@gmod/bam 1.1.16 → 1.1.17

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 (9) hide show
  1. package/CHANGELOG.md +5 -3
  2. package/dist/csi.d.ts +2 -2
  3. package/dist/csi.js +3 -6
  4. package/dist/csi.js.map +1 -1
  5. package/esm/csi.d.ts +2 -2
  6. package/esm/csi.js +3 -6
  7. package/esm/csi.js.map +1 -1
  8. package/package.json +15 -15
  9. package/src/csi.ts +4 -7
package/CHANGELOG.md CHANGED
@@ -1,12 +1,14 @@
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- ## [1.1.16](https://github.com/GMOD/bam-js/compare/v1.1.15...v1.1.16) (2022-03-30)
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+ ## [1.1.17](https://github.com/GMOD/bam-js/compare/v1.1.16...v1.1.17) (2022-07-18)
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- - Add src directory for better source maps
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+ - Bump devDeps and generic-filehandle to 3.0.0
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- ## [1.1.15](https://github.com/GMOD/bam-js/compare/v1.1.14...v1.1.15) (2022-03-18)
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+ ## [1.1.16](https://github.com/GMOD/bam-js/compare/v1.1.15...v1.1.16) (2022-03-30)
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+ - Add src directory for better source maps
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+ ## [1.1.15](https://github.com/GMOD/bam-js/compare/v1.1.14...v1.1.15) (2022-03-18)
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  - Fix for htsget failing with message 'input must be buffer, number, or string, received object'
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  - Speed improvement by caching chunks of features
package/dist/csi.d.ts CHANGED
@@ -28,8 +28,8 @@ export default class CSI extends IndexFile {
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  };
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  blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
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  /**
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- * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
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- * @returns {Array[number]}
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+ * calculate the list of bins that may overlap with region [beg,end)
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+ * (zero-based half-open)
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  */
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  reg2bins(beg: number, end: number): number[][];
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  }
package/dist/csi.js CHANGED
@@ -277,10 +277,7 @@ var CSI = /** @class */ (function (_super) {
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  return [4 /*yield*/, this.parse(opts)];
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  case 1:
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  indexData = _b.sent();
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- if (!indexData) {
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- return [2 /*return*/, []];
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- }
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- ba = indexData.indices[refId];
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+ ba = indexData === null || indexData === void 0 ? void 0 : indexData.indices[refId];
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  if (!ba) {
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  return [2 /*return*/, []];
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  }
@@ -305,8 +302,8 @@ var CSI = /** @class */ (function (_super) {
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  });
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  };
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  /**
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- * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
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- * @returns {Array[number]}
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+ * calculate the list of bins that may overlap with region [beg,end)
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+ * (zero-based half-open)
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  */
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  CSI.prototype.reg2bins = function (beg, end) {
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  beg -= 1; // < convert to 1-based closed
package/dist/csi.js.map CHANGED
@@ -1 +1 @@
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- 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1
+ {"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,8CAAuB;AACvB,yDAA6C;AAC7C,+DAA0D;AAC1D,kDAA2B;AAC3B,+BAAgF;AAEhF,0DAAmC;AAEnC,IAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,IAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAC,CAAA;AACpC,CAAC;AAED;IAAiC,uBAAS;IAIxC,aAAY,IAAS;QAArB,YACE,kBAAM,IAAI,CAAC,SAIZ;QAHC,KAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,KAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,KAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;;IACnB,CAAC;IACK,uBAAS,GAAf,UAAgB,KAAa;;;;;4BACT,qBAAM,IAAI,CAAC,KAAK,EAAE,EAAA;;wBAA9B,SAAS,GAAG,SAAkB;wBACpC,IAAI,CAAC,SAAS,EAAE;4BACd,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACK,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;wBACpC,IAAI,CAAC,GAAG,EAAE;4BACR,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACO,KAAK,GAAK,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,MAA7B,CAA6B;wBAC1C,IAAI,KAAK,EAAE;4BACT,sBAAO,KAAK,CAAC,SAAS,EAAA;yBACvB;wBACD,sBAAO,CAAC,CAAC,EAAA;;;;KACV;IAEK,sBAAQ,GAAd;;;gBACE,sBAAO,EAAE,EAAA;;;KACV;IAED,0BAAY,GAAZ,UAAa,KAAa,EAAE,MAAc,EAAE,SAAiB;QAC3D,IAAI,SAAS,GAAG,EAAE,EAAE;YAClB,OAAO,EAAE,CAAA;SACV;QAED,IAAM,IAAI,GAA2B,EAAE,CAAA;QACvC,IAAI,CAAC,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC5C,IAAI,CAAC,cAAc;YACjB,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACxE,IAAI,CAAC,MAAM,GACT,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAGnC,CAAC,IAAI,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACzB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,4CAAqC,IAAI,CAAC,WAAW,CAAE,CAAC,CAAA;SACzE;QACD,IAAI,CAAC,aAAa,GAAG;YACnB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QACzE,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,CAAC,MAAM,CACX,IAAI,EACJ,IAAI,CAAC,eAAe,CAClB,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CACF,CAAA;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,6BAAe,GAAf,UAAgB,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,IAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAM,WAAW,GAA8B,EAAE,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;gBAClB,IAAI,aAAa,GAAG,CAAC,EAAE;oBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;iBACjC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;aACf;SACF;QACD,OAAO,EAAE,WAAW,aAAA,EAAE,WAAW,aAAA,EAAE,CAAA;IACrC,CAAC;IAED,4BAA4B;IACtB,oBAAM,GAAZ,UAAa,IAA8B;;;;;;;wBACnC,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;wBACzD,qBAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAA;;wBAA9C,MAAM,GAAG,CAAC,SAAoC,CAAW;wBACjD,qBAAM,IAAA,uBAAK,EAAC,MAAM,CAAC;4BAEjC,0BAA0B;0BAFO;;wBAA3B,KAAK,GAAG,SAAmB;wBAEjC,0BAA0B;wBAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;4BACxC,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;yBACpB;6BAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;4BAC/C,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;yBACpB;6BAAM;4BACL,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;4BACjC,oDAAoD;yBACrD;wBAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACjC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;wBACrD,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;wBACvC,IAAI,SAAS,EAAE;4BACb,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,EAAE,SAAS,CAAC,CAAC,CAAA;yBAC7D;wBACD,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;wBAEjD,+CAA+C;wBAC/C,IAAI,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;wBACnC,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;wBAC1B,CAAC,GAAG,CAAC;;;6BAAE,CAAA,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAA;wBAC/B,qBAAM,IAAA,sBAAe,EAAC,IAAI,CAAC,MAAM,CAAC;4BAClC,oBAAoB;0BADc;;wBAAlC,SAAkC,CAAA;wBAE5B,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAC9C,UAAU,IAAI,CAAC,CAAA;wBACT,QAAQ,GAA+B,EAAE,CAAA;wBAC3C,KAAK,SAAA,CAAA;wBACT,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;4BAC9B,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;4BAC1C,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE;gCAC3B,yDAAyD;gCACzD,qCAAqC;gCACrC,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;gCAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;6BAClC;iCAAM;gCACC,OAAO,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UA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package/esm/csi.d.ts CHANGED
@@ -28,8 +28,8 @@ export default class CSI extends IndexFile {
28
28
  };
29
29
  blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
30
30
  /**
31
- * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
32
- * @returns {Array[number]}
31
+ * calculate the list of bins that may overlap with region [beg,end)
32
+ * (zero-based half-open)
33
33
  */
34
34
  reg2bins(beg: number, end: number): number[][];
35
35
  }
package/esm/csi.js CHANGED
@@ -151,10 +151,7 @@ export default class CSI extends IndexFile {
151
151
  min = 0;
152
152
  }
153
153
  const indexData = await this.parse(opts);
154
- if (!indexData) {
155
- return [];
156
- }
157
- const ba = indexData.indices[refId];
154
+ const ba = indexData === null || indexData === void 0 ? void 0 : indexData.indices[refId];
158
155
  if (!ba) {
159
156
  return [];
160
157
  }
@@ -174,8 +171,8 @@ export default class CSI extends IndexFile {
174
171
  return optimizeChunks(chunks, new VirtualOffset(0, 0));
175
172
  }
176
173
  /**
177
- * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
178
- * @returns {Array[number]}
174
+ * calculate the list of bins that may overlap with region [beg,end)
175
+ * (zero-based half-open)
179
176
  */
180
177
  reg2bins(beg, end) {
181
178
  beg -= 1; // < convert to 1-based closed
package/esm/csi.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "1.1.16",
3
+ "version": "1.1.17",
4
4
  "description": "Parser for BAM and BAM index (bai) files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bam-js",
@@ -39,33 +39,33 @@
39
39
  "genomics"
40
40
  ],
41
41
  "dependencies": {
42
- "@gmod/bgzf-filehandle": "^1.3.3",
42
+ "@gmod/bgzf-filehandle": "^1.4.4",
43
43
  "abortable-promise-cache": "^1.5.0",
44
44
  "buffer-crc32": "^0.2.13",
45
45
  "cross-fetch": "^3.0.2",
46
- "generic-filehandle": "^2.0.0",
46
+ "generic-filehandle": "^3.0.0",
47
47
  "long": "^4.0.0",
48
48
  "object.entries-ponyfill": "^1.0.1",
49
49
  "quick-lru": "^2.0.0"
50
50
  },
51
51
  "devDependencies": {
52
52
  "@types/buffer-crc32": "^0.2.0",
53
- "@types/jest": "^27.4.1",
54
- "@types/long": "^4.0.0",
55
- "@types/node": "^17.0.21",
53
+ "@types/jest": "^28.1.6",
54
+ "@types/long": "^4.0.2",
55
+ "@types/node": "^18.0.6",
56
56
  "@types/quick-lru": "^2.0.0",
57
- "@typescript-eslint/eslint-plugin": "^5.14.0",
58
- "@typescript-eslint/parser": "^5.14.0",
59
- "eslint": "^8.11.0",
57
+ "@typescript-eslint/eslint-plugin": "^5.30.7",
58
+ "@typescript-eslint/parser": "^5.30.7",
59
+ "eslint": "^8.20.0",
60
60
  "eslint-config-prettier": "^8.5.0",
61
- "eslint-plugin-import": "^2.25.4",
62
- "eslint-plugin-prettier": "^4.0.0",
63
- "jest": "^27.5.1",
64
- "prettier": "^2.4.1",
61
+ "eslint-plugin-import": "^2.26.0",
62
+ "eslint-plugin-prettier": "^4.2.1",
63
+ "jest": "^28.1.3",
64
+ "prettier": "^2.7.1",
65
65
  "rimraf": "^3.0.2",
66
66
  "standard-changelog": "^2.0.27",
67
- "ts-jest": "^27.1.3",
68
- "typescript": "^4.6.2"
67
+ "ts-jest": "^28.0.7",
68
+ "typescript": "^4.7.4"
69
69
  },
70
70
  "publishConfig": {
71
71
  "access": "public"
package/src/csi.ts CHANGED
@@ -188,16 +188,13 @@ export default class CSI extends IndexFile {
188
188
  }
189
189
 
190
190
  const indexData = await this.parse(opts)
191
- if (!indexData) {
192
- return []
193
- }
194
- const ba = indexData.indices[refId]
191
+ const ba = indexData?.indices[refId]
195
192
  if (!ba) {
196
193
  return []
197
194
  }
198
195
 
199
196
  const overlappingBins = this.reg2bins(min, max) // List of bin #s that overlap min, max
200
- const chunks: Chunk[] = []
197
+ const chunks = []
201
198
 
202
199
  // Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
203
200
  for (const [start, end] of overlappingBins) {
@@ -215,8 +212,8 @@ export default class CSI extends IndexFile {
215
212
  }
216
213
 
217
214
  /**
218
- * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
219
- * @returns {Array[number]}
215
+ * calculate the list of bins that may overlap with region [beg,end)
216
+ * (zero-based half-open)
220
217
  */
221
218
  reg2bins(beg: number, end: number) {
222
219
  beg -= 1 // < convert to 1-based closed