@gmod/bam 2.0.0 → 2.0.2

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 (48) hide show
  1. package/CHANGELOG.md +16 -7
  2. package/dist/bai.d.ts +2 -6
  3. package/dist/bai.js.map +1 -1
  4. package/dist/bamFile.d.ts +1 -3
  5. package/dist/bamFile.js +7 -11
  6. package/dist/bamFile.js.map +1 -1
  7. package/dist/chunk.js +1 -1
  8. package/dist/chunk.js.map +1 -1
  9. package/dist/csi.d.ts +5 -15
  10. package/dist/csi.js.map +1 -1
  11. package/dist/htsget.js +3 -3
  12. package/dist/htsget.js.map +1 -1
  13. package/dist/record.d.ts +1 -4
  14. package/dist/record.js +2 -4
  15. package/dist/record.js.map +1 -1
  16. package/dist/sam.js +3 -1
  17. package/dist/sam.js.map +1 -1
  18. package/dist/util.d.ts +1 -3
  19. package/dist/util.js.map +1 -1
  20. package/dist/virtualOffset.js.map +1 -1
  21. package/esm/bai.d.ts +2 -6
  22. package/esm/bai.js.map +1 -1
  23. package/esm/bamFile.d.ts +1 -3
  24. package/esm/bamFile.js +1 -1
  25. package/esm/bamFile.js.map +1 -1
  26. package/esm/chunk.js +1 -1
  27. package/esm/chunk.js.map +1 -1
  28. package/esm/csi.d.ts +5 -15
  29. package/esm/csi.js.map +1 -1
  30. package/esm/htsget.js +0 -1
  31. package/esm/htsget.js.map +1 -1
  32. package/esm/record.d.ts +1 -4
  33. package/esm/record.js +2 -4
  34. package/esm/record.js.map +1 -1
  35. package/esm/sam.js +3 -1
  36. package/esm/sam.js.map +1 -1
  37. package/esm/util.d.ts +1 -3
  38. package/esm/util.js.map +1 -1
  39. package/esm/virtualOffset.js.map +1 -1
  40. package/package.json +10 -11
  41. package/src/bai.ts +2 -2
  42. package/src/bamFile.ts +6 -6
  43. package/src/chunk.ts +1 -1
  44. package/src/csi.ts +3 -5
  45. package/src/htsget.ts +1 -1
  46. package/src/record.ts +5 -8
  47. package/src/sam.ts +3 -1
  48. package/src/util.ts +2 -2
package/esm/bai.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/bamFile.d.ts CHANGED
@@ -51,9 +51,7 @@ export default class BamFile {
51
51
  }[] | undefined>;
52
52
  getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
53
53
  _readRefSeqs(start: number, refSeqBytes: number, opts?: BaseOpts): Promise<{
54
- chrToIndex: {
55
- [key: string]: number;
56
- };
54
+ chrToIndex: Record<string, number>;
57
55
  indexToChr: {
58
56
  refName: string;
59
57
  length: number;
package/esm/bamFile.js CHANGED
@@ -117,7 +117,7 @@ export default class BamFile {
117
117
  buffer = res.buffer.subarray(0, Math.min(res.bytesRead, ret));
118
118
  }
119
119
  else {
120
- buffer = (await this.bam.readFile(opts));
120
+ buffer = await this.bam.readFile(opts);
121
121
  }
122
122
  const uncba = await unzip(buffer);
123
123
  if (uncba.readInt32LE(0) !== BAM_MAGIC) {
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/chunk.js CHANGED
@@ -7,7 +7,7 @@ export default class Chunk {
7
7
  this._fetchedSize = _fetchedSize;
8
8
  }
9
9
  toUniqueString() {
10
- return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
10
+ return `${this.minv.toString()}..${this.maxv.toString()} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
11
11
  }
12
12
  toString() {
13
13
  return this.toUniqueString();
package/esm/chunk.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAGxB,YACS,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAe;QACnB,SAAI,GAAJ,IAAI,CAAe;QACnB,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE;YACnC,OAAO,IAAI,CAAC,YAAY,CAAA;SACzB;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}
1
+ {"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAGxB,YACS,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAe;QACnB,SAAI,GAAJ,IAAI,CAAe;QACnB,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}
package/esm/csi.d.ts CHANGED
@@ -11,9 +11,7 @@ export default class CSI extends IndexFile {
11
11
  lineCount(refId: number, opts?: BaseOpts): Promise<number>;
12
12
  indexCov(): Promise<never[]>;
13
13
  parseAuxData(bytes: Buffer, offset: number): {
14
- refNameToId: {
15
- [key: string]: number;
16
- };
14
+ refNameToId: Record<string, number>;
17
15
  refIdToName: string[];
18
16
  columnNumbers: {
19
17
  ref: number;
@@ -30,9 +28,7 @@ export default class CSI extends IndexFile {
30
28
  _parse(opts: {
31
29
  signal?: AbortSignal;
32
30
  }): Promise<{
33
- refNameToId?: {
34
- [key: string]: number;
35
- } | undefined;
31
+ refNameToId?: Record<string, number> | undefined;
36
32
  refIdToName?: string[] | undefined;
37
33
  columnNumbers?: {
38
34
  ref: number;
@@ -48,9 +44,7 @@ export default class CSI extends IndexFile {
48
44
  csiVersion: number;
49
45
  firstDataLine: VirtualOffset | undefined;
50
46
  indices: {
51
- binIndex: {
52
- [key: string]: Chunk[];
53
- };
47
+ binIndex: Record<string, Chunk[]>;
54
48
  stats?: {
55
49
  lineCount: number;
56
50
  } | undefined;
@@ -66,9 +60,7 @@ export default class CSI extends IndexFile {
66
60
  */
67
61
  reg2bins(beg: number, end: number): number[][];
68
62
  parse(opts?: BaseOpts): Promise<{
69
- refNameToId?: {
70
- [key: string]: number;
71
- } | undefined;
63
+ refNameToId?: Record<string, number> | undefined;
72
64
  refIdToName?: string[] | undefined;
73
65
  columnNumbers?: {
74
66
  ref: number;
@@ -84,9 +76,7 @@ export default class CSI extends IndexFile {
84
76
  csiVersion: number;
85
77
  firstDataLine: VirtualOffset | undefined;
86
78
  indices: {
87
- binIndex: {
88
- [key: string]: Chunk[];
89
- };
79
+ binIndex: Record<string, Chunk[]>;
90
80
  stats?: {
91
81
  lineCount: number;
92
82
  } | undefined;
package/esm/csi.js.map CHANGED
@@ -1 +1 @@
1
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1
+ 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package/esm/htsget.js CHANGED
@@ -11,7 +11,6 @@ async function concat(arr, opts) {
11
11
  else {
12
12
  //remove referer header, it is not even allowed to be specified
13
13
  // @ts-expect-error
14
- //eslint-disable-next-line @typescript-eslint/no-unused-vars
15
14
  const { referer, ...rest } = headers;
16
15
  const res = await fetch(url, {
17
16
  ...opts,
package/esm/htsget.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAE/B,OAAO,OAAO,EAAE,EAAE,SAAS,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,EAAE,eAAe,EAAE,MAAM,OAAO,CAAA;AAMvC,KAAK,UAAU,MAAM,CAAC,GAAkB,EAAE,IAA0B;IAClE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,KAAK,EAAC,EAAE;QACpB,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE;YAC3B,OAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;SAChD;aAAM;YACL,+DAA+D;YAC/D,mBAAmB;YACnB,4DAA4D;YAC5D,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,CAAA;YACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;gBAC3B,GAAG,IAAI;gBACP,OAAO,EAAE,EAAE,GAAG,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,EAAE,GAAG,IAAI,EAAE;aACvC,CAAC,CAAA;YACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE;gBACX,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAC1D,CAAA;aACF;YACD,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;SAC5C;IACH,CAAC,CAAC,CACH,CAAA;IAED,OAAO,MAAM,CAAC,MAAM,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;AACrE,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,OAAO;IAK7C,YAAY,IAA0C;QACpD,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAA;QACvB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,CAAC,qBAAqB,CAC1B,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;;QAEd,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;QAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;QAC7E,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE;YACvB,MAAM,EAAE,CAAA;SACT;aAAM;YACL,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,CAAC,CAAA;YAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;gBACd,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;aACF;YACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;YAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;YAE3D,KAAK,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAC7B;gBACE,sCAAsC;gBACtC;oBACE,MAAM,EAAE,KAAK;oBACb,YAAY,EAAE,SAAS;oBACvB,GAAG,EAAE,CAAC;oBACN,SAAS;wBACP,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,cAAc;wBACZ,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;oBACD,WAAW;wBACT,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,CAAC;wBACf,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,MAAM,CAAC,gBAAgB;wBACrC,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,QAAQ;wBACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;iBACF;aACF,EACD,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA;SACF;IACH,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,EAAE,KAAK,EAAoC;QAC1D,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;SACnD;QACD,OAAO,EAAE,IAAI,EAAE,KAAK,CAAC,MAAM,EAAE,UAAU,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE,KAAK,EAAE,CAAA;IACtE,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAiB,EAAE;QACjC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;QAC3E,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;YACd,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;SACF;QACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;QAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;YACtC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;SAClC;QACD,MAAM,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACpC,MAAM,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;QACzD,MAAM,SAAS,GAAG,eAAe,CAAC,UAAU,CAAC,CAAA;QAE7C,oDAAoD;QACpD,+CAA+C;QAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;QAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;QACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE;YAC/C,IAAI,OAAO,GAAG,EAAE,CAAA;YAChB,IAAI,MAAM,GAAG,CAAC,CAAA;YACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE;gBAC9B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;oBACrB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;iBACrB;qBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;oBAC5B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;iBACrB;aACF;YACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;SACtC;QACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,OAAO,SAAS,CAAA;IAClB,CAAC;CACF"}
1
+ {"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAE/B,OAAO,OAAO,EAAE,EAAE,SAAS,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,EAAE,eAAe,EAAE,MAAM,OAAO,CAAA;AAMvC,KAAK,UAAU,MAAM,CAAC,GAAkB,EAAE,IAA0B;IAClE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,KAAK,EAAC,EAAE;QACpB,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;YAC5B,OAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjD,CAAC;aAAM,CAAC;YACN,+DAA+D;YAC/D,mBAAmB;YAEnB,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,CAAA;YACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;gBAC3B,GAAG,IAAI;gBACP,OAAO,EAAE,EAAE,GAAG,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,EAAE,GAAG,IAAI,EAAE;aACvC,CAAC,CAAA;YACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAC1D,CAAA;YACH,CAAC;YACD,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;QAC7C,CAAC;IACH,CAAC,CAAC,CACH,CAAA;IAED,OAAO,MAAM,CAAC,MAAM,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;AACrE,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,OAAO;IAK7C,YAAY,IAA0C;QACpD,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAA;QACvB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,CAAC,qBAAqB,CAC1B,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;;QAEd,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;QAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;QAC7E,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,MAAM,EAAE,CAAA;QACV,CAAC;aAAM,CAAC;YACN,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,CAAC,CAAA;YAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;YACH,CAAC;YACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;YAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;YAE3D,KAAK,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAC7B;gBACE,sCAAsC;gBACtC;oBACE,MAAM,EAAE,KAAK;oBACb,YAAY,EAAE,SAAS;oBACvB,GAAG,EAAE,CAAC;oBACN,SAAS;wBACP,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,cAAc;wBACZ,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;oBACD,WAAW;wBACT,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,CAAC;wBACf,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,MAAM,CAAC,gBAAgB;wBACrC,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,QAAQ;wBACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;iBACF;aACF,EACD,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA;QACH,CAAC;IACH,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,EAAE,KAAK,EAAoC;QAC1D,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;YAClB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;QACpD,CAAC;QACD,OAAO,EAAE,IAAI,EAAE,KAAK,CAAC,MAAM,EAAE,UAAU,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE,KAAK,EAAE,CAAA;IACtE,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAiB,EAAE;QACjC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;QAC3E,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;QACH,CAAC;QACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;QAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE,CAAC;YACvC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QACD,MAAM,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACpC,MAAM,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;QACzD,MAAM,SAAS,GAAG,eAAe,CAAC,UAAU,CAAC,CAAA;QAE7C,oDAAoD;QACpD,+CAA+C;QAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;QAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;QACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;YAChD,IAAI,OAAO,GAAG,EAAE,CAAA;YAChB,IAAI,MAAM,GAAG,CAAC,CAAA;YACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;gBAC/B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBACtB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;qBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;YACH,CAAC;YACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;QACvC,CAAC;QACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,OAAO,SAAS,CAAA;IAClB,CAAC;CACF"}
package/esm/record.d.ts CHANGED
@@ -65,7 +65,6 @@ export default class BamRecord {
65
65
  /** @returns {boolean} true if this is a supplementary alignment */
66
66
  isSupplementary(): boolean;
67
67
  cigar(): any;
68
- _flags(): void;
69
68
  length_on_ref(): any;
70
69
  _n_cigar_op(): number;
71
70
  _l_read_name(): number;
@@ -82,7 +81,5 @@ export default class BamRecord {
82
81
  _next_refid(): number;
83
82
  _next_pos(): number;
84
83
  template_length(): number;
85
- toJSON(): {
86
- [key: string]: any;
87
- };
84
+ toJSON(): Record<string, any>;
88
85
  }
package/esm/record.js CHANGED
@@ -1,4 +1,3 @@
1
- /* eslint-disable @typescript-eslint/no-empty-function */
2
1
  import Constants from './constants';
3
2
  const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
4
3
  const CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
@@ -58,7 +57,7 @@ export default class BamRecord {
58
57
  }
59
58
  tags = tags.concat(this._tagList || []);
60
59
  for (const k of Object.keys(this.data)) {
61
- if (k[0] !== '_' && k !== 'next_seq_id') {
60
+ if (!k.startsWith('_') && k !== 'next_seq_id') {
62
61
  tags.push(k);
63
62
  }
64
63
  }
@@ -426,7 +425,6 @@ export default class BamRecord {
426
425
  return cigar;
427
426
  }
428
427
  }
429
- _flags() { }
430
428
  length_on_ref() {
431
429
  if (this.data.length_on_ref) {
432
430
  return this.data.length_on_ref;
@@ -525,7 +523,7 @@ export default class BamRecord {
525
523
  toJSON() {
526
524
  const data = {};
527
525
  for (const k of Object.keys(this)) {
528
- if (k.charAt(0) === '_' || k === 'bytes') {
526
+ if (k.startsWith('_') || k === 'bytes') {
529
527
  continue;
530
528
  }
531
529
  //@ts-ignore
package/esm/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/sam.js CHANGED
@@ -7,7 +7,9 @@ export function parseHeaderText(text) {
7
7
  data.push({
8
8
  tag: tag.slice(1),
9
9
  data: fields.map(f => {
10
- const [fieldTag, value] = f.split(':', 2);
10
+ const r = f.indexOf(':');
11
+ const fieldTag = f.slice(0, r);
12
+ const value = f.slice(r + 1);
11
13
  return { tag: fieldTag, value };
12
14
  }),
13
15
  });
package/esm/sam.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,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"}
1
+ {"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,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,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,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,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,MAAM,QAAQ,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;oBAC9B,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;oBAC5B,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;gBACjC,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
package/esm/util.d.ts CHANGED
@@ -40,8 +40,6 @@ export declare function parsePseudoBin(bytes: Buffer, offset: number): {
40
40
  };
41
41
  export declare function findFirstData(firstDataLine: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
42
42
  export declare function parseNameBytes(namesBytes: Buffer, renameRefSeq?: (arg: string) => string): {
43
- refNameToId: {
44
- [key: string]: number;
45
- };
43
+ refNameToId: Record<string, number>;
46
44
  refIdToName: string[];
47
45
  };
package/esm/util.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/esm/virtualOffset.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,OAAO,OAAO,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;AACD,MAAM,UAAU,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"}
1
+ {"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,OAAO,OAAO,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,CAAC;YACpB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;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"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "2.0.0",
3
+ "version": "2.0.2",
4
4
  "description": "Parser for BAM and BAM index (bai) files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bam-js",
@@ -41,28 +41,27 @@
41
41
  "dependencies": {
42
42
  "@gmod/bgzf-filehandle": "^1.4.4",
43
43
  "abortable-promise-cache": "^1.5.0",
44
- "buffer-crc32": "^0.2.13",
44
+ "buffer-crc32": "^1.0.0",
45
45
  "generic-filehandle": "^3.0.0",
46
46
  "long": "^4.0.0",
47
47
  "quick-lru": "^4.0.0"
48
48
  },
49
49
  "devDependencies": {
50
- "@types/buffer-crc32": "^0.2.2",
51
50
  "@types/jest": "^29.5.1",
52
51
  "@types/long": "^4.0.0",
53
- "@types/node": "^18.16.0",
54
- "@typescript-eslint/eslint-plugin": "^5.59.6",
55
- "@typescript-eslint/parser": "^5.59.6",
52
+ "@types/node": "^20.11.19",
53
+ "@typescript-eslint/eslint-plugin": "^7.0.2",
54
+ "@typescript-eslint/parser": "^7.0.2",
56
55
  "eslint": "^8.40.0",
57
- "eslint-config-prettier": "^8.7.0",
56
+ "eslint-config-prettier": "^9.1.0",
58
57
  "eslint-plugin-import": "^2.27.5",
59
- "eslint-plugin-prettier": "^4.2.1",
60
- "eslint-plugin-unicorn": "^47.0.0",
58
+ "eslint-plugin-prettier": "^5.1.3",
59
+ "eslint-plugin-unicorn": "^51.0.1",
61
60
  "jest": "^29.5.0",
62
61
  "jest-fetch-mock": "^3.0.3",
63
- "prettier": "^2.8.8",
62
+ "prettier": "^3.2.5",
64
63
  "rimraf": "^5.0.0",
65
- "standard-changelog": "^2.0.27",
64
+ "standard-changelog": "^5.0.0",
66
65
  "ts-jest": "^29.1.0",
67
66
  "typescript": "^5.0.4"
68
67
  },
package/src/bai.ts CHANGED
@@ -50,7 +50,7 @@ export default class BAI extends IndexFile {
50
50
  let curr = 8
51
51
  let firstDataLine: VirtualOffset | undefined
52
52
 
53
- type BinIndex = { [key: string]: Chunk[] }
53
+ type BinIndex = Record<string, Chunk[]>
54
54
  type LinearIndex = VirtualOffset[]
55
55
  const indices = new Array<{
56
56
  binIndex: BinIndex
@@ -63,7 +63,7 @@ export default class BAI extends IndexFile {
63
63
  let stats
64
64
 
65
65
  curr += 4
66
- const binIndex: { [key: number]: Chunk[] } = {}
66
+ const binIndex: Record<number, Chunk[]> = {}
67
67
 
68
68
  for (let j = 0; j < binCount; j += 1) {
69
69
  const bin = bytes.readUInt32LE(curr)
package/src/bamFile.ts CHANGED
@@ -154,7 +154,7 @@ export default class BamFile {
154
154
  }
155
155
  buffer = res.buffer.subarray(0, Math.min(res.bytesRead, ret))
156
156
  } else {
157
- buffer = (await this.bam.readFile(opts)) as Buffer
157
+ buffer = await this.bam.readFile(opts)
158
158
  }
159
159
 
160
160
  const uncba = await unzip(buffer)
@@ -198,7 +198,7 @@ export default class BamFile {
198
198
  refSeqBytes: number,
199
199
  opts?: BaseOpts,
200
200
  ): Promise<{
201
- chrToIndex: { [key: string]: number }
201
+ chrToIndex: Record<string, number>
202
202
  indexToChr: { refName: string; length: number }[]
203
203
  }> {
204
204
  if (start > refSeqBytes) {
@@ -220,7 +220,7 @@ export default class BamFile {
220
220
  )
221
221
  const nRef = uncba.readInt32LE(start)
222
222
  let p = start + 4
223
- const chrToIndex: { [key: string]: number } = {}
223
+ const chrToIndex: Record<string, number> = {}
224
224
  const indexToChr: { refName: string; length: number }[] = []
225
225
  for (let i = 0; i < nRef; i += 1) {
226
226
  const lName = uncba.readInt32LE(p)
@@ -314,10 +314,10 @@ export default class BamFile {
314
314
 
315
315
  async fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts) {
316
316
  const { pairAcrossChr, maxInsertSize = 200000 } = opts
317
- const unmatedPairs: { [key: string]: boolean } = {}
318
- const readIds: { [key: string]: number } = {}
317
+ const unmatedPairs: Record<string, boolean> = {}
318
+ const readIds: Record<string, number> = {}
319
319
  feats.map(ret => {
320
- const readNames: { [key: string]: number } = {}
320
+ const readNames: Record<string, number> = {}
321
321
  for (const element of ret) {
322
322
  const name = element.name()
323
323
  const id = element.id()
package/src/chunk.ts CHANGED
@@ -12,7 +12,7 @@ export default class Chunk {
12
12
  ) {}
13
13
 
14
14
  toUniqueString() {
15
- return `${this.minv}..${this.maxv} (bin ${
15
+ return `${this.minv.toString()}..${this.maxv.toString()} (bin ${
16
16
  this.bin
17
17
  }, fetchedSize ${this.fetchedSize()})`
18
18
  }
package/src/csi.ts CHANGED
@@ -42,9 +42,7 @@ export default class CSI extends IndexFile {
42
42
  const coordinateType =
43
43
  formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed'
44
44
  const format = (
45
- { 0: 'generic', 1: 'SAM', 2: 'VCF' } as {
46
- [key: number]: string
47
- }
45
+ { 0: 'generic', 1: 'SAM', 2: 'VCF' } as Record<number, string>
48
46
  )[formatFlags & 0xf]
49
47
  if (!format) {
50
48
  throw new Error(`invalid Tabix preset format flags ${formatFlags}`)
@@ -97,7 +95,7 @@ export default class CSI extends IndexFile {
97
95
  const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined
98
96
  const refCount = bytes.readInt32LE(16 + auxLength)
99
97
 
100
- type BinIndex = { [key: string]: Chunk[] }
98
+ type BinIndex = Record<string, Chunk[]>
101
99
 
102
100
  // read the indexes for each reference sequence
103
101
  let curr = 16 + auxLength + 4
@@ -110,7 +108,7 @@ export default class CSI extends IndexFile {
110
108
  // the binning index
111
109
  const binCount = bytes.readInt32LE(curr)
112
110
  curr += 4
113
- const binIndex: { [key: string]: Chunk[] } = {}
111
+ const binIndex: Record<string, Chunk[]> = {}
114
112
  let stats // < provided by parsing a pseudo-bin, if present
115
113
  for (let j = 0; j < binCount; j++) {
116
114
  const bin = bytes.readUInt32LE(curr)