@gmod/bam 1.1.17 → 2.0.0

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 (83) hide show
  1. package/CHANGELOG.md +65 -25
  2. package/README.md +108 -57
  3. package/dist/bai.d.ts +34 -15
  4. package/dist/bai.js +180 -273
  5. package/dist/bai.js.map +1 -1
  6. package/dist/bamFile.d.ts +33 -27
  7. package/dist/bamFile.js +353 -572
  8. package/dist/bamFile.js.map +1 -1
  9. package/dist/chunk.d.ts +4 -8
  10. package/dist/chunk.js +13 -21
  11. package/dist/chunk.js.map +1 -1
  12. package/dist/csi.d.ts +74 -10
  13. package/dist/csi.js +157 -256
  14. package/dist/csi.js.map +1 -1
  15. package/dist/errors.js +12 -57
  16. package/dist/errors.js.map +1 -1
  17. package/dist/htsget.d.ts +5 -8
  18. package/dist/htsget.js +120 -209
  19. package/dist/htsget.js.map +1 -1
  20. package/dist/index.d.ts +5 -6
  21. package/dist/index.js +11 -11
  22. package/dist/index.js.map +1 -1
  23. package/dist/indexFile.d.ts +0 -6
  24. package/dist/indexFile.js +3 -77
  25. package/dist/indexFile.js.map +1 -1
  26. package/dist/nullIndex.d.ts +7 -0
  27. package/dist/nullIndex.js +33 -0
  28. package/dist/nullIndex.js.map +1 -0
  29. package/dist/record.d.ts +2 -2
  30. package/dist/record.js +200 -193
  31. package/dist/record.js.map +1 -1
  32. package/dist/sam.js +12 -10
  33. package/dist/sam.js.map +1 -1
  34. package/dist/util.d.ts +13 -1
  35. package/dist/util.js +55 -58
  36. package/dist/util.js.map +1 -1
  37. package/dist/virtualOffset.js +13 -20
  38. package/dist/virtualOffset.js.map +1 -1
  39. package/esm/bai.d.ts +34 -15
  40. package/esm/bai.js +86 -91
  41. package/esm/bai.js.map +1 -1
  42. package/esm/bamFile.d.ts +33 -27
  43. package/esm/bamFile.js +124 -120
  44. package/esm/bamFile.js.map +1 -1
  45. package/esm/chunk.d.ts +4 -8
  46. package/esm/chunk.js +2 -8
  47. package/esm/chunk.js.map +1 -1
  48. package/esm/csi.d.ts +74 -10
  49. package/esm/csi.js +85 -93
  50. package/esm/csi.js.map +1 -1
  51. package/esm/htsget.d.ts +5 -8
  52. package/esm/htsget.js +68 -43
  53. package/esm/htsget.js.map +1 -1
  54. package/esm/index.d.ts +5 -6
  55. package/esm/index.js +5 -6
  56. package/esm/index.js.map +1 -1
  57. package/esm/indexFile.d.ts +0 -6
  58. package/esm/indexFile.js +0 -22
  59. package/esm/indexFile.js.map +1 -1
  60. package/esm/nullIndex.d.ts +7 -0
  61. package/esm/nullIndex.js +16 -0
  62. package/esm/nullIndex.js.map +1 -0
  63. package/esm/record.d.ts +2 -2
  64. package/esm/record.js +34 -24
  65. package/esm/record.js.map +1 -1
  66. package/esm/sam.js +9 -7
  67. package/esm/sam.js.map +1 -1
  68. package/esm/util.d.ts +13 -1
  69. package/esm/util.js +40 -14
  70. package/esm/util.js.map +1 -1
  71. package/package.json +19 -20
  72. package/src/bai.ts +99 -102
  73. package/src/bamFile.ts +174 -198
  74. package/src/chunk.ts +6 -20
  75. package/src/csi.ts +102 -111
  76. package/src/htsget.ts +81 -61
  77. package/src/index.ts +5 -7
  78. package/src/indexFile.ts +0 -27
  79. package/src/nullIndex.ts +18 -0
  80. package/src/record.ts +34 -24
  81. package/src/sam.ts +9 -7
  82. package/src/util.ts +54 -13
  83. package/src/declare.d.ts +0 -2
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/sam.js CHANGED
@@ -2,18 +2,20 @@
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.parseHeaderText = void 0;
4
4
  function parseHeaderText(text) {
5
- var lines = text.split(/\r?\n/);
6
- var data = [];
7
- lines.forEach(function (line) {
8
- var _a = line.split(/\t/), tag = _a[0], fields = _a.slice(1);
9
- var parsedFields = fields.map(function (f) {
10
- var _a = f.split(':', 2), fieldTag = _a[0], value = _a[1];
11
- return { tag: fieldTag, value: value };
12
- });
5
+ const lines = text.split(/\r?\n/);
6
+ const data = [];
7
+ for (const line of lines) {
8
+ const [tag, ...fields] = line.split(/\t/);
13
9
  if (tag) {
14
- data.push({ tag: tag.substr(1), data: parsedFields });
10
+ data.push({
11
+ tag: tag.slice(1),
12
+ data: fields.map(f => {
13
+ const [fieldTag, value] = f.split(':', 2);
14
+ return { tag: fieldTag, value };
15
+ }),
16
+ });
15
17
  }
16
- });
18
+ }
17
19
  return data;
18
20
  }
19
21
  exports.parseHeaderText = parseHeaderText;
package/dist/sam.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;;AAAA,SAAgB,eAAe,CAAC,IAAY;IAC1C,IAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,IAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,CAAC,OAAO,CAAC,UAAA,IAAI;QACV,IAAA,KAAmB,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAlC,GAAG,QAAA,EAAK,MAAM,cAAoB,CAAA;QACzC,IAAM,YAAY,GAAG,MAAM,CAAC,GAAG,CAAC,UAAA,CAAC;YACzB,IAAA,KAAoB,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC,EAAlC,QAAQ,QAAA,EAAE,KAAK,QAAmB,CAAA;YACzC,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,OAAA,EAAE,CAAA;QACjC,CAAC,CAAC,CAAA;QACF,IAAI,GAAG,EAAE;YACP,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,CAAA;SACtD;IACH,CAAC,CAAC,CAAA;IACF,OAAO,IAAI,CAAA;AACb,CAAC;AAdD,0CAcC"}
1
+ {"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;;AAAA,SAAgB,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;QACxB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE;YACP,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,QAAQ,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;oBACzC,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;gBACjC,CAAC,CAAC;aACH,CAAC,CAAA;SACH;KACF;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAhBD,0CAgBC"}
package/dist/util.d.ts CHANGED
@@ -1,3 +1,5 @@
1
+ /// <reference types="node" />
2
+ import Long from 'long';
1
3
  import Chunk from './chunk';
2
4
  import VirtualOffset from './virtualOffset';
3
5
  export declare function timeout(ms: number): Promise<unknown>;
@@ -32,4 +34,14 @@ export interface BaseOpts {
32
34
  signal?: AbortSignal;
33
35
  }
34
36
  export declare function makeOpts(obj?: AbortSignal | BaseOpts): BaseOpts;
35
- export declare function optimizeChunks(chunks: Chunk[], lowest: VirtualOffset): Chunk[];
37
+ export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
38
+ export declare function parsePseudoBin(bytes: Buffer, offset: number): {
39
+ lineCount: number;
40
+ };
41
+ export declare function findFirstData(firstDataLine: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
42
+ export declare function parseNameBytes(namesBytes: Buffer, renameRefSeq?: (arg: string) => string): {
43
+ refNameToId: {
44
+ [key: string]: number;
45
+ };
46
+ refIdToName: string[];
47
+ };
package/dist/util.js CHANGED
@@ -8,37 +8,14 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
8
8
  step((generator = generator.apply(thisArg, _arguments || [])).next());
9
9
  });
10
10
  };
11
- var __generator = (this && this.__generator) || function (thisArg, body) {
12
- var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
13
- return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
14
- function verb(n) { return function (v) { return step([n, v]); }; }
15
- function step(op) {
16
- if (f) throw new TypeError("Generator is already executing.");
17
- while (_) try {
18
- if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
19
- if (y = 0, t) op = [op[0] & 2, t.value];
20
- switch (op[0]) {
21
- case 0: case 1: t = op; break;
22
- case 4: _.label++; return { value: op[1], done: false };
23
- case 5: _.label++; y = op[1]; op = [0]; continue;
24
- case 7: op = _.ops.pop(); _.trys.pop(); continue;
25
- default:
26
- if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
27
- if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
28
- if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
29
- if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
30
- if (t[2]) _.ops.pop();
31
- _.trys.pop(); continue;
32
- }
33
- op = body.call(thisArg, _);
34
- } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
35
- if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
36
- }
11
+ var __importDefault = (this && this.__importDefault) || function (mod) {
12
+ return (mod && mod.__esModule) ? mod : { "default": mod };
37
13
  };
38
14
  Object.defineProperty(exports, "__esModule", { value: true });
39
- exports.optimizeChunks = exports.makeOpts = exports.canMergeBlocks = exports.abortBreakPoint = exports.checkAbortSignal = exports.longToNumber = exports.timeout = void 0;
15
+ exports.parseNameBytes = exports.findFirstData = exports.parsePseudoBin = exports.optimizeChunks = exports.makeOpts = exports.canMergeBlocks = exports.abortBreakPoint = exports.checkAbortSignal = exports.longToNumber = exports.timeout = void 0;
16
+ const long_1 = __importDefault(require("long"));
40
17
  function timeout(ms) {
41
- return new Promise(function (resolve) { return setTimeout(resolve, ms); });
18
+ return new Promise(resolve => setTimeout(resolve, ms));
42
19
  }
43
20
  exports.timeout = timeout;
44
21
  function longToNumber(long) {
@@ -66,15 +43,15 @@ function checkAbortSignal(signal) {
66
43
  }
67
44
  if (signal.aborted) {
68
45
  // console.log('bam aborted!')
69
- if (typeof DOMException !== 'undefined') {
70
- throw new DOMException('aborted', 'AbortError');
71
- }
72
- else {
73
- var e = new Error('aborted');
46
+ if (typeof DOMException === 'undefined') {
47
+ const e = new Error('aborted');
74
48
  //@ts-ignore
75
49
  e.code = 'ERR_ABORTED';
76
50
  throw e;
77
51
  }
52
+ else {
53
+ throw new DOMException('aborted', 'AbortError');
54
+ }
78
55
  }
79
56
  }
80
57
  exports.checkAbortSignal = checkAbortSignal;
@@ -85,16 +62,9 @@ exports.checkAbortSignal = checkAbortSignal;
85
62
  * @param {AbortSignal} signal
86
63
  */
87
64
  function abortBreakPoint(signal) {
88
- return __awaiter(this, void 0, void 0, function () {
89
- return __generator(this, function (_a) {
90
- switch (_a.label) {
91
- case 0: return [4 /*yield*/, Promise.resolve()];
92
- case 1:
93
- _a.sent();
94
- checkAbortSignal(signal);
95
- return [2 /*return*/];
96
- }
97
- });
65
+ return __awaiter(this, void 0, void 0, function* () {
66
+ yield Promise.resolve();
67
+ checkAbortSignal(signal);
98
68
  });
99
69
  }
100
70
  exports.abortBreakPoint = abortBreakPoint;
@@ -103,29 +73,23 @@ function canMergeBlocks(chunk1, chunk2) {
103
73
  chunk2.maxv.blockPosition - chunk1.minv.blockPosition < 5000000);
104
74
  }
105
75
  exports.canMergeBlocks = canMergeBlocks;
106
- function makeOpts(obj) {
107
- if (obj === void 0) { obj = {}; }
76
+ function makeOpts(obj = {}) {
108
77
  return 'aborted' in obj ? { signal: obj } : obj;
109
78
  }
110
79
  exports.makeOpts = makeOpts;
111
80
  function optimizeChunks(chunks, lowest) {
112
- var mergedChunks = [];
113
- var lastChunk = null;
81
+ const mergedChunks = [];
82
+ let lastChunk;
114
83
  if (chunks.length === 0) {
115
84
  return chunks;
116
85
  }
117
- chunks.sort(function (c0, c1) {
118
- var dif = c0.minv.blockPosition - c1.minv.blockPosition;
119
- if (dif !== 0) {
120
- return dif;
121
- }
122
- else {
123
- return c0.minv.dataPosition - c1.minv.dataPosition;
124
- }
86
+ chunks.sort((c0, c1) => {
87
+ const dif = c0.minv.blockPosition - c1.minv.blockPosition;
88
+ return dif === 0 ? c0.minv.dataPosition - c1.minv.dataPosition : dif;
125
89
  });
126
- chunks.forEach(function (chunk) {
90
+ for (const chunk of chunks) {
127
91
  if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
128
- if (lastChunk === null) {
92
+ if (lastChunk === undefined) {
129
93
  mergedChunks.push(chunk);
130
94
  lastChunk = chunk;
131
95
  }
@@ -141,8 +105,41 @@ function optimizeChunks(chunks, lowest) {
141
105
  }
142
106
  }
143
107
  }
144
- });
108
+ }
145
109
  return mergedChunks;
146
110
  }
147
111
  exports.optimizeChunks = optimizeChunks;
112
+ function parsePseudoBin(bytes, offset) {
113
+ const lineCount = longToNumber(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset, offset + 8), true));
114
+ return { lineCount };
115
+ }
116
+ exports.parsePseudoBin = parsePseudoBin;
117
+ function findFirstData(firstDataLine, virtualOffset) {
118
+ return firstDataLine
119
+ ? firstDataLine.compareTo(virtualOffset) > 0
120
+ ? virtualOffset
121
+ : firstDataLine
122
+ : virtualOffset;
123
+ }
124
+ exports.findFirstData = findFirstData;
125
+ function parseNameBytes(namesBytes, renameRefSeq = s => s) {
126
+ let currRefId = 0;
127
+ let currNameStart = 0;
128
+ const refIdToName = [];
129
+ const refNameToId = {};
130
+ for (let i = 0; i < namesBytes.length; i += 1) {
131
+ if (!namesBytes[i]) {
132
+ if (currNameStart < i) {
133
+ let refName = namesBytes.toString('utf8', currNameStart, i);
134
+ refName = renameRefSeq(refName);
135
+ refIdToName[currRefId] = refName;
136
+ refNameToId[refName] = currRefId;
137
+ }
138
+ currNameStart = i + 1;
139
+ currRefId += 1;
140
+ }
141
+ }
142
+ return { refNameToId, refIdToName };
143
+ }
144
+ exports.parseNameBytes = parseNameBytes;
148
145
  //# sourceMappingURL=util.js.map
package/dist/util.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;AAAA,gDAAuB;AAIvB,SAAgB,OAAO,CAAC,EAAU;IAChC,OAAO,IAAI,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAFD,0BAEC;AAED,SAAgB,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC;QACA,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;KACpC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AARD,oCAQC;AAED;;;;;;;;;;GAUG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE;QACX,OAAM;KACP;IAED,IAAI,MAAM,CAAC,OAAO,EAAE;QAClB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE;YACvC,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;YAC9B,YAAY;YACZ,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;SACR;aAAM;YACL,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;SAChD;KACF;AACH,CAAC;AAhBD,4CAgBC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;QACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;QACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAC1B,CAAC;CAAA;AAHD,0CAGC;AAED,SAAgB,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AALD,wCAKC;AAaD,SAAgB,QAAQ,CAAC,MAA8B,EAAE;IACvD,OAAO,SAAS,IAAI,GAAG,CAAC,CAAC,CAAE,EAAE,MAAM,EAAE,GAAG,EAAe,CAAC,CAAC,CAAE,GAAgB,CAAA;AAC7E,CAAC;AAFD,4BAEC;AAED,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAA4B,CAAA;IAEhC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;QACvB,OAAO,MAAM,CAAA;KACd;IAED,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACrB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE;QAC1B,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE;YAC/C,IAAI,SAAS,KAAK,SAAS,EAAE;gBAC3B,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;aAClB;iBAAM;gBACL,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE;oBACpC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE;wBAC5C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;qBAC5B;iBACF;qBAAM;oBACL,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;iBAClB;aACF;SACF;KACF;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAhCD,wCAgCC;AAED,SAAgB,cAAc,CAAC,KAAa,EAAE,MAAc;IAC1D,MAAM,SAAS,GAAG,YAAY,CAC5B,cAAI,CAAC,WAAW,CACd,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,GAAG,CAAC,CAAC,EACrD,IAAI,CACL,CACF,CAAA;IACD,OAAO,EAAE,SAAS,EAAE,CAAA;AACtB,CAAC;AARD,wCAQC;AAED,SAAgB,aAAa,CAC3B,aAAwC,EACxC,aAA4B;IAE5B,OAAO,aAAa;QAClB,CAAC,CAAC,aAAa,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;YAC1C,CAAC,CAAC,aAAa;YACf,CAAC,CAAC,aAAa;QACjB,CAAC,CAAC,aAAa,CAAA;AACnB,CAAC;AATD,sCASC;AAED,SAAgB,cAAc,CAC5B,UAAkB,EAClB,eAAwC,CAAC,CAAC,EAAE,CAAC,CAAC;IAE9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,MAAM,WAAW,GAA8B,EAAE,CAAA;IACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;YAClB,IAAI,aAAa,GAAG,CAAC,EAAE;gBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;gBAC3D,OAAO,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;gBAC/B,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;gBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;aACjC;YACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;YACrB,SAAS,IAAI,CAAC,CAAA;SACf;KACF;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AArBD,wCAqBC"}
package/dist/virtualOffset.js CHANGED
@@ -1,24 +1,20 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.fromBytes = void 0;
4
- var VirtualOffset = /** @class */ (function () {
5
- function VirtualOffset(blockPosition, dataPosition) {
4
+ class VirtualOffset {
5
+ constructor(blockPosition, dataPosition) {
6
6
  this.blockPosition = blockPosition; // < offset of the compressed data block
7
7
  this.dataPosition = dataPosition; // < offset into the uncompressed data
8
8
  }
9
- VirtualOffset.prototype.toString = function () {
10
- return "".concat(this.blockPosition, ":").concat(this.dataPosition);
11
- };
12
- VirtualOffset.prototype.compareTo = function (b) {
9
+ toString() {
10
+ return `${this.blockPosition}:${this.dataPosition}`;
11
+ }
12
+ compareTo(b) {
13
13
  return (this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition);
14
- };
15
- VirtualOffset.min = function () {
16
- var args = [];
17
- for (var _i = 0; _i < arguments.length; _i++) {
18
- args[_i] = arguments[_i];
19
- }
20
- var min;
21
- var i = 0;
14
+ }
15
+ static min(...args) {
16
+ let min;
17
+ let i = 0;
22
18
  for (; !min; i += 1) {
23
19
  min = args[i];
24
20
  }
@@ -28,13 +24,10 @@ var VirtualOffset = /** @class */ (function () {
28
24
  }
29
25
  }
30
26
  return min;
31
- };
32
- return VirtualOffset;
33
- }());
27
+ }
28
+ }
34
29
  exports.default = VirtualOffset;
35
- function fromBytes(bytes, offset, bigendian) {
36
- if (offset === void 0) { offset = 0; }
37
- if (bigendian === void 0) { bigendian = false; }
30
+ function fromBytes(bytes, offset = 0, bigendian = false) {
38
31
  if (bigendian) {
39
32
  throw new Error('big-endian virtual file offsets not implemented');
40
33
  }
package/dist/virtualOffset.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AAAA;IAGE,uBAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,gCAAQ,GAAR;QACE,OAAO,UAAG,IAAI,CAAC,aAAa,cAAI,IAAI,CAAC,YAAY,CAAE,CAAA;IACrD,CAAC;IAED,iCAAS,GAAT,UAAU,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAEM,iBAAG,GAAV;QAAW,cAAwB;aAAxB,UAAwB,EAAxB,qBAAwB,EAAxB,IAAwB;YAAxB,yBAAwB;;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE;YACnB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;SACd;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC9B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE;gBAC9B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;aACd;SACF;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IACH,oBAAC;AAAD,CAAC,AA/BD,IA+BC;;AACD,SAAgB,SAAS,CAAC,KAAa,EAAE,MAAU,EAAE,SAAiB;IAA7B,uBAAA,EAAA,UAAU;IAAE,0BAAA,EAAA,iBAAiB;IACpE,IAAI,SAAS,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;KACnE;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC;AAdD,8BAcC"}
1
+ {"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AAAA,MAAqB,aAAa;IAGhC,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE;YACnB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;SACd;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC9B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE;gBAC9B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;aACd;SACF;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AA/BD,gCA+BC;AACD,SAAgB,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;KACnE;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC;AAdD,8BAcC"}
package/esm/bai.d.ts CHANGED
@@ -1,26 +1,45 @@
1
- /// <reference types="node" />
1
+ import VirtualOffset from './virtualOffset';
2
2
  import Chunk from './chunk';
3
- import IndexFile from './indexFile';
4
3
  import { BaseOpts } from './util';
4
+ import IndexFile from './indexFile';
5
5
  export default class BAI extends IndexFile {
6
- baiP?: Promise<Buffer>;
7
- parsePseudoBin(bytes: Buffer, offset: number): {
8
- lineCount: number;
9
- };
10
- lineCount(refId: number, opts?: BaseOpts): Promise<any>;
11
- fetchBai(opts?: BaseOpts): Promise<Buffer>;
12
- _parse(): Promise<{
13
- [key: string]: any;
6
+ setupP?: ReturnType<BAI['_parse']>;
7
+ lineCount(refId: number, opts?: BaseOpts): Promise<number>;
8
+ _parse(opts?: BaseOpts): Promise<{
9
+ bai: boolean;
10
+ firstDataLine: VirtualOffset | undefined;
11
+ maxBlockSize: number;
12
+ indices: {
13
+ binIndex: {
14
+ [key: string]: Chunk[];
15
+ };
16
+ linearIndex: VirtualOffset[];
17
+ stats?: {
18
+ lineCount: number;
19
+ } | undefined;
20
+ }[];
21
+ refCount: number;
14
22
  }>;
15
23
  indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<{
16
24
  start: number;
17
25
  end: number;
18
26
  score: number;
19
27
  }[]>;
20
- /**
21
- * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
22
- * @returns {Array[number]}
23
- */
24
- reg2bins(beg: number, end: number): number[][];
25
28
  blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
29
+ parse(opts?: BaseOpts): Promise<{
30
+ bai: boolean;
31
+ firstDataLine: VirtualOffset | undefined;
32
+ maxBlockSize: number;
33
+ indices: {
34
+ binIndex: {
35
+ [key: string]: Chunk[];
36
+ };
37
+ linearIndex: VirtualOffset[];
38
+ stats?: {
39
+ lineCount: number;
40
+ } | undefined;
41
+ }[];
42
+ refCount: number;
43
+ }>;
44
+ hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
26
45
  }