@jbrowse/plugin-comparative-adapters 2.6.3 → 2.7.0

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 (5) hide show
  1. package/dist/DeltaAdapter/util.js +2 -2
  2. package/dist/PAFAdapter/util.js +4 -8
  3. package/esm/DeltaAdapter/util.js +2 -2
  4. package/esm/PAFAdapter/util.js +4 -8
  5. package/package.json +3 -3
package/dist/DeltaAdapter/util.js CHANGED
@@ -91,8 +91,8 @@ function paf_delta2paf(buffer) {
91
91
  throw new Error(`inconsistent alignment on line ${i}`);
92
92
  }
93
93
  cigar.push((re - rs - x) << 4);
94
- for (let i = 0; i < cigar.length; ++i) {
95
- const rlen = cigar[i] >> 4;
94
+ for (const entry of cigar) {
95
+ const rlen = entry >> 4;
96
96
  blen += rlen;
97
97
  cigar_str.push(rlen + 'MID'.charAt(cigar[i] & 0xf));
98
98
  }
package/dist/PAFAdapter/util.js CHANGED
@@ -38,8 +38,7 @@ const util_1 = require("../util");
38
38
  // situations
39
39
  function getWeightedMeans(ret) {
40
40
  const scoreMap = {};
41
- for (let i = 0; i < ret.length; i++) {
42
- const entry = ret[i];
41
+ for (const entry of ret) {
43
42
  const query = entry.qname;
44
43
  const target = entry.tname;
45
44
  const key = query + '-' + target;
@@ -53,8 +52,7 @@ function getWeightedMeans(ret) {
53
52
  const vals = (0, util_1.zip)(val.quals, val.len);
54
53
  return [key, weightedMean(vals)];
55
54
  }));
56
- for (let i = 0; i < ret.length; i++) {
57
- const entry = ret[i];
55
+ for (const entry of ret) {
58
56
  const query = entry.qname;
59
57
  const target = entry.tname;
60
58
  const key = query + '-' + target;
@@ -62,13 +60,11 @@ function getWeightedMeans(ret) {
62
60
  }
63
61
  let min = 10000;
64
62
  let max = 0;
65
- for (let i = 0; i < ret.length; i++) {
66
- const entry = ret[i];
63
+ for (const entry of ret) {
67
64
  min = Math.min(entry.extra.meanScore || 0, min);
68
65
  max = Math.max(entry.extra.meanScore || 0, max);
69
66
  }
70
- for (let i = 0; i < ret.length; i++) {
71
- const entry = ret[i];
67
+ for (const entry of ret) {
72
68
  const b = entry.extra.meanScore || 0;
73
69
  entry.extra.meanScore = (b - min) / (max - min);
74
70
  }
package/esm/DeltaAdapter/util.js CHANGED
@@ -88,8 +88,8 @@ export function paf_delta2paf(buffer) {
88
88
  throw new Error(`inconsistent alignment on line ${i}`);
89
89
  }
90
90
  cigar.push((re - rs - x) << 4);
91
- for (let i = 0; i < cigar.length; ++i) {
92
- const rlen = cigar[i] >> 4;
91
+ for (const entry of cigar) {
92
+ const rlen = entry >> 4;
93
93
  blen += rlen;
94
94
  cigar_str.push(rlen + 'MID'.charAt(cigar[i] & 0xf));
95
95
  }
package/esm/PAFAdapter/util.js CHANGED
@@ -35,8 +35,7 @@ import { zip } from '../util';
35
35
  // situations
36
36
  export function getWeightedMeans(ret) {
37
37
  const scoreMap = {};
38
- for (let i = 0; i < ret.length; i++) {
39
- const entry = ret[i];
38
+ for (const entry of ret) {
40
39
  const query = entry.qname;
41
40
  const target = entry.tname;
42
41
  const key = query + '-' + target;
@@ -50,8 +49,7 @@ export function getWeightedMeans(ret) {
50
49
  const vals = zip(val.quals, val.len);
51
50
  return [key, weightedMean(vals)];
52
51
  }));
53
- for (let i = 0; i < ret.length; i++) {
54
- const entry = ret[i];
52
+ for (const entry of ret) {
55
53
  const query = entry.qname;
56
54
  const target = entry.tname;
57
55
  const key = query + '-' + target;
@@ -59,13 +57,11 @@ export function getWeightedMeans(ret) {
59
57
  }
60
58
  let min = 10000;
61
59
  let max = 0;
62
- for (let i = 0; i < ret.length; i++) {
63
- const entry = ret[i];
60
+ for (const entry of ret) {
64
61
  min = Math.min(entry.extra.meanScore || 0, min);
65
62
  max = Math.max(entry.extra.meanScore || 0, max);
66
63
  }
67
- for (let i = 0; i < ret.length; i++) {
68
- const entry = ret[i];
64
+ for (const entry of ret) {
69
65
  const b = entry.extra.meanScore || 0;
70
66
  entry.extra.meanScore = (b - min) / (max - min);
71
67
  }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-comparative-adapters",
3
- "version": "2.6.3",
3
+ "version": "2.7.0",
4
4
  "description": "JBrowse 2 comparative adapters",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -45,7 +45,7 @@
45
45
  "@jbrowse/plugin-linear-genome-view": "^2.0.0",
46
46
  "@mui/material": "^5.0.0",
47
47
  "mobx": "^6.0.0",
48
- "mobx-react": "^7.0.0",
48
+ "mobx-react": "^9.0.0",
49
49
  "mobx-state-tree": "^5.0.0",
50
50
  "prop-types": "^15.0.0",
51
51
  "react": ">=16.8.0",
@@ -58,5 +58,5 @@
58
58
  "publishConfig": {
59
59
  "access": "public"
60
60
  },
61
- "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
61
+ "gitHead": "dbe7fb1af01fc89f833d2744635eb44a17365b41"
62
62
  }