@jbrowse/plugin-alignments 2.2.0 → 2.2.2
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.
- package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +12 -13
- package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
- package/dist/BamAdapter/BamAdapter.d.ts +1 -1
- package/dist/BamAdapter/BamAdapter.js +1 -0
- package/dist/BamAdapter/BamAdapter.js.map +1 -1
- package/dist/BamAdapter/BamSlightlyLazyFeature.js +1 -0
- package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
- package/dist/BamAdapter/MismatchParser.d.ts +2 -2
- package/dist/BamAdapter/MismatchParser.js +4 -7
- package/dist/BamAdapter/MismatchParser.js.map +1 -1
- package/dist/BamAdapter/configSchema.js +1 -1
- package/dist/BamAdapter/configSchema.js.map +1 -1
- package/dist/BamAdapter/index.js +7 -5
- package/dist/BamAdapter/index.js.map +1 -1
- package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts +1 -10
- package/dist/CramAdapter/CramSlightlyLazyFeature.js +5 -218
- package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
- package/dist/CramAdapter/CramTestAdapters.d.ts +1 -1
- package/dist/CramAdapter/CramTestAdapters.js +3 -2
- package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
- package/dist/CramAdapter/configSchema.js +2 -2
- package/dist/CramAdapter/configSchema.js.map +1 -1
- package/dist/CramAdapter/index.js +7 -5
- package/dist/CramAdapter/index.js.map +1 -1
- package/dist/CramAdapter/util.d.ts +18 -0
- package/dist/CramAdapter/util.js +241 -0
- package/dist/CramAdapter/util.js.map +1 -0
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +1 -1
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
- package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts +1 -1
- package/dist/LinearAlignmentsDisplay/models/model.d.ts +5 -5
- package/dist/LinearAlignmentsDisplay/models/model.js +7 -7
- package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
- package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts +3 -1
- package/dist/LinearPileupDisplay/components/ColorByModifications.js +7 -22
- package/dist/LinearPileupDisplay/components/ColorByModifications.js.map +1 -1
- package/dist/LinearPileupDisplay/components/ColorByTag.js +2 -22
- package/dist/LinearPileupDisplay/components/ColorByTag.js.map +1 -1
- package/dist/LinearPileupDisplay/components/FilterByTag.js +2 -15
- package/dist/LinearPileupDisplay/components/FilterByTag.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +2 -19
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js +2 -18
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SortByTag.js +2 -23
- package/dist/LinearPileupDisplay/components/SortByTag.js.map +1 -1
- package/dist/LinearPileupDisplay/configSchema.d.ts +4 -4
- package/dist/LinearPileupDisplay/configSchema.js +2 -2
- package/dist/LinearPileupDisplay/configSchema.js.map +1 -1
- package/dist/LinearPileupDisplay/index.d.ts +3 -0
- package/dist/LinearPileupDisplay/index.js +3 -0
- package/dist/LinearPileupDisplay/index.js.map +1 -1
- package/dist/LinearPileupDisplay/model.d.ts +19 -9
- package/dist/LinearPileupDisplay/model.js +25 -30
- package/dist/LinearPileupDisplay/model.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +14 -10
- package/dist/LinearSNPCoverageDisplay/models/model.js +8 -6
- package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
- package/dist/PileupRPC/rpcMethods.d.ts +1 -1
- package/dist/PileupRPC/rpcMethods.js +12 -7
- package/dist/PileupRPC/rpcMethods.js.map +1 -1
- package/dist/PileupRenderer/PileupLayoutSession.d.ts +1 -1
- package/dist/PileupRenderer/PileupRenderer.js +32 -28
- package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
- package/dist/PileupRenderer/configSchema.js +1 -1
- package/dist/PileupRenderer/configSchema.js.map +1 -1
- package/dist/PileupRenderer/index.js +8 -6
- package/dist/PileupRenderer/index.js.map +1 -1
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +0 -51
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +3 -182
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/dist/SNPCoverageAdapter/configSchema.d.ts +2 -3
- package/dist/SNPCoverageAdapter/configSchema.js +6 -3
- package/dist/SNPCoverageAdapter/configSchema.js.map +1 -1
- package/dist/SNPCoverageAdapter/generateCoverageBins.d.ts +53 -0
- package/dist/SNPCoverageAdapter/generateCoverageBins.js +185 -0
- package/dist/SNPCoverageAdapter/generateCoverageBins.js.map +1 -0
- package/dist/SNPCoverageAdapter/index.d.ts +1 -2
- package/dist/SNPCoverageAdapter/index.js +17 -14
- package/dist/SNPCoverageAdapter/index.js.map +1 -1
- package/dist/index.d.ts +3 -2
- package/dist/index.js +4 -2
- package/dist/index.js.map +1 -1
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +12 -13
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
- package/esm/BamAdapter/BamAdapter.d.ts +1 -1
- package/esm/BamAdapter/BamAdapter.js +1 -0
- package/esm/BamAdapter/BamAdapter.js.map +1 -1
- package/esm/BamAdapter/BamSlightlyLazyFeature.js +1 -0
- package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
- package/esm/BamAdapter/MismatchParser.d.ts +2 -2
- package/esm/BamAdapter/MismatchParser.js +4 -7
- package/esm/BamAdapter/MismatchParser.js.map +1 -1
- package/esm/BamAdapter/configSchema.js +1 -1
- package/esm/BamAdapter/configSchema.js.map +1 -1
- package/esm/BamAdapter/index.js +7 -5
- package/esm/BamAdapter/index.js.map +1 -1
- package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +1 -10
- package/esm/CramAdapter/CramSlightlyLazyFeature.js +5 -218
- package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
- package/esm/CramAdapter/CramTestAdapters.d.ts +1 -1
- package/esm/CramAdapter/CramTestAdapters.js +3 -2
- package/esm/CramAdapter/CramTestAdapters.js.map +1 -1
- package/esm/CramAdapter/configSchema.js +2 -2
- package/esm/CramAdapter/configSchema.js.map +1 -1
- package/esm/CramAdapter/index.js +7 -5
- package/esm/CramAdapter/index.js.map +1 -1
- package/esm/CramAdapter/util.d.ts +18 -0
- package/esm/CramAdapter/util.js +236 -0
- package/esm/CramAdapter/util.js.map +1 -0
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +1 -1
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
- package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts +1 -1
- package/esm/LinearAlignmentsDisplay/models/model.d.ts +5 -5
- package/esm/LinearAlignmentsDisplay/models/model.js +7 -7
- package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
- package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +3 -1
- package/esm/LinearPileupDisplay/components/ColorByModifications.js +8 -23
- package/esm/LinearPileupDisplay/components/ColorByModifications.js.map +1 -1
- package/esm/LinearPileupDisplay/components/ColorByTag.js +3 -20
- package/esm/LinearPileupDisplay/components/ColorByTag.js.map +1 -1
- package/esm/LinearPileupDisplay/components/FilterByTag.js +3 -13
- package/esm/LinearPileupDisplay/components/FilterByTag.js.map +1 -1
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.js +3 -17
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
- package/esm/LinearPileupDisplay/components/SetMaxHeight.js +3 -16
- package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
- package/esm/LinearPileupDisplay/components/SortByTag.js +3 -21
- package/esm/LinearPileupDisplay/components/SortByTag.js.map +1 -1
- package/esm/LinearPileupDisplay/configSchema.d.ts +4 -4
- package/esm/LinearPileupDisplay/configSchema.js +2 -2
- package/esm/LinearPileupDisplay/configSchema.js.map +1 -1
- package/esm/LinearPileupDisplay/index.d.ts +3 -0
- package/esm/LinearPileupDisplay/index.js +1 -0
- package/esm/LinearPileupDisplay/index.js.map +1 -1
- package/esm/LinearPileupDisplay/model.d.ts +19 -9
- package/esm/LinearPileupDisplay/model.js +25 -30
- package/esm/LinearPileupDisplay/model.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +14 -10
- package/esm/LinearSNPCoverageDisplay/models/model.js +9 -7
- package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
- package/esm/PileupRPC/rpcMethods.d.ts +1 -1
- package/esm/PileupRPC/rpcMethods.js +12 -7
- package/esm/PileupRPC/rpcMethods.js.map +1 -1
- package/esm/PileupRenderer/PileupLayoutSession.d.ts +1 -1
- package/esm/PileupRenderer/PileupRenderer.js +32 -28
- package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
- package/esm/PileupRenderer/configSchema.js +1 -1
- package/esm/PileupRenderer/configSchema.js.map +1 -1
- package/esm/PileupRenderer/index.js +8 -6
- package/esm/PileupRenderer/index.js.map +1 -1
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +0 -51
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +4 -183
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/esm/SNPCoverageAdapter/configSchema.d.ts +2 -3
- package/esm/SNPCoverageAdapter/configSchema.js +6 -3
- package/esm/SNPCoverageAdapter/configSchema.js.map +1 -1
- package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts +53 -0
- package/esm/SNPCoverageAdapter/generateCoverageBins.js +182 -0
- package/esm/SNPCoverageAdapter/generateCoverageBins.js.map +1 -0
- package/esm/SNPCoverageAdapter/index.d.ts +1 -2
- package/esm/SNPCoverageAdapter/index.js +17 -15
- package/esm/SNPCoverageAdapter/index.js.map +1 -1
- package/esm/index.d.ts +3 -2
- package/esm/index.js +2 -2
- package/esm/index.js.map +1 -1
- package/package.json +4 -3
- package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +17 -16
- package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +1 -473
- package/src/AlignmentsFeatureDetail/index.test.js +6 -4
- package/src/BamAdapter/BamAdapter.ts +3 -2
- package/src/BamAdapter/BamSlightlyLazyFeature.ts +2 -1
- package/src/BamAdapter/MismatchParser.test.ts +21 -12
- package/src/BamAdapter/MismatchParser.ts +7 -10
- package/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap +135 -135
- package/src/BamAdapter/configSchema.ts +1 -1
- package/src/BamAdapter/index.ts +7 -8
- package/src/CombinationTest.test.ts +107 -0
- package/src/CramAdapter/CramSlightlyLazyFeature.ts +10 -219
- package/src/CramAdapter/CramTestAdapters.ts +2 -1
- package/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap +31 -31
- package/src/CramAdapter/__snapshots__/util.test.ts.snap +14 -0
- package/src/CramAdapter/configSchema.ts +2 -3
- package/src/CramAdapter/index.ts +7 -8
- package/src/CramAdapter/util.test.ts +26 -0
- package/src/CramAdapter/util.ts +251 -0
- package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +3 -1
- package/src/LinearAlignmentsDisplay/models/model.tsx +8 -7
- package/src/LinearPileupDisplay/components/ColorByModifications.tsx +5 -34
- package/src/LinearPileupDisplay/components/ColorByTag.tsx +2 -29
- package/src/LinearPileupDisplay/components/FilterByTag.tsx +2 -22
- package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +2 -22
- package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +2 -24
- package/src/LinearPileupDisplay/components/SortByTag.tsx +2 -31
- package/src/LinearPileupDisplay/configSchema.ts +3 -5
- package/src/LinearPileupDisplay/index.ts +5 -0
- package/src/LinearPileupDisplay/model.ts +31 -30
- package/src/LinearSNPCoverageDisplay/models/model.ts +12 -8
- package/src/PileupRPC/rpcMethods.ts +15 -20
- package/src/PileupRenderer/{PileupRenderer.tsx → PileupRenderer.ts} +48 -54
- package/src/PileupRenderer/configSchema.ts +1 -1
- package/src/PileupRenderer/index.ts +8 -9
- package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +5 -249
- package/src/SNPCoverageAdapter/configSchema.ts +14 -13
- package/src/SNPCoverageAdapter/generateCoverageBins.ts +245 -0
- package/src/SNPCoverageAdapter/index.ts +17 -18
- package/src/__snapshots__/index.test.ts.snap +1 -1
- package/src/index.ts +11 -4
|
@@ -2,33 +2,13 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
|
|
|
2
2
|
import SimpleFeature from '@jbrowse/core/util/simpleFeature';
|
|
3
3
|
import { ObservableCreate } from '@jbrowse/core/util/rxjs';
|
|
4
4
|
import { toArray } from 'rxjs/operators';
|
|
5
|
-
import
|
|
6
|
-
import {
|
|
7
|
-
function mismatchLen(mismatch) {
|
|
8
|
-
return !isInterbase(mismatch.type) ? mismatch.length : 1;
|
|
9
|
-
}
|
|
10
|
-
function isInterbase(type) {
|
|
11
|
-
return type === 'softclip' || type === 'hardclip' || type === 'insertion';
|
|
12
|
-
}
|
|
13
|
-
// eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
14
|
-
function inc(bin, strand, type, field) {
|
|
15
|
-
let thisBin = bin[type][field];
|
|
16
|
-
if (thisBin === undefined) {
|
|
17
|
-
thisBin = bin[type][field] = {
|
|
18
|
-
total: 0,
|
|
19
|
-
'-1': 0,
|
|
20
|
-
'0': 0,
|
|
21
|
-
'1': 0,
|
|
22
|
-
};
|
|
23
|
-
}
|
|
24
|
-
thisBin.total++;
|
|
25
|
-
thisBin[strand]++;
|
|
26
|
-
}
|
|
5
|
+
import generateCoverageBins from './generateCoverageBins';
|
|
6
|
+
import { fetchSequence } from '../util';
|
|
27
7
|
export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
|
|
28
8
|
async configure() {
|
|
29
9
|
var _a, _b;
|
|
30
10
|
const subadapterConfig = this.getConf('subadapter');
|
|
31
|
-
const sequenceConf =
|
|
11
|
+
const sequenceConf = subadapterConfig.sequenceAdapter;
|
|
32
12
|
const dataAdapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, subadapterConfig));
|
|
33
13
|
const sequenceAdapter = sequenceConf
|
|
34
14
|
? await ((_b = this.getSubAdapter) === null || _b === void 0 ? void 0 : _b.call(this, sequenceConf))
|
|
@@ -55,7 +35,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
|
|
|
55
35
|
.getFeatures(region, opts)
|
|
56
36
|
.pipe(toArray())
|
|
57
37
|
.toPromise();
|
|
58
|
-
const { bins, skipmap } = await
|
|
38
|
+
const { bins, skipmap } = await generateCoverageBins(feats, region, opts, arg => this.fetchSequence(arg));
|
|
59
39
|
bins.forEach((bin, index) => {
|
|
60
40
|
const start = region.start + index;
|
|
61
41
|
observer.next(new SimpleFeature({
|
|
@@ -95,165 +75,6 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
|
|
|
95
75
|
return subadapter.getRefNames(opts);
|
|
96
76
|
}
|
|
97
77
|
freeResources( /* { region } */) { }
|
|
98
|
-
async generateCoverageBins(features, region, opts) {
|
|
99
|
-
var _a;
|
|
100
|
-
const { colorBy } = opts;
|
|
101
|
-
const binMax = Math.ceil(region.end - region.start);
|
|
102
|
-
const skipmap = {};
|
|
103
|
-
const regionSeq = features.length && shouldFetchReferenceSequence((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type)
|
|
104
|
-
? await this.fetchSequence(region)
|
|
105
|
-
: undefined;
|
|
106
|
-
const bins = [];
|
|
107
|
-
for (let i = 0; i < features.length; i++) {
|
|
108
|
-
const feature = features[i];
|
|
109
|
-
const fstart = feature.get('start');
|
|
110
|
-
const fend = feature.get('end');
|
|
111
|
-
const fstrand = feature.get('strand');
|
|
112
|
-
for (let j = fstart; j < fend + 1; j++) {
|
|
113
|
-
const i = j - region.start;
|
|
114
|
-
if (i >= 0 && i < binMax) {
|
|
115
|
-
if (bins[i] === undefined) {
|
|
116
|
-
bins[i] = {
|
|
117
|
-
total: 0,
|
|
118
|
-
all: 0,
|
|
119
|
-
ref: 0,
|
|
120
|
-
'-1': 0,
|
|
121
|
-
'0': 0,
|
|
122
|
-
'1': 0,
|
|
123
|
-
lowqual: {},
|
|
124
|
-
cov: {},
|
|
125
|
-
delskips: {},
|
|
126
|
-
noncov: {},
|
|
127
|
-
};
|
|
128
|
-
}
|
|
129
|
-
if (j !== fend) {
|
|
130
|
-
bins[i].total++;
|
|
131
|
-
bins[i].all++;
|
|
132
|
-
bins[i].ref++;
|
|
133
|
-
bins[i][fstrand]++;
|
|
134
|
-
}
|
|
135
|
-
}
|
|
136
|
-
}
|
|
137
|
-
if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
|
|
138
|
-
const seq = feature.get('seq');
|
|
139
|
-
const mm = getTagAlt(feature, 'MM', 'Mm') || '';
|
|
140
|
-
const ops = parseCigar(feature.get('CIGAR'));
|
|
141
|
-
const fend = feature.get('end');
|
|
142
|
-
getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
|
|
143
|
-
const mod = `mod_${type}`;
|
|
144
|
-
for (const pos of getNextRefPos(ops, positions)) {
|
|
145
|
-
const epos = pos + fstart - region.start;
|
|
146
|
-
if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
|
|
147
|
-
const bin = bins[epos];
|
|
148
|
-
if (bin) {
|
|
149
|
-
inc(bin, fstrand, 'cov', mod);
|
|
150
|
-
}
|
|
151
|
-
else {
|
|
152
|
-
console.warn('Undefined position in modifications snpcoverage encountered');
|
|
153
|
-
}
|
|
154
|
-
}
|
|
155
|
-
}
|
|
156
|
-
});
|
|
157
|
-
}
|
|
158
|
-
// methylation based coloring takes into account both reference
|
|
159
|
-
// sequence CpG detection and reads
|
|
160
|
-
else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
|
|
161
|
-
if (!regionSeq) {
|
|
162
|
-
throw new Error('no region sequence detected, need sequenceAdapter configuration');
|
|
163
|
-
}
|
|
164
|
-
const seq = feature.get('seq');
|
|
165
|
-
const mm = getTagAlt(feature, 'MM', 'Mm') || '';
|
|
166
|
-
const methBins = new Array(region.end - region.start).fill(0);
|
|
167
|
-
const ops = parseCigar(feature.get('CIGAR'));
|
|
168
|
-
getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
|
|
169
|
-
// we are processing methylation
|
|
170
|
-
if (type === 'm') {
|
|
171
|
-
for (const pos of getNextRefPos(ops, positions)) {
|
|
172
|
-
const epos = pos + fstart - region.start;
|
|
173
|
-
if (epos >= 0 && epos < methBins.length) {
|
|
174
|
-
methBins[epos] = 1;
|
|
175
|
-
}
|
|
176
|
-
}
|
|
177
|
-
}
|
|
178
|
-
});
|
|
179
|
-
for (let j = fstart; j < fend; j++) {
|
|
180
|
-
const i = j - region.start;
|
|
181
|
-
if (i >= 0 && i < bins.length - 1) {
|
|
182
|
-
const l1 = regionSeq[i].toLowerCase();
|
|
183
|
-
const l2 = regionSeq[i + 1].toLowerCase();
|
|
184
|
-
const bin = bins[i];
|
|
185
|
-
const bin1 = bins[i + 1];
|
|
186
|
-
// color
|
|
187
|
-
if (l1 === 'c' && l2 === 'g') {
|
|
188
|
-
if (methBins[i] || methBins[i + 1]) {
|
|
189
|
-
inc(bin, fstrand, 'cov', 'meth');
|
|
190
|
-
inc(bin1, fstrand, 'cov', 'meth');
|
|
191
|
-
bins[i].ref--;
|
|
192
|
-
bins[i][fstrand]--;
|
|
193
|
-
bins[i + 1].ref--;
|
|
194
|
-
bins[i + 1][fstrand]--;
|
|
195
|
-
}
|
|
196
|
-
else {
|
|
197
|
-
inc(bin, fstrand, 'cov', 'unmeth');
|
|
198
|
-
inc(bin1, fstrand, 'cov', 'unmeth');
|
|
199
|
-
bins[i].ref--;
|
|
200
|
-
bins[i][fstrand]--;
|
|
201
|
-
bins[i + 1].ref--;
|
|
202
|
-
bins[i + 1][fstrand]--;
|
|
203
|
-
}
|
|
204
|
-
}
|
|
205
|
-
}
|
|
206
|
-
}
|
|
207
|
-
}
|
|
208
|
-
// normal SNP based coloring
|
|
209
|
-
const mismatches = feature.get('mismatches') || [];
|
|
210
|
-
const colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
|
|
211
|
-
for (let i = 0; i < mismatches.length; i++) {
|
|
212
|
-
const mismatch = mismatches[i];
|
|
213
|
-
const mstart = fstart + mismatch.start;
|
|
214
|
-
const mlen = mismatchLen(mismatch);
|
|
215
|
-
const mend = mstart + mlen;
|
|
216
|
-
for (let j = mstart; j < mstart + mlen; j++) {
|
|
217
|
-
const epos = j - region.start;
|
|
218
|
-
if (epos >= 0 && epos < bins.length) {
|
|
219
|
-
const bin = bins[epos];
|
|
220
|
-
const { base, type } = mismatch;
|
|
221
|
-
const interbase = isInterbase(type);
|
|
222
|
-
if (!interbase) {
|
|
223
|
-
bin.ref--;
|
|
224
|
-
bin[fstrand]--;
|
|
225
|
-
}
|
|
226
|
-
else {
|
|
227
|
-
inc(bin, fstrand, 'noncov', type);
|
|
228
|
-
}
|
|
229
|
-
if (type === 'deletion' || type === 'skip') {
|
|
230
|
-
inc(bin, fstrand, 'delskips', type);
|
|
231
|
-
bin.total--;
|
|
232
|
-
}
|
|
233
|
-
else if (!interbase && colorSNPs) {
|
|
234
|
-
inc(bin, fstrand, 'cov', base);
|
|
235
|
-
bin.refbase = mismatch.altbase;
|
|
236
|
-
}
|
|
237
|
-
}
|
|
238
|
-
}
|
|
239
|
-
if (mismatch.type === 'skip') {
|
|
240
|
-
const hash = `${mstart}_${mend}_${fstrand}`;
|
|
241
|
-
if (skipmap[hash] === undefined) {
|
|
242
|
-
skipmap[hash] = {
|
|
243
|
-
feature: feature,
|
|
244
|
-
start: mstart,
|
|
245
|
-
end: mend,
|
|
246
|
-
strand: fstrand,
|
|
247
|
-
xs: getTag(feature, 'XS') || getTag(feature, 'TS'),
|
|
248
|
-
score: 0,
|
|
249
|
-
};
|
|
250
|
-
}
|
|
251
|
-
skipmap[hash].score++;
|
|
252
|
-
}
|
|
253
|
-
}
|
|
254
|
-
}
|
|
255
|
-
return { bins, skipmap };
|
|
256
|
-
}
|
|
257
78
|
}
|
|
258
79
|
const { capabilities } = SNPCoverageAdapter;
|
|
259
80
|
export { capabilities };
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,
|
|
1
|
+
{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,EAAE,aAAa,EAAE,MAAM,SAAS,CAAA;AAEvC,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,sBAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,gBAAgB,CAAC,eAAe,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,aAAa,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,UAAU;iBAC3B,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC;iBACzB,IAAI,CAAC,OAAO,EAAE,CAAC;iBACf,SAAS,EAAE,CAAA;YAEd,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,oBAAoB,CAClD,KAAK,EACL,MAAM,EACN,IAAI,EACJ,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAC/B,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;gBAClC,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,KAAK,EAAE;oBACzB,IAAI,EAAE;wBACJ,KAAK,EAAE,GAAG,CAAC,KAAK;wBAChB,OAAO,EAAE,GAAG;wBACZ,KAAK;wBACL,GAAG,EAAE,KAAK,GAAG,CAAC;wBACd,OAAO,EAAE,MAAM,CAAC,OAAO;qBACxB;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,uCAAuC;YACvC,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE;gBAC9C,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG;oBACP,IAAI,EAAE;wBACJ,IAAI,EAAE,MAAM;wBACZ,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,GAAG,EAAE,IAAI,CAAC,GAAG;wBACb,MAAM,EAAE,IAAI,CAAC,MAAM;wBACnB,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,EAAE,EAAE,IAAI,CAAC,EAAE;qBACZ;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,OAAiB,EAAE,IAAkB;QAC9D,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,oBAAoB,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IACvD,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QACtC,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AAED,MAAM,EAAE,YAAY,EAAE,GAAG,kBAAkB,CAAA;AAC3C,OAAO,EAAE,YAAY,EAAE,CAAA"}
|
|
@@ -1,3 +1,2 @@
|
|
|
1
|
-
|
|
2
|
-
|
|
3
|
-
export default SNPCoverageAdapter;
|
|
1
|
+
declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
|
|
2
|
+
export default configSchema;
|
|
@@ -3,12 +3,15 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
|
|
|
3
3
|
* #config SNPCoverageAdapter
|
|
4
4
|
*/
|
|
5
5
|
function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
|
|
6
|
-
const
|
|
6
|
+
const configSchema = ConfigurationSchema('SNPCoverageAdapter', {
|
|
7
7
|
/**
|
|
8
8
|
* #slot
|
|
9
9
|
* normally refers to a BAM or CRAM adapter
|
|
10
10
|
*/
|
|
11
|
-
subadapter:
|
|
11
|
+
subadapter: {
|
|
12
|
+
type: 'frozen',
|
|
13
|
+
defaultValue: null,
|
|
14
|
+
},
|
|
12
15
|
}, { explicitlyTyped: true });
|
|
13
|
-
export default
|
|
16
|
+
export default configSchema;
|
|
14
17
|
//# sourceMappingURL=configSchema.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;
|
|
1
|
+
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,oBAAoB,EACpB;IACE;;;OAGG;IACH,UAAU,EAAE;QACV,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,YAAY,CAAA"}
|
|
@@ -0,0 +1,53 @@
|
|
|
1
|
+
import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
|
|
2
|
+
import { Feature } from '@jbrowse/core/util/simpleFeature';
|
|
3
|
+
export default function generateCoverageBins(features: Feature[], region: Region, opts: {
|
|
4
|
+
bpPerPx?: number;
|
|
5
|
+
colorBy?: {
|
|
6
|
+
type: string;
|
|
7
|
+
tag?: string;
|
|
8
|
+
};
|
|
9
|
+
}, fetchSequence: (arg: Region) => Promise<string>): Promise<{
|
|
10
|
+
bins: {
|
|
11
|
+
refbase?: string | undefined;
|
|
12
|
+
total: number;
|
|
13
|
+
all: number;
|
|
14
|
+
ref: number;
|
|
15
|
+
'-1': 0;
|
|
16
|
+
'0': 0;
|
|
17
|
+
'1': 0;
|
|
18
|
+
lowqual: {
|
|
19
|
+
total: number;
|
|
20
|
+
strands: {
|
|
21
|
+
[key: string]: number;
|
|
22
|
+
};
|
|
23
|
+
};
|
|
24
|
+
cov: {
|
|
25
|
+
total: number;
|
|
26
|
+
strands: {
|
|
27
|
+
[key: string]: number;
|
|
28
|
+
};
|
|
29
|
+
};
|
|
30
|
+
delskips: {
|
|
31
|
+
total: number;
|
|
32
|
+
strands: {
|
|
33
|
+
[key: string]: number;
|
|
34
|
+
};
|
|
35
|
+
};
|
|
36
|
+
noncov: {
|
|
37
|
+
total: number;
|
|
38
|
+
strands: {
|
|
39
|
+
[key: string]: number;
|
|
40
|
+
};
|
|
41
|
+
};
|
|
42
|
+
}[];
|
|
43
|
+
skipmap: {
|
|
44
|
+
[key: string]: {
|
|
45
|
+
score: number;
|
|
46
|
+
feature: unknown;
|
|
47
|
+
start: number;
|
|
48
|
+
end: number;
|
|
49
|
+
strand: number;
|
|
50
|
+
xs: string;
|
|
51
|
+
};
|
|
52
|
+
};
|
|
53
|
+
}>;
|
|
@@ -0,0 +1,182 @@
|
|
|
1
|
+
import { getTag, getTagAlt, shouldFetchReferenceSequence } from '../util';
|
|
2
|
+
import { parseCigar, getNextRefPos, getModificationPositions, } from '../BamAdapter/MismatchParser';
|
|
3
|
+
function mismatchLen(mismatch) {
|
|
4
|
+
return !isInterbase(mismatch.type) ? mismatch.length : 1;
|
|
5
|
+
}
|
|
6
|
+
function isInterbase(type) {
|
|
7
|
+
return type === 'softclip' || type === 'hardclip' || type === 'insertion';
|
|
8
|
+
}
|
|
9
|
+
// eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
10
|
+
function inc(bin, strand, type, field) {
|
|
11
|
+
let thisBin = bin[type][field];
|
|
12
|
+
if (thisBin === undefined) {
|
|
13
|
+
thisBin = bin[type][field] = {
|
|
14
|
+
total: 0,
|
|
15
|
+
'-1': 0,
|
|
16
|
+
'0': 0,
|
|
17
|
+
'1': 0,
|
|
18
|
+
};
|
|
19
|
+
}
|
|
20
|
+
thisBin.total++;
|
|
21
|
+
thisBin[strand]++;
|
|
22
|
+
}
|
|
23
|
+
export default async function generateCoverageBins(features, region, opts, fetchSequence) {
|
|
24
|
+
var _a;
|
|
25
|
+
const { colorBy } = opts;
|
|
26
|
+
const binMax = Math.ceil(region.end - region.start);
|
|
27
|
+
const skipmap = {};
|
|
28
|
+
const regionSeq = features.length && shouldFetchReferenceSequence((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type)
|
|
29
|
+
? await fetchSequence(region)
|
|
30
|
+
: undefined;
|
|
31
|
+
const bins = [];
|
|
32
|
+
for (let i = 0; i < features.length; i++) {
|
|
33
|
+
const feature = features[i];
|
|
34
|
+
const fstart = feature.get('start');
|
|
35
|
+
const fend = feature.get('end');
|
|
36
|
+
const fstrand = feature.get('strand');
|
|
37
|
+
for (let j = fstart; j < fend + 1; j++) {
|
|
38
|
+
const i = j - region.start;
|
|
39
|
+
if (i >= 0 && i < binMax) {
|
|
40
|
+
if (bins[i] === undefined) {
|
|
41
|
+
bins[i] = {
|
|
42
|
+
total: 0,
|
|
43
|
+
all: 0,
|
|
44
|
+
ref: 0,
|
|
45
|
+
'-1': 0,
|
|
46
|
+
'0': 0,
|
|
47
|
+
'1': 0,
|
|
48
|
+
lowqual: {},
|
|
49
|
+
cov: {},
|
|
50
|
+
delskips: {},
|
|
51
|
+
noncov: {},
|
|
52
|
+
};
|
|
53
|
+
}
|
|
54
|
+
if (j !== fend) {
|
|
55
|
+
bins[i].total++;
|
|
56
|
+
bins[i].all++;
|
|
57
|
+
bins[i].ref++;
|
|
58
|
+
bins[i][fstrand]++;
|
|
59
|
+
}
|
|
60
|
+
}
|
|
61
|
+
}
|
|
62
|
+
if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
|
|
63
|
+
const seq = feature.get('seq');
|
|
64
|
+
const mm = getTagAlt(feature, 'MM', 'Mm') || '';
|
|
65
|
+
const ops = parseCigar(feature.get('CIGAR'));
|
|
66
|
+
const fend = feature.get('end');
|
|
67
|
+
getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
|
|
68
|
+
const mod = `mod_${type}`;
|
|
69
|
+
for (const pos of getNextRefPos(ops, positions)) {
|
|
70
|
+
const epos = pos + fstart - region.start;
|
|
71
|
+
if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
|
|
72
|
+
const bin = bins[epos];
|
|
73
|
+
if (bin) {
|
|
74
|
+
inc(bin, fstrand, 'cov', mod);
|
|
75
|
+
}
|
|
76
|
+
else {
|
|
77
|
+
console.warn('Undefined position in modifications snpcoverage encountered');
|
|
78
|
+
}
|
|
79
|
+
}
|
|
80
|
+
}
|
|
81
|
+
});
|
|
82
|
+
}
|
|
83
|
+
// methylation based coloring takes into account both reference
|
|
84
|
+
// sequence CpG detection and reads
|
|
85
|
+
else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
|
|
86
|
+
if (!regionSeq) {
|
|
87
|
+
throw new Error('no region sequence detected, need sequenceAdapter configuration');
|
|
88
|
+
}
|
|
89
|
+
const seq = feature.get('seq');
|
|
90
|
+
const mm = getTagAlt(feature, 'MM', 'Mm') || '';
|
|
91
|
+
const methBins = new Array(region.end - region.start).fill(0);
|
|
92
|
+
const ops = parseCigar(feature.get('CIGAR'));
|
|
93
|
+
getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
|
|
94
|
+
// we are processing methylation
|
|
95
|
+
if (type === 'm') {
|
|
96
|
+
for (const pos of getNextRefPos(ops, positions)) {
|
|
97
|
+
const epos = pos + fstart - region.start;
|
|
98
|
+
if (epos >= 0 && epos < methBins.length) {
|
|
99
|
+
methBins[epos] = 1;
|
|
100
|
+
}
|
|
101
|
+
}
|
|
102
|
+
}
|
|
103
|
+
});
|
|
104
|
+
for (let j = fstart; j < fend; j++) {
|
|
105
|
+
const i = j - region.start;
|
|
106
|
+
if (i >= 0 && i < bins.length - 1) {
|
|
107
|
+
const l1 = regionSeq[i].toLowerCase();
|
|
108
|
+
const l2 = regionSeq[i + 1].toLowerCase();
|
|
109
|
+
const bin = bins[i];
|
|
110
|
+
const bin1 = bins[i + 1];
|
|
111
|
+
// color
|
|
112
|
+
if (l1 === 'c' && l2 === 'g') {
|
|
113
|
+
if (methBins[i] || methBins[i + 1]) {
|
|
114
|
+
inc(bin, fstrand, 'cov', 'meth');
|
|
115
|
+
inc(bin1, fstrand, 'cov', 'meth');
|
|
116
|
+
bins[i].ref--;
|
|
117
|
+
bins[i][fstrand]--;
|
|
118
|
+
bins[i + 1].ref--;
|
|
119
|
+
bins[i + 1][fstrand]--;
|
|
120
|
+
}
|
|
121
|
+
else {
|
|
122
|
+
inc(bin, fstrand, 'cov', 'unmeth');
|
|
123
|
+
inc(bin1, fstrand, 'cov', 'unmeth');
|
|
124
|
+
bins[i].ref--;
|
|
125
|
+
bins[i][fstrand]--;
|
|
126
|
+
bins[i + 1].ref--;
|
|
127
|
+
bins[i + 1][fstrand]--;
|
|
128
|
+
}
|
|
129
|
+
}
|
|
130
|
+
}
|
|
131
|
+
}
|
|
132
|
+
}
|
|
133
|
+
// normal SNP based coloring
|
|
134
|
+
const mismatches = feature.get('mismatches') || [];
|
|
135
|
+
const colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
|
|
136
|
+
for (let i = 0; i < mismatches.length; i++) {
|
|
137
|
+
const mismatch = mismatches[i];
|
|
138
|
+
const mstart = fstart + mismatch.start;
|
|
139
|
+
const mlen = mismatchLen(mismatch);
|
|
140
|
+
const mend = mstart + mlen;
|
|
141
|
+
for (let j = mstart; j < mstart + mlen; j++) {
|
|
142
|
+
const epos = j - region.start;
|
|
143
|
+
if (epos >= 0 && epos < bins.length) {
|
|
144
|
+
const bin = bins[epos];
|
|
145
|
+
const { base, type } = mismatch;
|
|
146
|
+
const interbase = isInterbase(type);
|
|
147
|
+
if (!interbase) {
|
|
148
|
+
bin.ref--;
|
|
149
|
+
bin[fstrand]--;
|
|
150
|
+
}
|
|
151
|
+
else {
|
|
152
|
+
inc(bin, fstrand, 'noncov', type);
|
|
153
|
+
}
|
|
154
|
+
if (type === 'deletion' || type === 'skip') {
|
|
155
|
+
inc(bin, fstrand, 'delskips', type);
|
|
156
|
+
bin.total--;
|
|
157
|
+
}
|
|
158
|
+
else if (!interbase && colorSNPs) {
|
|
159
|
+
inc(bin, fstrand, 'cov', base);
|
|
160
|
+
bin.refbase = mismatch.altbase;
|
|
161
|
+
}
|
|
162
|
+
}
|
|
163
|
+
}
|
|
164
|
+
if (mismatch.type === 'skip') {
|
|
165
|
+
const hash = `${mstart}_${mend}_${fstrand}`;
|
|
166
|
+
if (skipmap[hash] === undefined) {
|
|
167
|
+
skipmap[hash] = {
|
|
168
|
+
feature: feature,
|
|
169
|
+
start: mstart,
|
|
170
|
+
end: mend,
|
|
171
|
+
strand: fstrand,
|
|
172
|
+
xs: getTag(feature, 'XS') || getTag(feature, 'TS'),
|
|
173
|
+
score: 0,
|
|
174
|
+
};
|
|
175
|
+
}
|
|
176
|
+
skipmap[hash].score++;
|
|
177
|
+
}
|
|
178
|
+
}
|
|
179
|
+
}
|
|
180
|
+
return { bins, skipmap };
|
|
181
|
+
}
|
|
182
|
+
//# sourceMappingURL=generateCoverageBins.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"generateCoverageBins.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/generateCoverageBins.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,4BAA4B,EAAE,MAAM,SAAS,CAAA;AACzE,OAAO,EACL,UAAU,EACV,aAAa,EACb,wBAAwB,GAEzB,MAAM,8BAA8B,CAAA;AAErC,SAAS,WAAW,CAAC,QAAkB;IACrC,OAAO,CAAC,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;AAC1D,CAAC;AAED,SAAS,WAAW,CAAC,IAAY;IAC/B,OAAO,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,WAAW,CAAA;AAC3E,CAAC;AAED,8DAA8D;AAC9D,SAAS,GAAG,CAAC,GAAQ,EAAE,MAAc,EAAE,IAAY,EAAE,KAAa;IAChE,IAAI,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAA;IAC9B,IAAI,OAAO,KAAK,SAAS,EAAE;QACzB,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,GAAG;YAC3B,KAAK,EAAE,CAAC;YACR,IAAI,EAAE,CAAC;YACP,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;SACP,CAAA;KACF;IACD,OAAO,CAAC,KAAK,EAAE,CAAA;IACf,OAAO,CAAC,MAAM,CAAC,EAAE,CAAA;AACnB,CAAC;AAED,MAAM,CAAC,OAAO,CAAC,KAAK,UAAU,oBAAoB,CAChD,QAAmB,EACnB,MAAc,EACd,IAAoE,EACpE,aAA+C;;IAE/C,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;IACxB,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAEnD,MAAM,OAAO,GAAG,EASf,CAAA;IAQD,MAAM,SAAS,GACb,QAAQ,CAAC,MAAM,IAAI,4BAA4B,CAAC,MAAA,IAAI,CAAC,OAAO,0CAAE,IAAI,CAAC;QACjE,CAAC,CAAC,MAAM,aAAa,CAAC,MAAM,CAAC;QAC7B,CAAC,CAAC,SAAS,CAAA;IAEf,MAAM,IAAI,GAAG,EAYV,CAAA;IAEH,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;QAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QACnC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAe,CAAA;QAEnD,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACtC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;YAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,MAAM,EAAE;gBACxB,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;oBACzB,IAAI,CAAC,CAAC,CAAC,GAAG;wBACR,KAAK,EAAE,CAAC;wBACR,GAAG,EAAE,CAAC;wBACN,GAAG,EAAE,CAAC;wBACN,IAAI,EAAE,CAAC;wBACP,GAAG,EAAE,CAAC;wBACN,GAAG,EAAE,CAAC;wBACN,OAAO,EAAE,EAAa;wBACtB,GAAG,EAAE,EAAa;wBAClB,QAAQ,EAAE,EAAa;wBACvB,MAAM,EAAE,EAAa;qBACtB,CAAA;iBACF;gBACD,IAAI,CAAC,KAAK,IAAI,EAAE;oBACd,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,EAAE,CAAA;oBACf,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;oBACb,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;oBACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;iBACnB;aACF;SACF;QAED,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,EAAE;YACrC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAW,CAAA;YACxC,MAAM,EAAE,GAAI,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAY,IAAI,EAAE,CAAA;YAC3D,MAAM,GAAG,GAAG,UAAU,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;YAC5C,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAE/B,wBAAwB,CAAC,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,CAAC,OAAO,CAChD,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,OAAO,IAAI,EAAE,CAAA;gBACzB,KAAK,MAAM,GAAG,IAAI,aAAa,CAAC,GAAG,EAAE,SAAS,CAAC,EAAE;oBAC/C,MAAM,IAAI,GAAG,GAAG,GAAG,MAAM,GAAG,MAAM,CAAC,KAAK,CAAA;oBACxC,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,IAAI,CAAC,MAAM,IAAI,GAAG,GAAG,MAAM,GAAG,IAAI,EAAE;wBAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAA;wBACtB,IAAI,GAAG,EAAE;4BACP,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;yBAC9B;6BAAM;4BACL,OAAO,CAAC,IAAI,CACV,6DAA6D,CAC9D,CAAA;yBACF;qBACF;iBACF;YACH,CAAC,CACF,CAAA;SACF;QAED,+DAA+D;QAC/D,mCAAmC;aAC9B,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,EAAE;YACxC,IAAI,CAAC,SAAS,EAAE;gBACd,MAAM,IAAI,KAAK,CACb,iEAAiE,CAClE,CAAA;aACF;YACD,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAC9B,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAA;YAC/C,MAAM,QAAQ,GAAG,IAAI,KAAK,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YAC7D,MAAM,GAAG,GAAG,UAAU,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;YAE5C,wBAAwB,CAAC,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,CAAC,OAAO,CAChD,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,EAAE,EAAE;gBACtB,gCAAgC;gBAChC,IAAI,IAAI,KAAK,GAAG,EAAE;oBAChB,KAAK,MAAM,GAAG,IAAI,aAAa,CAAC,GAAG,EAAE,SAAS,CAAC,EAAE;wBAC/C,MAAM,IAAI,GAAG,GAAG,GAAG,MAAM,GAAG,MAAM,CAAC,KAAK,CAAA;wBACxC,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,QAAQ,CAAC,MAAM,EAAE;4BACvC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;yBACnB;qBACF;iBACF;YACH,CAAC,CACF,CAAA;YAED,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;gBAClC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;gBAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE;oBACjC,MAAM,EAAE,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;oBACrC,MAAM,EAAE,GAAG,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;oBACzC,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;oBACnB,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;oBAExB,QAAQ;oBACR,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;wBAC5B,IAAI,QAAQ,CAAC,CAAC,CAAC,IAAI,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE;4BAClC,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;4BAChC,GAAG,CAAC,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;4BACjC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;4BACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;4BAClB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;4BACjB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;yBACvB;6BAAM;4BACL,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,QAAQ,CAAC,CAAA;4BAClC,GAAG,CAAC,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,QAAQ,CAAC,CAAA;4BACnC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;4BACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;4BAClB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;4BACjB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;yBACvB;qBACF;iBACF;aACF;SACF;QAED,4BAA4B;QAC5B,MAAM,UAAU,GAAI,OAAO,CAAC,GAAG,CAAC,YAAY,CAAgB,IAAI,EAAE,CAAA;QAClE,MAAM,SAAS,GACb,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,CAAA;QAEtE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC1C,MAAM,QAAQ,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YAC9B,MAAM,MAAM,GAAG,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAA;YACtC,MAAM,IAAI,GAAG,WAAW,CAAC,QAAQ,CAAC,CAAA;YAClC,MAAM,IAAI,GAAG,MAAM,GAAG,IAAI,CAAA;YAC1B,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,MAAM,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;gBAC3C,MAAM,IAAI,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;gBAC7B,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,IAAI,CAAC,MAAM,EAAE;oBACnC,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAA;oBACtB,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,QAAQ,CAAA;oBAC/B,MAAM,SAAS,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;oBACnC,IAAI,CAAC,SAAS,EAAE;wBACd,GAAG,CAAC,GAAG,EAAE,CAAA;wBACT,GAAG,CAAC,OAAO,CAAC,EAAE,CAAA;qBACf;yBAAM;wBACL,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAA;qBAClC;oBAED,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,MAAM,EAAE;wBAC1C,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,UAAU,EAAE,IAAI,CAAC,CAAA;wBACnC,GAAG,CAAC,KAAK,EAAE,CAAA;qBACZ;yBAAM,IAAI,CAAC,SAAS,IAAI,SAAS,EAAE;wBAClC,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;wBAC9B,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,OAAO,CAAA;qBAC/B;iBACF;aACF;YAED,IAAI,QAAQ,CAAC,IAAI,KAAK,MAAM,EAAE;gBAC5B,MAAM,IAAI,GAAG,GAAG,MAAM,IAAI,IAAI,IAAI,OAAO,EAAE,CAAA;gBAC3C,IAAI,OAAO,CAAC,IAAI,CAAC,KAAK,SAAS,EAAE;oBAC/B,OAAO,CAAC,IAAI,CAAC,GAAG;wBACd,OAAO,EAAE,OAAO;wBAChB,KAAK,EAAE,MAAM;wBACb,GAAG,EAAE,IAAI;wBACT,MAAM,EAAE,OAAO;wBACf,EAAE,EAAE,MAAM,CAAC,OAAO,EAAE,IAAI,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,IAAI,CAAC;wBAClD,KAAK,EAAE,CAAC;qBACT,CAAA;iBACF;gBACD,OAAO,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,CAAA;aACtB;SACF;KACF;IAED,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,CAAA;AAC1B,CAAC"}
|
|
@@ -1,18 +1,20 @@
|
|
|
1
1
|
import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
|
|
2
|
-
import
|
|
2
|
+
import configSchema from './configSchema';
|
|
3
3
|
import { capabilities } from './SNPCoverageAdapter';
|
|
4
|
-
export default (pluginManager)
|
|
5
|
-
pluginManager.addAdapterType(() =>
|
|
6
|
-
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
};
|
|
4
|
+
export default function (pluginManager) {
|
|
5
|
+
pluginManager.addAdapterType(() => {
|
|
6
|
+
return new AdapterType({
|
|
7
|
+
name: 'SNPCoverageAdapter',
|
|
8
|
+
adapterMetadata: {
|
|
9
|
+
category: null,
|
|
10
|
+
displayName: null,
|
|
11
|
+
hiddenFromGUI: true,
|
|
12
|
+
description: null,
|
|
13
|
+
},
|
|
14
|
+
getAdapterClass: () => import('./SNPCoverageAdapter').then(r => r.default),
|
|
15
|
+
configSchema,
|
|
16
|
+
adapterCapabilities: capabilities,
|
|
17
|
+
});
|
|
18
|
+
});
|
|
19
|
+
}
|
|
18
20
|
//# sourceMappingURL=index.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,EAAE,YAAY,EAAE,MAAM,sBAAsB,CAAA;AAEnD,MAAM,CAAC,OAAO,WAAW,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,oBAAoB;YAC1B,eAAe,EAAE;gBACf,QAAQ,EAAE,IAAI;gBACd,WAAW,EAAE,IAAI;gBACjB,aAAa,EAAE,IAAI;gBACnB,WAAW,EAAE,IAAI;aAClB;YACD,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,sBAAsB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;YACrD,YAAY;YACZ,mBAAmB,EAAE,YAAY;SAClC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}
|
package/esm/index.d.ts
CHANGED
|
@@ -2,9 +2,10 @@ import Plugin from '@jbrowse/core/Plugin';
|
|
|
2
2
|
import PluginManager from '@jbrowse/core/PluginManager';
|
|
3
3
|
import * as MismatchParser from './BamAdapter/MismatchParser';
|
|
4
4
|
import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
|
|
5
|
-
|
|
6
|
-
export type { LinearPileupDisplayModel };
|
|
5
|
+
import { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory } from './LinearPileupDisplay';
|
|
7
6
|
export default class AlignmentsPlugin extends Plugin {
|
|
8
7
|
name: string;
|
|
9
8
|
install(pluginManager: PluginManager): void;
|
|
10
9
|
}
|
|
10
|
+
export { linearPileupDisplayConfigSchemaFactory, linearPileupDisplayStateModelFactory, MismatchParser, };
|
|
11
|
+
export type { LinearPileupDisplayModel };
|
package/esm/index.js
CHANGED
|
@@ -8,12 +8,11 @@ import SNPCoverageRendererF from './SNPCoverageRenderer';
|
|
|
8
8
|
import PileupRendererF from './PileupRenderer';
|
|
9
9
|
import LinearAlignmentsDisplayF from './LinearAlignmentsDisplay';
|
|
10
10
|
import LinearSNPCoverageDisplayF from './LinearSNPCoverageDisplay';
|
|
11
|
-
import LinearPileupDisplayF from './LinearPileupDisplay';
|
|
11
|
+
import LinearPileupDisplayF, { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, } from './LinearPileupDisplay';
|
|
12
12
|
import AlignmentsTrackF from './AlignmentsTrack';
|
|
13
13
|
import AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail';
|
|
14
14
|
import { PileupGetGlobalValueForTag, PileupGetVisibleModifications, } from './PileupRPC/rpcMethods';
|
|
15
15
|
import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
|
|
16
|
-
export { MismatchParser };
|
|
17
16
|
export default class AlignmentsPlugin extends Plugin {
|
|
18
17
|
constructor() {
|
|
19
18
|
super(...arguments);
|
|
@@ -88,4 +87,5 @@ export default class AlignmentsPlugin extends Plugin {
|
|
|
88
87
|
pluginManager.addRpcMethod(() => new PileupGetVisibleModifications(pluginManager));
|
|
89
88
|
}
|
|
90
89
|
}
|
|
90
|
+
export { linearPileupDisplayConfigSchemaFactory, linearPileupDisplayStateModelFactory, MismatchParser, };
|
|
91
91
|
//# sourceMappingURL=index.js.map
|
package/esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AACA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,KAAK,cAAc,MAAM,6BAA6B,CAAA;AAG7D,OAAO,WAAW,MAAM,eAAe,CAAA;AACvC,OAAO,YAAY,MAAM,cAAc,CAAA;AACvC,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,mBAAmB,MAAM,sBAAsB,CAAA;AACtD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,eAAe,MAAM,kBAAkB,CAAA;AAC9C,OAAO,wBAAwB,MAAM,2BAA2B,CAAA;AAChE,OAAO,yBAAyB,MAAM,4BAA4B,CAAA;AAClE,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AACA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,KAAK,cAAc,MAAM,6BAA6B,CAAA;AAG7D,OAAO,WAAW,MAAM,eAAe,CAAA;AACvC,OAAO,YAAY,MAAM,cAAc,CAAA;AACvC,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,mBAAmB,MAAM,sBAAsB,CAAA;AACtD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,eAAe,MAAM,kBAAkB,CAAA;AAC9C,OAAO,wBAAwB,MAAM,2BAA2B,CAAA;AAChE,OAAO,yBAAyB,MAAM,4BAA4B,CAAA;AAClE,OAAO,oBAAoB,EAAE,EAC3B,oCAAoC,EACpC,sCAAsC,GACvC,MAAM,uBAAuB,CAAA;AAC9B,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,wBAAwB,MAAM,2BAA2B,CAAA;AAEhE,OAAO,EACL,0BAA0B,EAC1B,6BAA6B,GAC9B,MAAM,wBAAwB,CAAA;AAC/B,OAAO,EACL,SAAS,EACT,aAAa,EACb,WAAW,GAGZ,MAAM,2BAA2B,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,gBAAiB,SAAQ,MAAM;IAApD;;QACE,SAAI,GAAG,kBAAkB,CAAA;IA4F3B,CAAC;IA1FC,OAAO,CAAC,aAA4B;QAClC,CAAC;QAAA;YACC,YAAY;YACZ,WAAW;YACX,oBAAoB;YACpB,yBAAyB;YACzB,gBAAgB;YAChB,mBAAmB;YACnB,iBAAiB;YACjB,eAAe;YACf,oBAAoB;YACpB,wBAAwB;YACxB,wBAAwB;SACzB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAA;QAE5B,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,UAAU,CAAA;gBAC7B,MAAM,WAAW,GAAG,aAAa,CAAA;gBACjC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,YAAY,EAAE,IAAI;oBAClB,YAAY,EAAE,KAAK,IAAI,SAAS,CAAC,IAAI,EAAE,OAAO,CAAC;iBAChD,CAAA;gBACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,SAAS,CAAA;gBAC5B,MAAM,WAAW,GAAG,YAAY,CAAA;gBAChC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,SAAS,GAAG,KAAK,IAAI,WAAW,CAAC,KAAK,CAAC,CAAA;gBAE7C,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,WAAW,EAAE,IAAI;oBACjB,KAAK,EAAE;wBACL,QAAQ,EAAE,KAAK,IAAI,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC;wBAC1C,SAAS,EAAE,aAAa,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;qBAClD;iBACF,CAAA;gBACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;YACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;gBAC7B,IAAI,WAAW,KAAK,YAAY,IAAI,WAAW,KAAK,aAAa,EAAE;oBACjE,OAAO,iBAAiB,CAAA;iBACzB;gBACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;YACtC,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,YAAY,CACxB,GAAG,EAAE,CAAC,IAAI,0BAA0B,CAAC,aAAa,CAAC,CACpD,CAAA;QACD,aAAa,CAAC,YAAY,CACxB,GAAG,EAAE,CAAC,IAAI,6BAA6B,CAAC,aAAa,CAAC,CACvD,CAAA;IACH,CAAC;CACF;AAED,OAAO,EACL,sCAAsC,EACtC,oCAAoC,EACpC,cAAc,GACf,CAAA"}
|