nmr-processing 8.7.0 → 9.0.0

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 (71) hide show
  1. package/lib/peaks/peakToXY.d.ts +3 -3
  2. package/lib/peaks/peakToXY.js +1 -1
  3. package/lib/peaks/peakToXY.js.map +1 -1
  4. package/lib/peaks/peaksToRanges.d.ts +1 -1
  5. package/lib/peaks/peaksToRanges.js +2 -2
  6. package/lib/peaks/peaksToRanges.js.map +1 -1
  7. package/lib/peaks/peaksToXY.d.ts +11 -2
  8. package/lib/peaks/peaksToXY.js +4 -3
  9. package/lib/peaks/peaksToXY.js.map +1 -1
  10. package/lib/peaks/util/convertWidth.d.ts +13 -0
  11. package/lib/peaks/util/convertWidth.js +34 -0
  12. package/lib/peaks/util/convertWidth.js.map +1 -0
  13. package/lib/peaks/util/convertWidthToHz.d.ts +2 -0
  14. package/lib/peaks/util/convertWidthToHz.js +9 -0
  15. package/lib/peaks/util/convertWidthToHz.js.map +1 -0
  16. package/lib/peaks/util/convertWidthToPPM.d.ts +2 -0
  17. package/lib/peaks/util/convertWidthToPPM.js +9 -0
  18. package/lib/peaks/util/convertWidthToPPM.js.map +1 -0
  19. package/lib/{peaks/util → ranges/utils}/joinRanges.d.ts +0 -0
  20. package/lib/{peaks/util → ranges/utils}/joinRanges.js +0 -0
  21. package/lib/ranges/utils/joinRanges.js.map +1 -0
  22. package/lib/{peaks/util → signals/utils}/jAnalyzer.d.ts +1 -1
  23. package/lib/{peaks/util → signals/utils}/jAnalyzer.js +0 -0
  24. package/lib/signals/utils/jAnalyzer.js.map +1 -0
  25. package/lib/xy/xyAutoPeaksPicking.d.ts +9 -1
  26. package/lib/xy/xyAutoPeaksPicking.js +6 -4
  27. package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
  28. package/lib/xy/xyAutoRangesPicking.d.ts +2 -2
  29. package/lib/xy/xyAutoRangesPicking.js +1 -1
  30. package/lib/xy/xyAutoRangesPicking.js.map +1 -1
  31. package/lib/xyz/xyzJResAnalyzer.d.ts +1 -1
  32. package/lib/xyz/xyzJResAnalyzer.js +1 -1
  33. package/lib/xyz/xyzJResAnalyzer.js.map +1 -1
  34. package/lib-esm/peaks/peakToXY.js +1 -1
  35. package/lib-esm/peaks/peakToXY.js.map +1 -1
  36. package/lib-esm/peaks/peaksToRanges.js +2 -2
  37. package/lib-esm/peaks/peaksToRanges.js.map +1 -1
  38. package/lib-esm/peaks/peaksToXY.js +4 -3
  39. package/lib-esm/peaks/peaksToXY.js.map +1 -1
  40. package/lib-esm/peaks/util/convertWidth.js +30 -0
  41. package/lib-esm/peaks/util/convertWidth.js.map +1 -0
  42. package/lib-esm/peaks/util/convertWidthToHz.js +5 -0
  43. package/lib-esm/peaks/util/convertWidthToHz.js.map +1 -0
  44. package/lib-esm/peaks/util/convertWidthToPPM.js +5 -0
  45. package/lib-esm/peaks/util/convertWidthToPPM.js.map +1 -0
  46. package/lib-esm/{peaks/util → ranges/utils}/joinRanges.js +0 -0
  47. package/lib-esm/ranges/utils/joinRanges.js.map +1 -0
  48. package/lib-esm/{peaks/util → signals/utils}/jAnalyzer.js +0 -0
  49. package/{lib/peaks/util → lib-esm/signals/utils}/jAnalyzer.js.map +1 -1
  50. package/lib-esm/xy/xyAutoPeaksPicking.js +6 -4
  51. package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
  52. package/lib-esm/xy/xyAutoRangesPicking.js +1 -1
  53. package/lib-esm/xy/xyAutoRangesPicking.js.map +1 -1
  54. package/lib-esm/xyz/xyzJResAnalyzer.js +1 -1
  55. package/lib-esm/xyz/xyzJResAnalyzer.js.map +1 -1
  56. package/package.json +1 -1
  57. package/src/peaks/peakToXY.ts +3 -5
  58. package/src/peaks/peaksToRanges.ts +3 -3
  59. package/src/peaks/peaksToXY.ts +18 -4
  60. package/src/peaks/util/convertWidth.ts +40 -0
  61. package/src/peaks/util/convertWidthToHz.ts +7 -0
  62. package/src/peaks/util/convertWidthToPPM.ts +7 -0
  63. package/src/ranges/markSolventSignal.ts +1 -1
  64. package/src/{peaks/util → ranges/utils}/joinRanges.ts +0 -0
  65. package/src/{peaks/util → signals/utils}/jAnalyzer.ts +1 -1
  66. package/src/xy/xyAutoPeaksPicking.ts +14 -2
  67. package/src/xy/xyAutoRangesPicking.ts +2 -2
  68. package/src/xyz/xyzJResAnalyzer.ts +2 -2
  69. package/lib/peaks/util/joinRanges.js.map +0 -1
  70. package/lib-esm/peaks/util/jAnalyzer.js.map +0 -1
  71. package/lib-esm/peaks/util/joinRanges.js.map +0 -1
package/lib-esm/ranges/utils/joinRanges.js.map ADDED
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package/{lib/peaks/util → lib-esm/signals/utils}/jAnalyzer.js.map RENAMED
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package/lib-esm/xy/xyAutoPeaksPicking.js CHANGED
@@ -1,7 +1,8 @@
1
1
  import { gsd, optimizePeaks, joinBroadPeaks } from 'ml-gsd';
2
2
  import { xyExtract, xNoiseSanPlot, xAbsoluteMedian, } from 'ml-spectra-processing';
3
- export function xyAutoPeaksPicking(data, options = {}) {
4
- const { from, to, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, direction = 'positive', } = options;
3
+ import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
4
+ export function xyAutoPeaksPicking(data, options) {
5
+ const { from, to, frequency, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, direction = 'positive', } = options;
5
6
  const { windowSize = 9, polynomial = 3 } = sgOptions;
6
7
  if (data.x.length < windowSize)
7
8
  return [];
@@ -11,6 +12,7 @@ export function xyAutoPeaksPicking(data, options = {}) {
11
12
  const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
12
13
  let getPeakOptions = {
13
14
  shape,
15
+ frequency,
14
16
  broadWidth,
15
17
  optimize,
16
18
  factorLimits,
@@ -49,7 +51,7 @@ function getNegativePeaks(data, cutOff, getPeakOptions) {
49
51
  return getPeakList(data, getPeakOptions);
50
52
  }
51
53
  function getPeakList(data, options) {
52
- const { shape, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
54
+ const { shape, frequency, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
53
55
  let peakList = gsd(data, {
54
56
  shape,
55
57
  sgOptions,
@@ -74,7 +76,7 @@ function getPeakList(data, options) {
74
76
  optimization,
75
77
  });
76
78
  }
77
- return peakList;
79
+ return convertWidthToHz(peakList, frequency);
78
80
  }
79
81
  function getCutOff(data, options) {
80
82
  const { noiseLevel, useSanPlot, thresholdFactor } = options;
package/lib-esm/xy/xyAutoPeaksPicking.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/lib-esm/xy/xyAutoRangesPicking.js CHANGED
@@ -4,7 +4,7 @@ import { xyAutoPeaksPicking } from './xyAutoPeaksPicking';
4
4
  /**
5
5
  * Detect peaks, optimize parameters and compile multiplicity if required.
6
6
  */
7
- export function xyAutoRangesPicking(data, options = {}) {
7
+ export function xyAutoRangesPicking(data, options) {
8
8
  let peaks = xyAutoPeaksPicking(data, options.peakPicking);
9
9
  peaks = peaksFilterImpurities(peaks, options.impurities);
10
10
  return peaksToRanges(data, peaks, options.ranges);
package/lib-esm/xy/xyAutoRangesPicking.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"xyAutoRangesPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoRangesPicking.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAC;AAEvE,OAAO,EAAwB,aAAa,EAAE,MAAM,wBAAwB,CAAC;AAE7E,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAS1D;;GAEG;AACH,MAAM,UAAU,mBAAmB,CACjC,IAAY,EACZ,UAAsC,EAAE;IAExC,IAAI,KAAK,GAAG,kBAAkB,CAAC,IAAI,EAAE,OAAO,CAAC,WAAW,CAAC,CAAC;IAC1D,KAAK,GAAG,qBAAqB,CAAC,KAAK,EAAE,OAAO,CAAC,UAAU,CAAC,CAAC;IACzD,OAAO,aAAa,CAAC,IAAI,EAAE,KAAK,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC;AACpD,CAAC"}
1
+ {"version":3,"file":"xyAutoRangesPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoRangesPicking.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAC;AAEvE,OAAO,EAAwB,aAAa,EAAE,MAAM,wBAAwB,CAAC;AAE7E,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAS1D;;GAEG;AACH,MAAM,UAAU,mBAAmB,CACjC,IAAY,EACZ,OAAmC;IAEnC,IAAI,KAAK,GAAG,kBAAkB,CAAC,IAAI,EAAE,OAAO,CAAC,WAAW,CAAC,CAAC;IAC1D,KAAK,GAAG,qBAAqB,CAAC,KAAK,EAAE,OAAO,CAAC,UAAU,CAAC,CAAC;IACzD,OAAO,aAAa,CAAC,IAAI,EAAE,KAAK,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC;AACpD,CAAC"}
package/lib-esm/xyz/xyzJResAnalyzer.js CHANGED
@@ -1,5 +1,5 @@
1
1
  import simpleClustering from 'ml-simple-clustering';
2
- import jAnalyzer from '../peaks/util/jAnalyzer';
2
+ import jAnalyzer from '../signals/utils/jAnalyzer';
3
3
  import { formatZones } from './util/formatZone';
4
4
  export function xyzJResAnalyzer(signals, options = {}) {
5
5
  let { reference = 0, getZones = false, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
package/lib-esm/xyz/xyzJResAnalyzer.js.map CHANGED
@@ -1 +1 @@
1
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "nmr-processing",
3
- "version": "8.7.0",
3
+ "version": "9.0.0",
4
4
  "description": "Pure functions allowing to process NMR spectra.",
5
5
  "main": "./lib/index.js",
6
6
  "module": "./lib-esm/index.js",
package/src/peaks/peakToXY.ts CHANGED
@@ -1,8 +1,6 @@
1
- import { PeakXYWidth } from 'cheminfo-types';
2
- import { OptionsSG1D } from 'spectrum-generator';
1
+ import { NMRPeak1D } from './NMRPeak1D';
2
+ import { peaksToXY, PeaksToXYOptions } from './peaksToXY';
3
3
 
4
- import { peaksToXY } from './peaksToXY';
5
-
6
- export function peakToXY(peak: PeakXYWidth, options: OptionsSG1D = {}) {
4
+ export function peakToXY(peak: NMRPeak1D, options: PeaksToXYOptions) {
7
5
  return peaksToXY([peak], options);
8
6
  }
package/src/peaks/peaksToRanges.ts CHANGED
@@ -1,14 +1,14 @@
1
1
  import type { DataXY } from 'cheminfo-types';
2
2
  import { xyIntegration } from 'ml-spectra-processing';
3
3
 
4
+ import { joinRanges } from '../ranges/utils/joinRanges';
4
5
  import type { NMRSignal1D } from '../signals/NMRSignal1D';
6
+ import jAnalyzer from '../signals/utils/jAnalyzer';
7
+ import type { SignalIntern, Peak1DIntern } from '../signals/utils/jAnalyzer';
5
8
  import type { MakeMandatory } from '../utilities/MakeMandatory';
6
9
  import type { NMRRange } from '../xy/NMRRange';
7
10
 
8
11
  import type { NMRPeak1D } from './NMRPeak1D';
9
- import jAnalyzer from './util/jAnalyzer';
10
- import type { SignalIntern, Peak1DIntern } from './util/jAnalyzer';
11
- import { joinRanges } from './util/joinRanges';
12
12
 
13
13
  export interface OptionsPeaksToRanges {
14
14
  /**
package/src/peaks/peaksToXY.ts CHANGED
@@ -1,9 +1,23 @@
1
- import { PeakXYWidth } from 'cheminfo-types';
2
1
  import { generateSpectrum, OptionsSG1D } from 'spectrum-generator';
3
2
 
4
- export function peaksToXY(peaks: PeakXYWidth[], options: OptionsSG1D = {}) {
5
- const { from, to, nbPoints = 1024, shape } = options;
6
- return generateSpectrum(peaks, {
3
+ import { NMRPeak1D } from './NMRPeak1D';
4
+ import { convertWidthToPPM } from './util/convertWidthToPPM';
5
+
6
+ /**
7
+ * Convert an array of peaks assuming that width/fwhm is in Hz
8
+ */
9
+
10
+ export interface PeaksToXYOptions extends OptionsSG1D {
11
+ /**
12
+ * frequency of the spectrum
13
+ */
14
+ frequency: number;
15
+ }
16
+
17
+ export function peaksToXY(peaks: NMRPeak1D[], options: PeaksToXYOptions) {
18
+ const { from, to, nbPoints = 1024, shape, frequency } = options;
19
+
20
+ return generateSpectrum(convertWidthToPPM(peaks, frequency), {
7
21
  generator: {
8
22
  from,
9
23
  to,
package/src/peaks/util/convertWidth.ts ADDED
@@ -0,0 +1,40 @@
1
+ import { MakeMandatory } from '../../utilities/MakeMandatory';
2
+ import { NMRPeak1D } from '../NMRPeak1D';
3
+
4
+ export type NMRPeak1DWithShape = MakeMandatory<NMRPeak1D, 'shape'>;
5
+
6
+ export interface ConvertWidthOptions {
7
+ convertTo: string & { _kind?: 'hz' | 'ppm' };
8
+ frequency: number;
9
+ }
10
+ /**
11
+ * convert width and fwhm to ppm
12
+ */
13
+ export function convertWidth(peaks: NMRPeak1D[], options: ConvertWidthOptions) {
14
+ const { frequency, convertTo } = options;
15
+ const convert = getConverter(convertTo, frequency);
16
+ return peaks.map((peak) => {
17
+ peak.width = convert(peak.width);
18
+ if (hasShape(peak)) {
19
+ if (peak.shape.fwhm) {
20
+ peak.shape.fwhm = convert(peak.shape.fwhm);
21
+ }
22
+ }
23
+ return peak;
24
+ });
25
+ }
26
+
27
+ function hasShape(peak: NMRPeak1D): peak is NMRPeak1DWithShape {
28
+ return 'shape' in peak;
29
+ }
30
+
31
+ function getConverter(convertTo: string, frequency: number) {
32
+ switch (convertTo) {
33
+ case 'ppm':
34
+ return (x: number) => x / frequency;
35
+ case 'hz':
36
+ return (x: number) => x * frequency;
37
+ default:
38
+ throw new Error(`Does not support convert to ${convertTo}`);
39
+ }
40
+ }
package/src/peaks/util/convertWidthToHz.ts ADDED
@@ -0,0 +1,7 @@
1
+ import { NMRPeak1D } from '../NMRPeak1D';
2
+
3
+ import { convertWidth } from './convertWidth';
4
+
5
+ export function convertWidthToHz(peaks: NMRPeak1D[], frequency: number) {
6
+ return convertWidth(peaks, { frequency, convertTo: 'hz' });
7
+ }
package/src/peaks/util/convertWidthToPPM.ts ADDED
@@ -0,0 +1,7 @@
1
+ import { NMRPeak1D } from '../NMRPeak1D';
2
+
3
+ import { convertWidth } from './convertWidth';
4
+
5
+ export function convertWidthToPPM(peaks: NMRPeak1D[], frequency: number) {
6
+ return convertWidth(peaks, { frequency, convertTo: 'ppm' });
7
+ }
package/src/ranges/markSolventSignal.ts CHANGED
@@ -4,8 +4,8 @@ import { addIDs } from '../assignment/utils/getAssignment/checkIDs';
4
4
  import { NMRPeak1D } from '../peaks/NMRPeak1D';
5
5
  import { detectSignals } from '../peaks/peaksToRanges';
6
6
  import { solventSuppression } from '../peaks/solventSuppression';
7
- import { SignalIntern } from '../peaks/util/jAnalyzer';
8
7
  import { NMRSignal1D } from '../signals/NMRSignal1D';
8
+ import { SignalIntern } from '../signals/utils/jAnalyzer';
9
9
  import { NMRRange } from '../xy/NMRRange';
10
10
 
11
11
  interface NMRPeak1DWithSignalID extends NMRPeak1D {
package/src/{peaks/util → ranges/utils}/joinRanges.ts RENAMED
File without changes
package/src/{peaks/util → signals/utils}/jAnalyzer.ts RENAMED
@@ -1,5 +1,5 @@
1
+ import type { NMRPeak1D } from '../../peaks/NMRPeak1D';
1
2
  import type { MakeMandatory } from '../../utilities/MakeMandatory';
2
- import type { NMRPeak1D } from '../NMRPeak1D';
3
3
 
4
4
  /*
5
5
  * This library implements the J analyser described by Cobas et al in the paper:
package/src/xy/xyAutoPeaksPicking.ts CHANGED
@@ -12,6 +12,7 @@ import {
12
12
  } from 'ml-spectra-processing';
13
13
 
14
14
  import { NMRPeak1D } from '..';
15
+ import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
15
16
 
16
17
  /**
17
18
  * Implementation of the peak picking method described by Cobas in:
@@ -35,6 +36,10 @@ export interface GetPeakListOptions
35
36
  * @default false
36
37
  */
37
38
  optimize: boolean;
39
+ /**
40
+ * frequency used to convert width and fwhm to Hz
41
+ */
42
+ frequency: number;
38
43
  }
39
44
 
40
45
  export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
@@ -61,15 +66,20 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
61
66
  * @default false
62
67
  */
63
68
  useSanPlot?: boolean;
69
+ /**
70
+ * frequency used to convert width and fwhm to Hz
71
+ */
72
+ frequency: number;
64
73
  }
65
74
 
66
75
  export function xyAutoPeaksPicking(
67
76
  data: DataXY,
68
- options: OptionsXYAutoPeaksPicking = {},
77
+ options: OptionsXYAutoPeaksPicking,
69
78
  ): NMRPeak1D[] {
70
79
  const {
71
80
  from,
72
81
  to,
82
+ frequency,
73
83
  noiseLevel,
74
84
  thresholdFactor = 3,
75
85
  minMaxRatio = 0.05,
@@ -98,6 +108,7 @@ export function xyAutoPeaksPicking(
98
108
 
99
109
  let getPeakOptions: GetPeakListOptions = {
100
110
  shape,
111
+ frequency,
101
112
  broadWidth,
102
113
  optimize,
103
114
  factorLimits,
@@ -145,6 +156,7 @@ function getNegativePeaks(
145
156
  function getPeakList(data: DataXY, options: GetPeakListOptions) {
146
157
  const {
147
158
  shape,
159
+ frequency,
148
160
  broadWidth,
149
161
  optimize,
150
162
  maxCriteria,
@@ -185,7 +197,7 @@ function getPeakList(data: DataXY, options: GetPeakListOptions) {
185
197
  });
186
198
  }
187
199
 
188
- return peakList;
200
+ return convertWidthToHz(peakList, frequency);
189
201
  }
190
202
 
191
203
  function getCutOff(data: number[] | Float64Array, options: OptionsGetCutOff) {
package/src/xy/xyAutoRangesPicking.ts CHANGED
@@ -8,7 +8,7 @@ import { xyAutoPeaksPicking } from './xyAutoPeaksPicking';
8
8
  import type { OptionsXYAutoPeaksPicking } from './xyAutoPeaksPicking';
9
9
 
10
10
  interface OptionsXYAutoRangesPicking {
11
- peakPicking?: OptionsXYAutoPeaksPicking;
11
+ peakPicking: OptionsXYAutoPeaksPicking;
12
12
  impurities?: OptionsPeaksFilterImpurities;
13
13
  ranges?: OptionsPeaksToRanges;
14
14
  }
@@ -18,7 +18,7 @@ interface OptionsXYAutoRangesPicking {
18
18
  */
19
19
  export function xyAutoRangesPicking(
20
20
  data: DataXY,
21
- options: OptionsXYAutoRangesPicking = {},
21
+ options: OptionsXYAutoRangesPicking,
22
22
  ) {
23
23
  let peaks = xyAutoPeaksPicking(data, options.peakPicking);
24
24
  peaks = peaksFilterImpurities(peaks, options.impurities);
package/src/xyz/xyzJResAnalyzer.ts CHANGED
@@ -1,8 +1,8 @@
1
1
  import type { Peak2D } from 'ml-matrix-peaks-finder';
2
2
  import simpleClustering from 'ml-simple-clustering';
3
3
 
4
- import type { JAxisKeys } from '../peaks/util/jAnalyzer';
5
- import jAnalyzer from '../peaks/util/jAnalyzer';
4
+ import type { JAxisKeys } from '../signals/utils/jAnalyzer';
5
+ import jAnalyzer from '../signals/utils/jAnalyzer';
6
6
  import type { MakeMandatory } from '../utilities/MakeMandatory';
7
7
 
8
8
  import type { NMRSignal2D } from './NMRSignal2D';
package/lib/peaks/util/joinRanges.js.map DELETED
@@ -1 +0,0 @@
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package/lib-esm/peaks/util/jAnalyzer.js.map DELETED
@@ -1 +0,0 @@
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- 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package/lib-esm/peaks/util/joinRanges.js.map DELETED
@@ -1 +0,0 @@
1
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