1,651 +0,0 @@
1
- import { A as J, L as K } from "./index-CCJIjehY.js";
2
- import { b as Q } from "./index-BftNdA0O.js";
3
- import { L as R } from "./__vite-browser-external-C--ziKoh.js";
4
- import { R as F } from "./remoteFile-BuaqFGWk.js";
5
- import { u as $, L as H, a as Z } from "./long-B-FASCSo.js";
6
- function j(o) {
7
- if (o.greaterThan(Number.MAX_SAFE_INTEGER) || o.lessThan(Number.MIN_SAFE_INTEGER))
8
- throw new Error("integer overflow");
9
- return o.toNumber();
10
- }
11
- class ee extends Error {
12
- }
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- function _(o) {
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- if (o && o.aborted) {
15
- if (typeof DOMException < "u")
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- throw new DOMException("aborted", "AbortError");
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- {
18
- const e = new ee("aborted");
19
- throw e.code = "ERR_ABORTED", e;
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- }
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- }
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- }
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- function te(o, e) {
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- return e.minv.blockPosition - o.maxv.blockPosition < 65e3 && e.maxv.blockPosition - o.minv.blockPosition < 5e6;
25
- }
26
- function X(o, e) {
27
- const t = [];
28
- let n = null;
29
- return o.length === 0 ? o : (o.sort(function(i, s) {
30
- const a = i.minv.blockPosition - s.minv.blockPosition;
31
- return a !== 0 ? a : i.minv.dataPosition - s.minv.dataPosition;
32
- }), o.forEach((i) => {
33
- (!e || i.maxv.compareTo(e) > 0) && (n === null ? (t.push(i), n = i) : te(n, i) ? i.maxv.compareTo(n.maxv) > 0 && (n.maxv = i.maxv) : (t.push(i), n = i));
34
- }), t);
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- }
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- class V {
37
- constructor(e, t) {
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- this.blockPosition = e, this.dataPosition = t;
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- }
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- toString() {
41
- return `${this.blockPosition}:${this.dataPosition}`;
42
- }
43
- compareTo(e) {
44
- return this.blockPosition - e.blockPosition || this.dataPosition - e.dataPosition;
45
- }
46
- }
47
- function T(o, e = 0, t = !1) {
48
- if (t)
49
- throw new Error("big-endian virtual file offsets not implemented");
50
- return new V(o[e + 7] * 1099511627776 + o[e + 6] * 4294967296 + o[e + 5] * 16777216 + o[e + 4] * 65536 + o[e + 3] * 256 + o[e + 2], o[e + 1] << 8 | o[e]);
51
- }
52
- class D {
53
- constructor(e, t, n, i = void 0) {
54
- this.minv = e, this.maxv = t, this.bin = n, this._fetchedSize = i;
55
- }
56
- toUniqueString() {
57
- return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
58
- }
59
- toString() {
60
- return this.toUniqueString();
61
- }
62
- compareTo(e) {
63
- return this.minv.compareTo(e.minv) || this.maxv.compareTo(e.maxv) || this.bin - e.bin;
64
- }
65
- fetchedSize() {
66
- return this._fetchedSize !== void 0 ? this._fetchedSize : this.maxv.blockPosition + 65536 - this.minv.blockPosition;
67
- }
68
- }
69
- class W {
70
- constructor({ filehandle: e, renameRefSeqs: t = (n) => n }) {
71
- this.filehandle = e, this.renameRefSeq = t;
72
- }
73
- async getMetadata(e = {}) {
74
- const { indices: t, ...n } = await this.parse(e);
75
- return n;
76
- }
77
- _findFirstData(e, t) {
78
- return e ? e.compareTo(t) > 0 ? t : e : t;
79
- }
80
- async parse(e = {}) {
81
- return this.parseP || (this.parseP = this._parse(e).catch((t) => {
82
- throw this.parseP = void 0, t;
83
- })), this.parseP;
84
- }
85
- async hasRefSeq(e, t = {}) {
86
- var n;
87
- return !!(!((n = (await this.parse(t)).indices[e]) === null || n === void 0) && n.binIndex);
88
- }
89
- }
90
- const ne = 21578324, U = 14;
91
- function ie(o, e) {
92
- return o += 1, e -= 1, [
93
- [0, 0],
94
- [1 + (o >> 26), 1 + (e >> 26)],
95
- [9 + (o >> 23), 9 + (e >> 23)],
96
- [73 + (o >> 20), 73 + (e >> 20)],
97
- [585 + (o >> 17), 585 + (e >> 17)],
98
- [4681 + (o >> 14), 4681 + (e >> 14)]
99
- ];
100
- }
101
- class y extends W {
102
- async lineCount(e, t = {}) {
103
- const n = await this.parse(t), i = n.refNameToId[e];
104
- if (i === void 0 || !n.indices[i])
105
- return -1;
106
- const { stats: a } = n.indices[i];
107
- return a ? a.lineCount : -1;
108
- }
109
- // fetch and parse the index
110
- async _parse(e = {}) {
111
- const t = await this.filehandle.readFile(e), n = await $(t);
112
- if (_(e.signal), n.readUInt32LE(0) !== ne)
113
- throw new Error("Not a TBI file");
114
- const i = n.readInt32LE(4), s = n.readInt32LE(8), a = s & 65536 ? "zero-based-half-open" : "1-based-closed", f = {
115
- 0: "generic",
116
- 1: "SAM",
117
- 2: "VCF"
118
- }[s & 15];
119
- if (!f)
120
- throw new Error(`invalid Tabix preset format flags ${s}`);
121
- const d = {
122
- ref: n.readInt32LE(12),
123
- start: n.readInt32LE(16),
124
- end: n.readInt32LE(20)
125
- }, u = n.readInt32LE(24), h = 5, c = ((1 << (h + 1) * 3) - 1) / 7, b = 2 ** (14 + h * 3), I = u ? String.fromCharCode(u) : null, m = n.readInt32LE(28), w = n.readInt32LE(32), { refNameToId: x, refIdToName: p } = this._parseNameBytes(n.slice(36, 36 + w));
126
- let l = 36 + w, g;
127
- return {
128
- indices: new Array(i).fill(0).map(() => {
129
- const E = n.readInt32LE(l);
130
- l += 4;
131
- const v = {};
132
- let N;
133
- for (let C = 0; C < E; C += 1) {
134
- const A = n.readUInt32LE(l);
135
- if (l += 4, A > c + 1)
136
- throw new Error("tabix index contains too many bins, please use a CSI index");
137
- if (A === c + 1) {
138
- const k = n.readInt32LE(l);
139
- l += 4, k === 2 && (N = this.parsePseudoBin(n, l)), l += 16 * k;
140
- } else {
141
- const k = n.readInt32LE(l);
142
- l += 4;
143
- const O = new Array(k);
144
- for (let M = 0; M < k; M += 1) {
145
- const q = T(n, l), Y = T(n, l + 8);
146
- l += 16, g = this._findFirstData(g, q), O[M] = new D(q, Y, A);
147
- }
148
- v[A] = O;
149
- }
150
- }
151
- const B = n.readInt32LE(l);
152
- l += 4;
153
- const L = new Array(B);
154
- for (let C = 0; C < B; C += 1)
155
- L[C] = T(n, l), l += 8, g = this._findFirstData(g, L[C]);
156
- return { binIndex: v, linearIndex: L, stats: N };
157
- }),
158
- metaChar: I,
159
- maxBinNumber: c,
160
- maxRefLength: b,
161
- skipLines: m,
162
- firstDataLine: g,
163
- columnNumbers: d,
164
- coordinateType: a,
165
- format: f,
166
- refIdToName: p,
167
- refNameToId: x,
168
- maxBlockSize: 65536
169
- };
170
- }
171
- parsePseudoBin(e, t) {
172
- return { lineCount: j(H.fromBytesLE(e.slice(t + 16, t + 24), !0)) };
173
- }
174
- _parseNameBytes(e) {
175
- let t = 0, n = 0;
176
- const i = [], s = {};
177
- for (let a = 0; a < e.length; a += 1)
178
- if (!e[a]) {
179
- if (n < a) {
180
- let r = e.toString("utf8", n, a);
181
- r = this.renameRefSeq(r), i[t] = r, s[r] = t;
182
- }
183
- n = a + 1, t += 1;
184
- }
185
- return { refNameToId: s, refIdToName: i };
186
- }
187
- async blocksForRange(e, t, n, i = {}) {
188
- t < 0 && (t = 0);
189
- const s = await this.parse(i), a = s.refNameToId[e];
190
- if (a === void 0)
191
- return [];
192
- const r = s.indices[a];
193
- if (!r)
194
- return [];
195
- (r.linearIndex.length ? r.linearIndex[t >> U >= r.linearIndex.length ? r.linearIndex.length - 1 : t >> U] : new V(0, 0)) || console.warn("querying outside of possible tabix range");
196
- const d = ie(t, n), u = [];
197
- for (const [m, w] of d)
198
- for (let x = m; x <= w; x++)
199
- if (r.binIndex[x])
200
- for (const p of r.binIndex[x])
201
- u.push(new D(p.minv, p.maxv, x));
202
- const h = r.linearIndex.length;
203
- let c = null;
204
- const b = Math.min(t >> 14, h - 1), I = Math.min(n >> 14, h - 1);
205
- for (let m = b; m <= I; ++m) {
206
- const w = r.linearIndex[m];
207
- w && (!c || w.compareTo(c) < 0) && (c = w);
208
- }
209
- return X(u, c);
210
- }
211
- }
212
- const re = 21582659, se = 38359875;
213
- function ae(o, e) {
214
- return o * 2 ** e;
215
- }
216
- function G(o, e) {
217
- return Math.floor(o / 2 ** e);
218
- }
219
- class z extends W {
220
- constructor(e) {
221
- super(e), this.maxBinNumber = 0, this.depth = 0, this.minShift = 0;
222
- }
223
- async lineCount(e, t = {}) {
224
- const n = await this.parse(t), i = n.refNameToId[e];
225
- if (i === void 0 || !n.indices[i])
226
- return -1;
227
- const { stats: a } = n.indices[i];
228
- return a ? a.lineCount : -1;
229
- }
230
- indexCov() {
231
- throw new Error("CSI indexes do not support indexcov");
232
- }
233
- parseAuxData(e, t) {
234
- const n = e.readInt32LE(t), i = n & 65536 ? "zero-based-half-open" : "1-based-closed", s = { 0: "generic", 1: "SAM", 2: "VCF" }[n & 15];
235
- if (!s)
236
- throw new Error(`invalid Tabix preset format flags ${n}`);
237
- const a = {
238
- ref: e.readInt32LE(t + 4),
239
- start: e.readInt32LE(t + 8),
240
- end: e.readInt32LE(t + 12)
241
- }, r = e.readInt32LE(t + 16), f = r ? String.fromCharCode(r) : null, d = e.readInt32LE(t + 20), u = e.readInt32LE(t + 24), { refIdToName: h, refNameToId: c } = this._parseNameBytes(e.slice(t + 28, t + 28 + u));
242
- return {
243
- refIdToName: h,
244
- refNameToId: c,
245
- skipLines: d,
246
- metaChar: f,
247
- columnNumbers: a,
248
- format: s,
249
- coordinateType: i
250
- };
251
- }
252
- _parseNameBytes(e) {
253
- let t = 0, n = 0;
254
- const i = [], s = {};
255
- for (let a = 0; a < e.length; a += 1)
256
- if (!e[a]) {
257
- if (n < a) {
258
- let r = e.toString("utf8", n, a);
259
- r = this.renameRefSeq(r), i[t] = r, s[r] = t;
260
- }
261
- n = a + 1, t += 1;
262
- }
263
- return { refNameToId: s, refIdToName: i };
264
- }
265
- // fetch and parse the index
266
- async _parse(e = {}) {
267
- const t = await $(await this.filehandle.readFile(e));
268
- let n;
269
- if (t.readUInt32LE(0) === re)
270
- n = 1;
271
- else if (t.readUInt32LE(0) === se)
272
- n = 2;
273
- else
274
- throw new Error("Not a CSI file");
275
- this.minShift = t.readInt32LE(4), this.depth = t.readInt32LE(8), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
276
- const i = 2 ** (this.minShift + this.depth * 3), s = t.readInt32LE(12), a = s && s >= 30 ? this.parseAuxData(t, 16) : {
277
- refIdToName: [],
278
- refNameToId: {},
279
- metaChar: null,
280
- columnNumbers: { ref: 0, start: 1, end: 2 },
281
- coordinateType: "zero-based-half-open",
282
- format: "generic"
283
- }, r = t.readInt32LE(16 + s);
284
- let f, d = 16 + s + 4;
285
- const u = new Array(r).fill(0).map(() => {
286
- const h = t.readInt32LE(d);
287
- d += 4;
288
- const c = {};
289
- let b;
290
- for (let I = 0; I < h; I += 1) {
291
- const m = t.readUInt32LE(d);
292
- if (m > this.maxBinNumber)
293
- b = this.parsePseudoBin(t, d + 4), d += 48;
294
- else {
295
- const w = T(t, d + 4);
296
- f = this._findFirstData(f, w);
297
- const x = t.readInt32LE(d + 12);
298
- d += 16;
299
- const p = new Array(x);
300
- for (let l = 0; l < x; l += 1) {
301
- const g = T(t, d), P = T(t, d + 8);
302
- d += 16, p[l] = new D(g, P, m);
303
- }
304
- c[m] = p;
305
- }
306
- }
307
- return { binIndex: c, stats: b };
308
- });
309
- return {
310
- ...a,
311
- csi: !0,
312
- refCount: r,
313
- maxBlockSize: 65536,
314
- firstDataLine: f,
315
- csiVersion: n,
316
- indices: u,
317
- depth: this.depth,
318
- maxBinNumber: this.maxBinNumber,
319
- maxRefLength: i
320
- };
321
- }
322
- parsePseudoBin(e, t) {
323
- return { lineCount: j(H.fromBytesLE(e.slice(t + 28, t + 36), !0)) };
324
- }
325
- async blocksForRange(e, t, n, i = {}) {
326
- t < 0 && (t = 0);
327
- const s = await this.parse(i), a = s.refNameToId[e];
328
- if (a === void 0)
329
- return [];
330
- const r = s.indices[a];
331
- if (!r)
332
- return [];
333
- const f = this.reg2bins(t, n), d = [];
334
- for (const [u, h] of f)
335
- for (let c = u; c <= h; c++)
336
- if (r.binIndex[c])
337
- for (const b of r.binIndex[c])
338
- d.push(new D(b.minv, b.maxv, c));
339
- return X(d, new V(0, 0));
340
- }
341
- /**
342
- * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
343
- */
344
- reg2bins(e, t) {
345
- e -= 1, e < 1 && (e = 1), t > 2 ** 50 && (t = 2 ** 34), t -= 1;
346
- let n = 0, i = 0, s = this.minShift + this.depth * 3;
347
- const a = [];
348
- for (; n <= this.depth; s -= 3, i += ae(1, n * 3), n += 1) {
349
- const r = i + G(e, s), f = i + G(t, s);
350
- if (f - r + a.length > this.maxBinNumber)
351
- throw new Error(`query ${e}-${t} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);
352
- a.push([r, f]);
353
- }
354
- return a;
355
- }
356
- }
357
- function oe(o) {
358
- return /^[\u0000-\u007F]*$/.test(o);
359
- }
360
- const S = typeof TextDecoder < "u" ? new TextDecoder("utf8") : void 0;
361
- class ue {
362
- /**
363
- * @param {object} args
364
- *
365
- * @param {string} [args.path]
366
- *
367
- * @param {filehandle} [args.filehandle]
368
- *
369
- * @param {string} [args.tbiPath]
370
- *
371
- * @param {filehandle} [args.tbiFilehandle]
372
- *
373
- * @param {string} [args.csiPath]
374
- *
375
- * @param {filehandle} [args.csiFilehandle]
376
- *
377
- * @param {url} [args.url]
378
- *
379
- * @param {csiUrl} [args.csiUrl]
380
- *
381
- * @param {tbiUrl} [args.tbiUrl]
382
- *
383
- * @param {function} [args.renameRefSeqs] optional function with sig `string
384
- * => string` to transform reference sequence names for the purpose of
385
- * indexing and querying. note that the data that is returned is not altered,
386
- * just the names of the reference sequences that are used for querying.
387
- */
388
- constructor({ path: e, filehandle: t, url: n, tbiPath: i, tbiUrl: s, tbiFilehandle: a, csiPath: r, csiUrl: f, csiFilehandle: d, renameRefSeqs: u = (c) => c, chunkCacheSize: h = 5 * 2 ** 20 }) {
389
- if (t)
390
- this.filehandle = t;
391
- else if (e)
392
- this.filehandle = new R(e);
393
- else if (n)
394
- this.filehandle = new F(n);
395
- else
396
- throw new TypeError("must provide either filehandle or path");
397
- if (a)
398
- this.index = new y({
399
- filehandle: a,
400
- renameRefSeqs: u
401
- });
402
- else if (d)
403
- this.index = new z({
404
- filehandle: d,
405
- renameRefSeqs: u
406
- });
407
- else if (i)
408
- this.index = new y({
409
- filehandle: new R(i),
410
- renameRefSeqs: u
411
- });
412
- else if (r)
413
- this.index = new z({
414
- filehandle: new R(r),
415
- renameRefSeqs: u
416
- });
417
- else if (e)
418
- this.index = new y({
419
- filehandle: new R(`${e}.tbi`),
420
- renameRefSeqs: u
421
- });
422
- else if (f)
423
- this.index = new z({
424
- filehandle: new F(f)
425
- });
426
- else if (s)
427
- this.index = new y({
428
- filehandle: new F(s)
429
- });
430
- else if (n)
431
- this.index = new y({
432
- filehandle: new F(`${n}.tbi`)
433
- });
434
- else
435
- throw new TypeError("must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl");
436
- this.renameRefSeq = u, this.chunkCache = new J({
437
- cache: new K({ maxSize: Math.floor(h / 65536) }),
438
- fill: (c, b) => this.readChunk(c, { signal: b })
439
- });
440
- }
441
- /**
442
- * @param refName name of the reference sequence
443
- *
444
- * @param start start of the region (in 0-based half-open coordinates)
445
- *
446
- * @param end end of the region (in 0-based half-open coordinates)
447
- *
448
- * @param opts callback called for each line in the region. can also pass a
449
- * object param containing obj.lineCallback, obj.signal, etc
450
- *
451
- * @returns promise that is resolved when the whole read is finished,
452
- * rejected on error
453
- */
454
- async getLines(e, t, n, i) {
455
- var s, a;
456
- let r, f = {}, d;
457
- typeof i == "function" ? d = i : (f = i, d = i.lineCallback, r = i.signal);
458
- const u = await this.index.getMetadata(f);
459
- _(r);
460
- const h = t ?? 0, c = n ?? u.maxRefLength;
461
- if (!(h <= c))
462
- throw new TypeError("invalid start and end coordinates. start must be less than or equal to end");
463
- if (h === c)
464
- return;
465
- const b = await this.index.blocksForRange(e, h, c, f);
466
- _(r);
467
- for (const I of b) {
468
- const { buffer: m, cpositions: w, dpositions: x } = await this.chunkCache.get(I.toString(), I, r);
469
- _(r);
470
- let p = 0, l = 0;
471
- const g = (s = S == null ? void 0 : S.decode(m)) !== null && s !== void 0 ? s : m.toString(), P = m.length < 5e8 && oe(g);
472
- for (; p < g.length; ) {
473
- let E, v;
474
- if (P) {
475
- if (v = g.indexOf(`
476
- `, p), v === -1)
477
- break;
478
- E = g.slice(p, v);
479
- } else {
480
- if (v = m.indexOf(`
481
- `, p), v === -1)
482
- break;
483
- const L = m.slice(p, v);
484
- E = (a = S == null ? void 0 : S.decode(L)) !== null && a !== void 0 ? a : L.toString();
485
- }
486
- if (x) {
487
- for (; p + I.minv.dataPosition >= x[l++]; )
488
- ;
489
- l--;
490
- }
491
- const { startCoordinate: N, overlaps: B } = this.checkLine(u, e, h, c, E);
492
- if (B)
493
- d(
494
- E,
495
- // cpositions[pos] refers to actual file offset of a bgzip block
496
- // boundaries
497
- //
498
- // we multiply by (1 <<8) in order to make sure each block has a
499
- // "unique" address space so that data in that block could never
500
- // overlap
501
- //
502
- // then the blockStart-dpositions is an uncompressed file offset
503
- // from that bgzip block boundary, and since the cpositions are
504
- // multiplied by (1 << 8) these uncompressed offsets get a unique
505
- // space
506
- w[l] * 256 + (p - x[l]) + I.minv.dataPosition + 1
507
- );
508
- else if (N !== void 0 && N >= c)
509
- return;
510
- p = v + 1;
511
- }
512
- }
513
- }
514
- async getMetadata(e = {}) {
515
- return this.index.getMetadata(e);
516
- }
517
- /**
518
- * get a buffer containing the "header" region of the file, which are the
519
- * bytes up to the first non-meta line
520
- */
521
- async getHeaderBuffer(e = {}) {
522
- const { firstDataLine: t, metaChar: n, maxBlockSize: i } = await this.getMetadata(e);
523
- _(e.signal);
524
- const s = ((t == null ? void 0 : t.blockPosition) || 0) + i, a = await this._readRegion(0, s, e), r = await $(a);
525
- if (n) {
526
- let f = -1;
527
- const d = 10, u = n.charCodeAt(0);
528
- for (let h = 0; h < r.length && !(h === f + 1 && r[h] !== u); h += 1)
529
- r[h] === d && (f = h);
530
- return r.subarray(0, f + 1);
531
- }
532
- return r;
533
- }
534
- /**
535
- * get a string containing the "header" region of the file, is the portion up
536
- * to the first non-meta line
537
- *
538
- * @returns {Promise} for a string
539
- */
540
- async getHeader(e = {}) {
541
- return (await this.getHeaderBuffer(e)).toString("utf8");
542
- }
543
- /**
544
- * get an array of reference sequence names, in the order in which they occur
545
- * in the file. reference sequence renaming is not applied to these names.
546
- */
547
- async getReferenceSequenceNames(e = {}) {
548
- return (await this.getMetadata(e)).refIdToName;
549
- }
550
- /**
551
- * @param {object} metadata metadata object from the parsed index, containing
552
- * columnNumbers, metaChar, and format
553
- *
554
- * @param {string} regionRefName
555
- *
556
- * @param {number} regionStart region start coordinate (0-based-half-open)
557
- *
558
- * @param {number} regionEnd region end coordinate (0-based-half-open)
559
- *
560
- * @param {array[string]} line
561
- *
562
- * @returns {object} like `{startCoordinate, overlaps}`. overlaps is boolean,
563
- * true if line is a data line that overlaps the given region
564
- */
565
- checkLine(e, t, n, i, s) {
566
- const { columnNumbers: a, metaChar: r, coordinateType: f, format: d } = e;
567
- if (r && s.startsWith(r))
568
- return { overlaps: !1 };
569
- let { ref: u, start: h, end: c } = a;
570
- u || (u = 0), h || (h = 0), c || (c = 0), d === "VCF" && (c = 8);
571
- const b = Math.max(u, h, c);
572
- let I = 1, m = 0, w = "", x = -1 / 0;
573
- const p = s.length;
574
- for (let l = 0; l < p + 1; l++)
575
- if (s[l] === " " || l === p) {
576
- if (I === u) {
577
- if (this.renameRefSeq(s.slice(m, l)) !== t)
578
- return {
579
- overlaps: !1
580
- };
581
- } else if (I === h) {
582
- if (x = parseInt(s.slice(m, l), 10), f === "1-based-closed" && (x -= 1), x >= i)
583
- return {
584
- startCoordinate: x,
585
- overlaps: !1
586
- };
587
- if ((c === 0 || c === h) && x + 1 <= n)
588
- return {
589
- startCoordinate: x,
590
- overlaps: !1
591
- };
592
- } else if (d === "VCF" && I === 4)
593
- w = s.slice(m, l);
594
- else if (I === c && (d === "VCF" ? this._getVcfEnd(x, w, s.slice(m, l)) : Number.parseInt(s.slice(m, l), 10)) <= n)
595
- return {
596
- overlaps: !1
597
- };
598
- if (m = l + 1, I += 1, I > b)
599
- break;
600
- }
601
- return {
602
- startCoordinate: x,
603
- overlaps: !0
604
- };
605
- }
606
- _getVcfEnd(e, t, n) {
607
- let i = e + t.length;
608
- const s = n.includes("SVTYPE=TRA");
609
- if (n[0] !== "." && !s) {
610
- let a = ";";
611
- for (let r = 0; r < n.length; r += 1) {
612
- if (a === ";" && n.slice(r, r + 4) === "END=") {
613
- let f = n.indexOf(";", r);
614
- f === -1 && (f = n.length), i = parseInt(n.slice(r + 4, f), 10);
615
- break;
616
- }
617
- a = n[r];
618
- }
619
- } else if (s)
620
- return e + 1;
621
- return i;
622
- }
623
- /**
624
- * return the approximate number of data lines in the given reference
625
- * sequence
626
- *
627
- * @param refSeq reference sequence name
628
- *
629
- * @returns number of data lines present on that reference sequence
630
- */
631
- async lineCount(e, t = {}) {
632
- return this.index.lineCount(e, t);
633
- }
634
- async _readRegion(e, t, n = {}) {
635
- const i = Q.Buffer.alloc(t), { bytesRead: s, buffer: a } = await this.filehandle.read(i, 0, t, e, n);
636
- return a.subarray(0, s);
637
- }
638
- /**
639
- * read and uncompress the data in a chunk (composed of one or more
640
- * contiguous bgzip blocks) of the file
641
- */
642
- async readChunk(e, t = {}) {
643
- const n = await this._readRegion(e.minv.blockPosition, e.fetchedSize(), t);
644
- return Z(n, e);
645
- }
646
- }
647
- export {
648
- z as CSI,
649
- y as TBI,
650
- ue as TabixIndexedFile
651
- };