diff --git a/packages/core/util/simpleFeature.ts b/packages/core/util/simpleFeature.ts index 055e00de31..53cb6282bc 100644 --- a/packages/core/util/simpleFeature.ts +++ b/packages/core/util/simpleFeature.ts @@ -11,18 +11,6 @@ export interface Feature { get(name: 'subfeatures'): Feature[] | undefined get(name: string): any - - /** - * Set an item of data. - */ - - set(name: string, val: any): void - - /** - * Get an array listing which data keys are present in this feature. - */ - tags(): string[] - /** * Get the unique ID of this feature. */ diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json index 67f7c6137a..0d5d220ae1 100644 --- a/plugins/alignments/package.json +++ b/plugins/alignments/package.json @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@gmod/bam": "^2.0.0", + "@gmod/bam": "^3.0.0", "@gmod/cram": "^3.0.3", "@jbrowse/sv-core": "^2.16.1", "@mui/icons-material": "^6.0.0", diff --git a/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx b/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx index 450ac41419..035de5da3a 100644 --- a/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +++ b/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx @@ -18,8 +18,6 @@ import Formatter from './Formatter' const SupplementaryAlignments = lazy(() => import('./SupplementaryAlignments')) const LinkedPairedAlignments = lazy(() => import('./LinkedPairedAlignments')) -const omit = ['clipPos', 'flags'] - const AlignmentsFeatureDetails = observer(function (props: { model: AlignmentFeatureWidgetModel }) { @@ -32,7 +30,6 @@ const AlignmentsFeatureDetails = observer(function (props: { - prop.startsWith('_get_') && - prop !== '_get_mismatches' && - prop !== '_get_tags', - ) - .map(methodName => methodName.replace('_get_', '')) - .concat(this.record._tags()), - ), - ] - } - id() { - return `${this.adapter.id}-${this.record.id()}` + return `${this.adapter.id}-${this.record.id}` } get(field: string): any { - const methodName = `_get_${field}` - // @ts-expect-error - if (this[methodName]) { - // @ts-expect-error - return this[methodName]() - } - return this.record.get(field) - } - - _get_refName() { - return this.adapter.refIdToName(this.record.seq_id()) + return field === 'mismatches' + ? getMismatches( + this.record.CIGAR, + this.record.tags.MD as string | undefined, + this.record.seq, + this.ref, + this.record.qualRaw, + ) + : this.fields[field] } parent() { @@ -115,33 +41,62 @@ export default class BamSlightlyLazyFeature implements Feature { return undefined } - pairedFeature() { - return false + get parsedCigar() { + return parseCigar(this.record.CIGAR) } - toJSON(): SimpleFeatureSerialized { + get fields(): SimpleFeatureSerialized { + const r = this.record + const a = this.adapter + const p = r.isPaired() return { - ...Object.fromEntries( - this.tags() - .map(t => [t, this.get(t)]) - .filter(elt => elt[1] !== undefined), - ), + id: this.id(), + start: r.start, + name: r.name, + end: r.end, + score: r.score, + qual: r.qual, + strand: r.strand, + template_length: r.template_length, + flags: r.flags, + tags: r.tags, + refName: a.refIdToName(r.ref_id)!, + CIGAR: r.CIGAR, + seq: r.seq, + type: 'match', + pair_orientation: r.pair_orientation, + next_ref: p ? a.refIdToName(r.next_refid) : undefined, + next_pos: p ? r.next_pos : undefined, + next_segment_position: p + ? `${a.refIdToName(r.next_refid)}:${r.next_pos + 1}` + : undefined, uniqueId: this.id(), } } - _get_mismatches() { - return getMismatches( - this.get('CIGAR'), - this.get('MD'), - this.get('seq'), - this.ref, - this.qualRaw(), - ) + toJSON(): SimpleFeatureSerialized { + return this.fields + } +} + +function cacheGetter(ctor: { prototype: T }, prop: keyof T): void { + const desc = Object.getOwnPropertyDescriptor(ctor.prototype, prop) + if (!desc) { + throw new Error('t1') } - _get_clipPos() { - const cigar = this.get('CIGAR') || '' - return getClip(cigar, this.get('strand')) + const getter = desc.get + if (!getter) { + throw new Error('t2') } + Object.defineProperty(ctor.prototype, prop, { + get() { + const ret = getter.call(this) + Object.defineProperty(this, prop, { value: ret }) + return ret + }, + }) } + +cacheGetter(BamSlightlyLazyFeature, 'fields') +cacheGetter(BamSlightlyLazyFeature, 'parsedCigar') diff --git a/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap b/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap index 1529ea1f7d..b32635fa67 100644 --- a/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap +++ b/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap @@ -4,270 +4,300 @@ exports[`adapter can fetch features from volvox.bam 1`] = ` [ { "CIGAR": "100M", - "MD": "22A32C15T12A15", - "MQ": 37, - "NM": 4, - "X0": 1, - "X1": 0, - "XG": 0, - "XM": 4, - "XO": 0, - "XT": "U", - "clipPos": 0, "end": 5540, "flags": 16, - "length_on_ref": 100, + "id": "test-10158054", "name": "ctgA_5060_5540_1:0:0_3:1:0_15a3", + "next_pos": undefined, + "next_ref": undefined, + "next_segment_position": undefined, + "pair_orientation": "", "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, "seq": "TACACTGGTTCGGAGACGGTTCGTGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATGAGCGGCCGCTGACCGGCGGCACGACTAATATAGTGCAAGA", - "seq_length": 100, "start": 5440, "strand": -1, + "tags": { + "MD": "22A32C15T12A15", + "NM": 4, + "X0": 1, + "X1": 0, + "XG": 0, + "XM": 4, + "XO": 0, + "XT": "U", + }, "template_length": 0, "type": "match", "uniqueId": "test-10158054", }, { "CIGAR": "100M", - "MD": "66G33", - "MQ": 37, - "NM": 1, - "X0": 1, - "X1": 0, - "XG": 0, - "XM": 1, - "XO": 0, - "XT": "U", - "clipPos": 0, "end": 5541, "flags": 16, - "length_on_ref": 100, + "id": "test-10158322", "name": "ctgA_4973_5541_1:0:0_1:0:0_1569", + "next_pos": undefined, + "next_ref": undefined, + "next_segment_position": undefined, + "pair_orientation": "", "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, "seq": "ACACTGGTTCGGAGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCCCTGTCCGGCGGCACGAATAATATAGTGCAAGAA", - "seq_length": 100, "start": 5441, "strand": -1, + "tags": { + "MD": "66G33", + "NM": 1, + "X0": 1, + "X1": 0, + "XG": 0, + "XM": 1, + "XO": 0, + "XT": "U", + }, "template_length": 0, "type": "match", "uniqueId": "test-10158322", }, { "CIGAR": "100M", - "MD": "25G23C1C24A23", - "MQ": 37, - "NM": 4, - "X0": 1, - "X1": 0, - "XG": 0, - "XM": 4, - "XO": 0, - "XT": "U", - "clipPos": 0, "end": 5544, "flags": 0, - "length_on_ref": 100, + "id": "test-10158581", "name": "ctgA_5445_5947_3:1:0_2:0:0_2b9", + "next_pos": undefined, + "next_ref": undefined, + "next_segment_position": undefined, + "pair_orientation": "", "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, "seq": "CTGGTTCGGAGACGGTTCATGACGACCGCGCTATATGTCGGCATCTGCGTCGCATGAGCGGCCGCTGTCCGGCGGCTCGAATAATATAGTGCAAGAAAAA", - "seq_length": 100, "start": 5444, "strand": 1, + "tags": { + "MD": "25G23C1C24A23", + "NM": 4, + "X0": 1, + "X1": 0, + "XG": 0, + "XM": 4, + "XO": 0, + "XT": "U", + }, "template_length": 0, "type": "match", "uniqueId": "test-10158581", }, { "CIGAR": "100M", - "MD": "42C57", - "MQ": 37, - "NM": 1, - "X0": 1, - "X1": 0, - "XG": 0, - "XM": 1, - "XO": 0, - "XT": "U", - "clipPos": 0, "end": 5553, "flags": 0, - "length_on_ref": 100, + "id": "test-10158847", "name": "ctgA_5454_5906_0:1:0_2:0:0_d8a", + "next_pos": undefined, + "next_ref": undefined, + "next_segment_position": undefined, + "pair_orientation": "", "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, "seq": "AGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACT", - "seq_length": 100, "start": 5453, "strand": 1, + "tags": { + "MD": "42C57", + "NM": 1, + "X0": 1, + "X1": 0, + "XG": 0, + "XM": 1, + "XO": 0, + "XT": "U", + }, "template_length": 0, "type": "match", "uniqueId": "test-10158847", }, { "CIGAR": "100M", - "MD": "49G11G38", - "MQ": 37, - "NM": 2, - "X0": 1, - "X1": 0, - "XG": 0, - "XM": 2, - "XO": 0, - "XT": "U", - "clipPos": 0, "end": 5554, "flags": 0, - "length_on_ref": 100, + "id": "test-12607066", "name": "ctgA_5455_5964_2:0:0_2:0:0_23e2", + "next_pos": undefined, + "next_ref": undefined, + "next_segment_position": undefined, + "pair_orientation": "", "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, "seq": "GACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCCGCCGCTGTCCGACGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTA", - "seq_length": 100, "start": 5454, "strand": 1, + "tags": { + "MD": "49G11G38", + "NM": 2, + "X0": 1, + "X1": 0, + "XG": 0, + "XM": 2, + "XO": 0, + "XT": "U", + }, "template_length": 0, "type": "match", "uniqueId": "test-12607066", }, { "CIGAR": "100M", - "MD": "22T13C63", - "MQ": 37, - "NM": 2, - "X0": 1, - "X1": 0, - "XG": 0, - "XM": 2, - "XO": 0, - "XT": "U", - "clipPos": 0, "end": 5559, "flags": 16, - "length_on_ref": 100, + "id": "test-12607328", "name": "ctgA_5153_5559_3:0:0_1:1:0_11ac", + "next_pos": undefined, + "next_ref": undefined, + "next_segment_position": undefined, + "pair_orientation": "", "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, "seq": "TTCATGACGAGCGCGCTATATGACGGCATCTGCGCCGCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTT", - "seq_length": 100, "start": 5459, "strand": -1, + "tags": { + "MD": "22T13C63", + "NM": 2, + "X0": 1, + "X1": 0, + "XG": 0, + "XM": 2, + "XO": 0, + "XT": "U", + }, "template_length": 0, "type": "match", "uniqueId": "test-12607328", }, { "CIGAR": "100M", - "MD": "35C3G60", - "MQ": 37, - "NM": 2, - "X0": 1, - "X1": 0, - "XG": 0, - "XM": 2, - "XO": 0, - "XT": "U", - "clipPos": 0, "end": 5560, "flags": 0, - "length_on_ref": 100, + "id": "test-12607590", "name": "ctgA_5461_5986_1:1:0_3:0:0_200e", + "next_pos": undefined, + "next_ref": undefined, + "next_segment_position": undefined, + "pair_orientation": "", "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, "seq": "TCATGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATCAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTA", - "seq_length": 100, "start": 5460, "strand": 1, + "tags": { + "MD": "35C3G60", + "NM": 2, + "X0": 1, + "X1": 0, + "XG": 0, + "XM": 2, + "XO": 0, + "XT": "U", + }, "template_length": 0, "type": "match", "uniqueId": "test-12607590", }, { "CIGAR": "100M", - "MD": "100", - "MQ": 37, - "NM": 0, - "X0": 1, - "X1": 0, - "XG": 0, - "XM": 0, - "XO": 0, - "XT": "U", - "clipPos": 0, "end": 5568, "flags": 0, - "length_on_ref": 100, + "id": "test-12607851", "name": "ctgA_5469_5932_0:0:0_2:0:0_6f8", + "next_pos": undefined, + "next_ref": undefined, + "next_segment_position": undefined, + "pair_orientation": "", "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, "seq": "AGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGAT", - "seq_length": 100, "start": 5468, "strand": 1, + "tags": { + "MD": "100", + "NM": 0, + "X0": 1, + "X1": 0, + "XG": 0, + "XM": 0, + "XO": 0, + "XT": "U", + }, "template_length": 0, "type": "match", "uniqueId": "test-12607851", }, { "CIGAR": "100M", - "MD": "52G43A3", - "MQ": 37, - "NM": 2, - "X0": 1, - "X1": 0, - "XG": 0, - "XM": 2, - "XO": 0, - "XT": "U", - "clipPos": 0, "end": 5594, "flags": 16, - "length_on_ref": 100, + "id": "test-12608107", "name": "ctgA_5079_5594_1:0:0_2:0:0_d64", + "next_pos": undefined, + "next_ref": undefined, + "next_segment_position": undefined, + "pair_orientation": "", "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, "seq": "CCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCTAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTCTCACA", - "seq_length": 100, "start": 5494, "strand": -1, + "tags": { + "MD": "52G43A3", + "NM": 2, + "X0": 1, + "X1": 0, + "XG": 0, + "XM": 2, + "XO": 0, + "XT": "U", + }, "template_length": 0, "type": "match", "uniqueId": "test-12608107", }, { "CIGAR": "100M", - "MD": "92C7", - "MQ": 37, - "NM": 1, - "X0": 1, - "X1": 0, - "XG": 0, - "XM": 1, - "XO": 0, - "XT": "U", - "clipPos": 0, "end": 5596, "flags": 0, - "length_on_ref": 100, + "id": "test-12608367", "name": "ctgA_5497_6082_1:0:0_2:0:0_b2", + "next_pos": undefined, + "next_ref": undefined, + "next_segment_position": undefined, + "pair_orientation": "", "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, "seq": "CATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTGTAACAGG", - "seq_length": 100, "start": 5496, "strand": 1, + "tags": { + "MD": "92C7", + "NM": 1, + "X0": 1, + "X1": 0, + "XG": 0, + "XM": 1, + "XO": 0, + "XT": "U", + }, "template_length": 0, "type": "match", "uniqueId": "test-12608367", diff --git a/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts b/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts index 6da467f996..35230dae4c 100644 --- a/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts +++ b/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts @@ -17,8 +17,7 @@ import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/rendere // locals import { FilterModel, IFilter, getUniqueModificationValues } from '../../shared' -import { createAutorun, modificationColors } from '../../util' -import { randomColor } from '../../util' +import { createAutorun, getColorForModification } from '../../util' // lazies const Tooltip = lazy(() => import('../components/Tooltip')) @@ -111,14 +110,11 @@ function stateModelFactory( * #action */ updateModificationColorMap(uniqueModifications: string[]) { - uniqueModifications.forEach(value => { - if (!self.modificationTagMap.has(value)) { - self.modificationTagMap.set( - value, - modificationColors[value] || randomColor(value), - ) + for (const m of uniqueModifications) { + if (!self.modificationTagMap.has(m)) { + self.modificationTagMap.set(m, getColorForModification(m)) } - }) + } }, })) .views(self => { diff --git a/plugins/alignments/src/MismatchParser/index.ts b/plugins/alignments/src/MismatchParser/index.ts index 4573515930..9d8f5ede15 100644 --- a/plugins/alignments/src/MismatchParser/index.ts +++ b/plugins/alignments/src/MismatchParser/index.ts @@ -213,7 +213,7 @@ export function mdToMismatches( } export function getMismatches( - cigar: string, + cigar?: string, md?: string, seq?: string, ref?: string, @@ -221,7 +221,6 @@ export function getMismatches( ) { let mismatches: Mismatch[] = [] const ops = parseCigar(cigar) - // parse the CIGAR tag if it has one if (cigar) { mismatches = mismatches.concat(cigarToMismatches(ops, seq, ref, qual)) @@ -278,7 +277,7 @@ export function getModificationProbabilities(feature: Feature) { .map(elt => Math.min(1, elt / 50)) } -export function getMethBins(feature: Feature) { +export function getMethBins(feature: Feature, cigarOps: string[]) { const fstart = feature.get('start') const fend = feature.get('end') const fstrand = feature.get('strand') as -1 | 0 | 1 @@ -288,13 +287,12 @@ export function getMethBins(feature: Feature) { const methProbs = new Array(flen) const seq = feature.get('seq') as string | undefined if (seq) { - const ops = parseCigar(feature.get('CIGAR')) const probabilities = getModificationProbabilities(feature) const modifications = getModificationPositions(mm, seq, fstrand) let probIndex = 0 for (const { type, positions } of modifications) { if (type === 'm') { - for (const ref of getNextRefPos(ops, positions)) { + for (const ref of getNextRefPos(cigarOps, positions)) { const prob = probabilities?.[probIndex] || 0 probIndex++ if (ref >= 0 && ref < flen) { @@ -338,8 +336,7 @@ export function getModificationPositions( // this logic also based on parse_mm.pl from hts-specs is that in the // sequence of the read, if we have a modification type e.g. C+m;2 and a - // sequence ACGTACGTAC we skip the two instances of C and go to the last - // C + // sequence ACGTACGTAC we skip the two instances of C and go to the last C for (const type of types) { let i = 0 const positions = [] @@ -459,9 +456,8 @@ export function getClip(cigar: string, strand: number) { : +(endClip.exec(cigar) || [])[1]! || 0 } -export function getTag(f: Feature, tag: string) { - const tags = f.get('tags') - return tags ? tags[tag] : f.get(tag) +export function getTag(feature: Feature, tag: string) { + return feature.get('tags')[tag] } // produces a list of "feature-like" object from parsing supplementary diff --git a/plugins/alignments/src/PileupRPC/methods/GetReducedFeatures.ts b/plugins/alignments/src/PileupRPC/methods/GetReducedFeatures.ts index 4c840c8ca9..ba547ec261 100644 --- a/plugins/alignments/src/PileupRPC/methods/GetReducedFeatures.ts +++ b/plugins/alignments/src/PileupRPC/methods/GetReducedFeatures.ts @@ -8,6 +8,7 @@ import { firstValueFrom } from 'rxjs' import { filterForPairs, getInsertSizeStats } from '../util' import PileupBaseRPC from '../base' import { getTag } from '../../util' +import { getClip } from '../../MismatchParser' // specialized get features to return limited data about alignments export default class PileupGetReducedFeatures extends PileupBaseRPC { @@ -47,7 +48,7 @@ export default class PileupGetReducedFeatures extends PileupBaseRPC { pair_orientation: f.get('pair_orientation'), next_ref: f.get('next_ref'), next_pos: f.get('next_pos'), - clipPos: f.get('clipPos'), + clipPos: getClip(f.get('CIGAR'), f.get('strand')), SA: getTag(f, 'SA'), })), f => f.id, diff --git a/plugins/alignments/src/PileupRenderer/makeImageData.ts b/plugins/alignments/src/PileupRenderer/makeImageData.ts index dddf5d5258..4bffdbe2a6 100644 --- a/plugins/alignments/src/PileupRenderer/makeImageData.ts +++ b/plugins/alignments/src/PileupRenderer/makeImageData.ts @@ -12,6 +12,7 @@ import { import { renderAlignment } from './renderAlignment' import { renderMismatches } from './renderMismatches' import { renderSoftClipping } from './renderSoftClipping' +import { parseCigar } from '../MismatchParser' export type RenderArgsWithColor = RenderArgsDeserializedWithFeaturesAndLayout @@ -49,6 +50,7 @@ export function makeImageData({ const drawSNPsMuted = shouldDrawSNPsMuted(colorBy?.type) const drawIndels = shouldDrawIndels() for (const feat of layoutRecords) { + const cigarOps = parseCigar(feat.feature.get('CIGAR')) renderAlignment({ ctx, feat, @@ -59,6 +61,7 @@ export function makeImageData({ charWidth, charHeight, canvasWidth, + cigarOps, }) renderMismatches({ ctx, @@ -84,6 +87,7 @@ export function makeImageData({ config, theme, canvasWidth, + cigarOps, }) } } diff --git a/plugins/alignments/src/PileupRenderer/renderAlignment.ts b/plugins/alignments/src/PileupRenderer/renderAlignment.ts index 896e42b7a8..fa5b51d274 100644 --- a/plugins/alignments/src/PileupRenderer/renderAlignment.ts +++ b/plugins/alignments/src/PileupRenderer/renderAlignment.ts @@ -18,6 +18,7 @@ export function renderAlignment({ charHeight, defaultColor, canvasWidth, + cigarOps, }: { ctx: CanvasRenderingContext2D feat: LayoutFeature @@ -28,6 +29,7 @@ export function renderAlignment({ charHeight: number defaultColor: boolean canvasWidth: number + cigarOps: string[] }) { const { config, bpPerPx, regions, colorBy, colorTagMap = {} } = renderArgs const { tag = '', type: colorType = '' } = colorBy || {} @@ -43,7 +45,7 @@ export function renderAlignment({ colorTagMap, }) - renderAlignmentShape({ ctx, feat, renderArgs }) + renderAlignmentShape({ cigarOps, ctx, feat, renderArgs }) // second pass for color types that render per-base things that go over the // existing drawing @@ -55,6 +57,7 @@ export function renderAlignment({ region, bpPerPx, canvasWidth, + cigarOps, }) break @@ -69,6 +72,7 @@ export function renderAlignment({ charWidth, charHeight, canvasWidth, + cigarOps, }) break @@ -80,6 +84,7 @@ export function renderAlignment({ bpPerPx, renderArgs, canvasWidth, + cigarOps, }) break @@ -91,6 +96,7 @@ export function renderAlignment({ bpPerPx, renderArgs, canvasWidth, + cigarOps, }) break } diff --git a/plugins/alignments/src/PileupRenderer/renderAlignmentShape.ts b/plugins/alignments/src/PileupRenderer/renderAlignmentShape.ts index f67ec586cd..70dce244d0 100644 --- a/plugins/alignments/src/PileupRenderer/renderAlignmentShape.ts +++ b/plugins/alignments/src/PileupRenderer/renderAlignmentShape.ts @@ -6,40 +6,139 @@ export function renderAlignmentShape({ ctx, feat, renderArgs, + cigarOps, }: { ctx: CanvasRenderingContext2D feat: LayoutFeature renderArgs: RenderArgsDeserialized + cigarOps: string[] }) { const { regions, bpPerPx } = renderArgs const { heightPx, topPx, feature } = feat const region = regions[0]! const s = feature.get('start') const e = feature.get('end') - const [leftPx, rightPx] = bpSpanPx(s, e, region, bpPerPx) + const CIGAR = feature.get('CIGAR') const flip = region.reversed ? -1 : 1 const strand = feature.get('strand') * flip - if (bpPerPx < 10 && heightPx > 5) { - if (strand === -1) { - ctx.beginPath() - ctx.moveTo(leftPx - 5, topPx + heightPx / 2) - ctx.lineTo(leftPx, topPx + heightPx) - ctx.lineTo(rightPx, topPx + heightPx) - ctx.lineTo(rightPx, topPx) - ctx.lineTo(leftPx, topPx) - ctx.closePath() - ctx.fill() - } else { - ctx.beginPath() - ctx.moveTo(leftPx, topPx) - ctx.lineTo(leftPx, topPx + heightPx) - ctx.lineTo(rightPx, topPx + heightPx) - ctx.lineTo(rightPx + 5, topPx + heightPx / 2) - ctx.lineTo(rightPx, topPx) - ctx.closePath() - ctx.fill() + const renderChevrons = bpPerPx < 10 && heightPx > 5 + if (CIGAR) { + if (strand === 1) { + let drawLen = 0 + let drawStart = s + for (let i = 0; i < cigarOps.length; i += 2) { + const opLen = +cigarOps[i]! + const op = cigarOps[i + 1]! + if (op === 'M' || op === 'X' || op === '=' || op === 'D') { + drawLen += opLen + } else if (op === 'N') { + if (drawStart !== drawLen) { + const [leftPx, rightPx] = bpSpanPx( + drawStart, + drawStart + drawLen, + region, + bpPerPx, + ) + const w = rightPx - leftPx + ctx.fillRect(leftPx, topPx, w, heightPx) + } + drawStart += drawLen + opLen + drawLen = 0 + } + } + + if (drawStart !== drawLen) { + const [leftPx, rightPx] = bpSpanPx( + drawStart, + drawStart + drawLen, + region, + bpPerPx, + ) + const w = rightPx - leftPx + + if (renderChevrons) { + ctx.beginPath() + ctx.moveTo(leftPx, topPx) + ctx.lineTo(leftPx, topPx + heightPx) + ctx.lineTo(rightPx, topPx + heightPx) + ctx.lineTo(rightPx + 5, topPx + heightPx / 2) + ctx.lineTo(rightPx, topPx) + ctx.closePath() + ctx.fill() + } else { + ctx.fillRect(leftPx, topPx, w, heightPx) + } + } + } else if (strand === -1) { + let drawLen = 0 + let drawStart = e + for (let i = cigarOps.length - 2; i >= 0; i -= 2) { + const opLen = +cigarOps[i]! + const op = cigarOps[i + 1]! + if (op === 'M' || op === 'X' || op === '=' || op === 'D') { + drawLen += opLen + } else if (op === 'N') { + if (drawLen !== 0) { + const [leftPx, rightPx] = bpSpanPx( + drawStart - drawLen, + drawStart, + region, + bpPerPx, + ) + ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx) + } + drawStart -= drawLen + opLen + drawLen = 0 + } + } + + if (drawLen !== 0) { + const [leftPx, rightPx] = bpSpanPx( + drawStart - drawLen, + drawStart, + region, + bpPerPx, + ) + const w = rightPx - leftPx + + if (renderChevrons) { + ctx.beginPath() + ctx.moveTo(leftPx - 5, topPx + heightPx / 2) + ctx.lineTo(leftPx, topPx + heightPx) + ctx.lineTo(rightPx, topPx + heightPx) + ctx.lineTo(rightPx, topPx) + ctx.lineTo(leftPx, topPx) + ctx.closePath() + ctx.fill() + } else { + ctx.fillRect(leftPx, topPx, w, heightPx) + } + } } } else { - ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx) + const [leftPx, rightPx] = bpSpanPx(s, e, region, bpPerPx) + if (bpPerPx < 10 && heightPx > 5) { + if (strand === -1) { + ctx.beginPath() + ctx.moveTo(leftPx - 5, topPx + heightPx / 2) + ctx.lineTo(leftPx, topPx + heightPx) + ctx.lineTo(rightPx, topPx + heightPx) + ctx.lineTo(rightPx, topPx) + ctx.lineTo(leftPx, topPx) + ctx.closePath() + ctx.fill() + } else { + ctx.beginPath() + ctx.moveTo(leftPx, topPx) + ctx.lineTo(leftPx, topPx + heightPx) + ctx.lineTo(rightPx, topPx + heightPx) + ctx.lineTo(rightPx + 5, topPx + heightPx / 2) + ctx.lineTo(rightPx, topPx) + ctx.closePath() + ctx.fill() + } + } else { + ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx) + } } } diff --git a/plugins/alignments/src/PileupRenderer/renderMethylation.ts b/plugins/alignments/src/PileupRenderer/renderMethylation.ts index 8415cbb034..0913d22a7f 100644 --- a/plugins/alignments/src/PileupRenderer/renderMethylation.ts +++ b/plugins/alignments/src/PileupRenderer/renderMethylation.ts @@ -13,6 +13,7 @@ export function renderMethylation({ bpPerPx, renderArgs, canvasWidth, + cigarOps, }: { ctx: CanvasRenderingContext2D feat: LayoutFeature @@ -20,6 +21,7 @@ export function renderMethylation({ bpPerPx: number renderArgs: RenderArgsWithColor canvasWidth: number + cigarOps: string[] }) { const { regionSequence } = renderArgs const { feature, topPx, heightPx } = feat @@ -33,7 +35,7 @@ export function renderMethylation({ } const fstart = feature.get('start') const fend = feature.get('end') - const { methBins, methProbs } = getMethBins(feature) + const { methBins, methProbs } = getMethBins(feature, cigarOps) function getCol(k: number) { if (methBins[k]) { diff --git a/plugins/alignments/src/PileupRenderer/renderMismatches.ts b/plugins/alignments/src/PileupRenderer/renderMismatches.ts index 7814e2fa5f..ee066b3d52 100644 --- a/plugins/alignments/src/PileupRenderer/renderMismatches.ts +++ b/plugins/alignments/src/PileupRenderer/renderMismatches.ts @@ -42,8 +42,8 @@ export function renderMismatches({ const mismatches = feature.get('mismatches') as Mismatch[] | undefined const heightLim = charHeight - 2 - // extraHorizontallyFlippedOffset is used to draw interbase items, which - // are located to the left when forward and right when reversed + // extraHorizontallyFlippedOffset is used to draw interbase items, which are + // located to the left when forward and right when reversed const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx + 1 : -1 if (!mismatches) { @@ -142,20 +142,16 @@ export function renderMismatches({ } else if (mismatch.type === 'skip') { // fix to avoid bad rendering note that this was also related to chrome // bug https://bugs.chromium.org/p/chromium/issues/detail?id=1131528 + // // also affected firefox ref #1236 #2750 if (leftPx + widthPx > 0) { // make small exons more visible when zoomed far out const adjustPx = widthPx - (bpPerPx > 10 ? 1.5 : 0) - ctx.clearRect(leftPx, topPx, adjustPx, heightPx) - fillRect( - ctx, - Math.max(0, leftPx), - topPx + heightPx / 2 - 1, - adjustPx + Math.min(leftPx, 0), - 2, - canvasWidth, - '#333', - ) + const l = Math.max(0, leftPx) + const t = topPx + heightPx / 2 - 1 + const w = adjustPx + Math.min(leftPx, 0) + const h = 1 + fillRect(ctx, l, t, w, h, canvasWidth, 'rgb(151,184,201)') } } } diff --git a/plugins/alignments/src/PileupRenderer/renderModifications.ts b/plugins/alignments/src/PileupRenderer/renderModifications.ts index 3eaa8d42aa..cad194ea6f 100644 --- a/plugins/alignments/src/PileupRenderer/renderModifications.ts +++ b/plugins/alignments/src/PileupRenderer/renderModifications.ts @@ -3,7 +3,6 @@ import { getModificationPositions, getModificationProbabilities, getNextRefPos, - parseCigar, } from '../MismatchParser' import { getTagAlt } from '../util' import { fillRect, LayoutFeature } from './util' @@ -27,6 +26,7 @@ export function renderModifications({ bpPerPx, renderArgs, canvasWidth, + cigarOps, }: { ctx: CanvasRenderingContext2D feat: LayoutFeature @@ -34,6 +34,7 @@ export function renderModifications({ bpPerPx: number renderArgs: RenderArgsWithColor canvasWidth: number + cigarOps: string[] }) { const { feature, topPx, heightPx } = feat const { modificationTagMap = {} } = renderArgs @@ -44,10 +45,8 @@ export function renderModifications({ return } const mm = (getTagAlt(feature, 'MM', 'Mm') as string) || '' - const cigar = feature.get('CIGAR') const start = feature.get('start') const strand = feature.get('strand') - const cigarOps = parseCigar(cigar) const probabilities = getModificationProbabilities(feature) const modifications = getModificationPositions(mm, seq, strand) diff --git a/plugins/alignments/src/PileupRenderer/renderPerBaseLettering.ts b/plugins/alignments/src/PileupRenderer/renderPerBaseLettering.ts index 47f17dc96e..ecec413eac 100644 --- a/plugins/alignments/src/PileupRenderer/renderPerBaseLettering.ts +++ b/plugins/alignments/src/PileupRenderer/renderPerBaseLettering.ts @@ -1,5 +1,4 @@ import { bpSpanPx, Region } from '@jbrowse/core/util' -import { parseCigar } from '../MismatchParser' import { fillRect, LayoutFeature } from './util' export function renderPerBaseLettering({ @@ -12,6 +11,7 @@ export function renderPerBaseLettering({ charWidth, charHeight, canvasWidth, + cigarOps, }: { ctx: CanvasRenderingContext2D feat: LayoutFeature @@ -22,11 +22,11 @@ export function renderPerBaseLettering({ charWidth: number charHeight: number canvasWidth: number + cigarOps: string[] }) { const heightLim = charHeight - 2 const { feature, topPx, heightPx } = feat const seq = feature.get('seq') as string | undefined - const cigarOps = parseCigar(feature.get('CIGAR')) const w = 1 / bpPerPx const start = feature.get('start') let soffset = 0 diff --git a/plugins/alignments/src/PileupRenderer/renderPerBaseQuality.ts b/plugins/alignments/src/PileupRenderer/renderPerBaseQuality.ts index dae87601aa..92128c1656 100644 --- a/plugins/alignments/src/PileupRenderer/renderPerBaseQuality.ts +++ b/plugins/alignments/src/PileupRenderer/renderPerBaseQuality.ts @@ -1,5 +1,4 @@ import { bpSpanPx, Region } from '@jbrowse/core/util' -import { parseCigar } from '../MismatchParser' import { fillRect, LayoutFeature } from './util' export function renderPerBaseQuality({ @@ -8,17 +7,18 @@ export function renderPerBaseQuality({ region, bpPerPx, canvasWidth, + cigarOps, }: { ctx: CanvasRenderingContext2D feat: LayoutFeature region: Region bpPerPx: number canvasWidth: number + cigarOps: string[] }) { const { feature, topPx, heightPx } = feat const qual: string = feature.get('qual') || '' const scores = qual.split(' ').map(val => +val) - const cigarOps = parseCigar(feature.get('CIGAR')) const w = 1 / bpPerPx const start = feature.get('start') let soffset = 0 // sequence offset diff --git a/plugins/alignments/src/PileupRenderer/renderSoftClipping.ts b/plugins/alignments/src/PileupRenderer/renderSoftClipping.ts index 7ad73f2516..23197e8c92 100644 --- a/plugins/alignments/src/PileupRenderer/renderSoftClipping.ts +++ b/plugins/alignments/src/PileupRenderer/renderSoftClipping.ts @@ -6,7 +6,7 @@ import { bpSpanPx } from '@jbrowse/core/util' import { Theme } from '@mui/material' // locals -import { Mismatch, parseCigar } from '../MismatchParser' +import { Mismatch } from '../MismatchParser' import { RenderArgsDeserializedWithFeaturesAndLayout } from './PileupRenderer' import { fillRect, getCharWidthHeight, LayoutFeature } from './util' @@ -18,6 +18,7 @@ export function renderSoftClipping({ theme, colorForBase, canvasWidth, + cigarOps, }: { ctx: CanvasRenderingContext2D feat: LayoutFeature @@ -26,6 +27,7 @@ export function renderSoftClipping({ colorForBase: Record theme: Theme canvasWidth: number + cigarOps: string[] }) { const { feature, topPx, heightPx } = feat const { regions, bpPerPx } = renderArgs @@ -41,12 +43,11 @@ export function renderSoftClipping({ } const heightLim = charHeight - 2 - const CIGAR = parseCigar(feature.get('CIGAR')) let seqOffset = 0 let refOffset = 0 - for (let i = 0; i < CIGAR.length; i += 2) { - const op = CIGAR[i + 1]! - const len = +CIGAR[i]! + for (let i = 0; i < cigarOps.length; i += 2) { + const op = cigarOps[i + 1]! + const len = +cigarOps[i]! if (op === 'S') { for (let k = 0; k < len; k++) { const base = seq[seqOffset + k]! diff --git a/plugins/alignments/src/SNPCoverageAdapter/SNPCoverageAdapter.ts b/plugins/alignments/src/SNPCoverageAdapter/SNPCoverageAdapter.ts index 923a0be18f..51c2434745 100644 --- a/plugins/alignments/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +++ b/plugins/alignments/src/SNPCoverageAdapter/SNPCoverageAdapter.ts @@ -84,7 +84,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter { end: skip.end, strand: skip.strand, score: skip.score, - xs: skip.xs, + effectiveStrand: skip.effectiveStrand, }, }), ) diff --git a/plugins/alignments/src/SNPCoverageAdapter/generateCoverageBins.ts b/plugins/alignments/src/SNPCoverageAdapter/generateCoverageBins.ts index 7192c19ec8..8c62476e7a 100644 --- a/plugins/alignments/src/SNPCoverageAdapter/generateCoverageBins.ts +++ b/plugins/alignments/src/SNPCoverageAdapter/generateCoverageBins.ts @@ -131,7 +131,8 @@ export default async function generateCoverageBins( if (!seq) { continue } - const { methBins, methProbs } = getMethBins(feature) + const cigarOps = parseCigar(feature.get('CIGAR')) + const { methBins, methProbs } = getMethBins(feature, cigarOps) const dels = mismatches.filter(f => f.type === 'deletion') // methylation based coloring takes into account both reference sequence @@ -233,14 +234,31 @@ export default async function generateCoverageBins( } if (mismatch.type === 'skip') { - const hash = `${mstart}_${mend}_${fstrand}` + const xs = getTag(feature, 'XS') + const ts = getTag(feature, 'ts') + const TS = getTag(feature, 'TS') + let effectiveStrand = 0 + if (xs === '+') { + effectiveStrand = 1 + } else if (xs === '-') { + effectiveStrand = -1 + } else if (ts === '-') { + effectiveStrand = fstrand * -1 + } else if (ts === '+') { + effectiveStrand = fstrand + } else if (TS === '-') { + effectiveStrand = -1 + } else if (TS === '+') { + effectiveStrand = 1 + } + const hash = `${mstart}_${mend}_${effectiveStrand}` if (skipmap[hash] === undefined) { skipmap[hash] = { feature: feature, start: mstart, end: mend, strand: fstrand, - xs: getTag(feature, 'XS') || getTag(feature, 'TS'), + effectiveStrand, score: 0, } } @@ -249,5 +267,8 @@ export default async function generateCoverageBins( } } - return { bins, skipmap } + return { + bins, + skipmap, + } } diff --git a/plugins/alignments/src/SNPCoverageAdapter/util.ts b/plugins/alignments/src/SNPCoverageAdapter/util.ts index 9eab21d732..b71e8d25d3 100644 --- a/plugins/alignments/src/SNPCoverageAdapter/util.ts +++ b/plugins/alignments/src/SNPCoverageAdapter/util.ts @@ -6,7 +6,7 @@ export type SkipMap = Record< start: number end: number strand: number - xs: string + effectiveStrand: number } > diff --git a/plugins/alignments/src/SNPCoverageRenderer/SNPCoverageRenderer.ts b/plugins/alignments/src/SNPCoverageRenderer/SNPCoverageRenderer.ts index 1df7aa0ef0..201957ddcf 100644 --- a/plugins/alignments/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +++ b/plugins/alignments/src/SNPCoverageRenderer/SNPCoverageRenderer.ts @@ -103,13 +103,14 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer { } const feats = [...features.values()] - const coverage = feats.filter(f => f.get('type') !== 'skip') - const skips = feats.filter(f => f.get('type') === 'skip') // Use two pass rendering, which helps in visualizing the SNPs at higher // bpPerPx First pass: draw the gray background ctx.fillStyle = colorForBase.total! - for (const feature of coverage) { + for (const feature of feats) { + if (feature.get('type') === 'skip') { + continue + } const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx) const w = rightPx - leftPx + fudgeFactor const score = feature.get('score') as number @@ -131,7 +132,10 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer { // which can be wider than the actual bpPerPx This reduces overdrawing of // the grey background over the SNPs - for (const feature of coverage) { + for (const feature of feats) { + if (feature.get('type') === 'skip') { + continue + } const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx) const score = feature.get('score') as number @@ -210,28 +214,23 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer { } if (drawArcs) { - for (const f of skips) { - const [left, right] = bpSpanPx( - f.get('start'), - f.get('end'), - region, - bpPerPx, - ) + for (const f of feats) { + if (f.get('type') !== 'skip') { + continue + } + const s = f.get('start') + const e = f.get('end') + const [left, right] = bpSpanPx(s, e, region, bpPerPx) ctx.beginPath() - const str = f.get('strand') as number - const xs = f.get('xs') as string + const effectiveStrand = f.get('effectiveStrand') const pos = 'rgba(255,200,200,0.7)' const neg = 'rgba(200,200,255,0.7)' const neutral = 'rgba(200,200,200,0.7)' - if (xs === '+') { + if (effectiveStrand === 1) { ctx.strokeStyle = pos - } else if (xs === '-') { - ctx.strokeStyle = neg - } else if (str === 1) { - ctx.strokeStyle = pos - } else if (str === -1) { + } else if (effectiveStrand === -1) { ctx.strokeStyle = neg } else { ctx.strokeStyle = neutral @@ -247,12 +246,12 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer { if (displayCrossHatches) { ctx.lineWidth = 1 ctx.strokeStyle = 'rgba(140,140,140,0.8)' - ticks.values.forEach(tick => { + for (const tick of ticks.values) { ctx.beginPath() ctx.moveTo(0, Math.round(toY(tick))) ctx.lineTo(width, Math.round(toY(tick))) ctx.stroke() - }) + } } return undefined } diff --git a/plugins/alignments/src/util.ts b/plugins/alignments/src/util.ts index 8313836e7b..2eafd6a54a 100644 --- a/plugins/alignments/src/util.ts +++ b/plugins/alignments/src/util.ts @@ -159,3 +159,7 @@ export function randomColor(str: string) { } return `hsl(${sum * 10}, 20%, 50%)` } + +export function getColorForModification(str: string) { + return modificationColors[str] || randomColor(str) +} diff --git a/plugins/arc/src/LinearPairedArcDisplay/util.ts b/plugins/arc/src/LinearPairedArcDisplay/util.ts index aa23ccd51b..da2bbc27ac 100644 --- a/plugins/arc/src/LinearPairedArcDisplay/util.ts +++ b/plugins/arc/src/LinearPairedArcDisplay/util.ts @@ -8,8 +8,7 @@ import { IAutorunOptions, autorun } from 'mobx' // get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and // BAM does not export function getTag(feature: Feature, tag: string) { - const tags = feature.get('tags') - return tags !== undefined ? tags[tag] : feature.get(tag) + return feature.get('tags')[tag] } // use fallback alt tag, used in situations where upper case/lower case tags diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx index 358d0d5cc5..ee99252c15 100644 --- a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx @@ -55,9 +55,9 @@ const AlignmentConnections = observer(function ({ : getMatchedAlignmentFeatures(allFeatures), ) if (!hasPaired) { - layoutMatches.forEach(m => { - m.sort((a, b) => a.feature.get('clipPos') - b.feature.get('clipPos')) - }) + for (const m of layoutMatches) { + m.sort((a, b) => a.clipPos - b.clipPos) + } } return layoutMatches }, [allFeatures, trackId, hasPaired, model]) diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/model.ts b/plugins/breakpoint-split-view/src/BreakpointSplitView/model.ts index e8bb9b26b2..1b0dd46d6f 100644 --- a/plugins/breakpoint-split-view/src/BreakpointSplitView/model.ts +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/model.ts @@ -37,6 +37,14 @@ interface Track { displays: Display[] } +const startClip = new RegExp(/(\d+)[SH]$/) +const endClip = new RegExp(/^(\d+)([SH])/) + +export function getClip(cigar: string, strand: number) { + return strand === -1 + ? +(startClip.exec(cigar) || [])[1]! || 0 + : +(endClip.exec(cigar) || [])[1]! || 0 +} function calc(track: Track, f: Feature) { return track.displays[0]!.searchFeatureByID?.(f.id()) } @@ -241,6 +249,10 @@ export default function stateModelFactory(pluginManager: PluginManager) { feature, layout: calc(tracks[level], feature), level, + clipPos: getClip( + feature.get('CIGAR'), + feature.get('strand'), + ), } : undefined }) diff --git a/products/jbrowse-web/src/tests/__image_snapshots__/alignment-arcs-test-tsx-toggle-long-read-arc-display-1-snap.png b/products/jbrowse-web/src/tests/__image_snapshots__/alignment-arcs-test-tsx-toggle-long-read-arc-display-1-snap.png index 1e651f50f3..5fdfcad145 100644 Binary files a/products/jbrowse-web/src/tests/__image_snapshots__/alignment-arcs-test-tsx-toggle-long-read-arc-display-1-snap.png and b/products/jbrowse-web/src/tests/__image_snapshots__/alignment-arcs-test-tsx-toggle-long-read-arc-display-1-snap.png differ diff --git a/products/jbrowse-web/src/tests/__image_snapshots__/alignments-color-by-test-tsx-color-by-stranded-rna-seq-1-snap.png b/products/jbrowse-web/src/tests/__image_snapshots__/alignments-color-by-test-tsx-color-by-stranded-rna-seq-1-snap.png index fd7ac448b4..1cd6dcf255 100644 Binary files a/products/jbrowse-web/src/tests/__image_snapshots__/alignments-color-by-test-tsx-color-by-stranded-rna-seq-1-snap.png and b/products/jbrowse-web/src/tests/__image_snapshots__/alignments-color-by-test-tsx-color-by-stranded-rna-seq-1-snap.png differ diff --git a/test_data/config_demo.json b/test_data/config_demo.json index 89a08cde1a..3f37b7d7a9 100644 --- a/test_data/config_demo.json +++ b/test_data/config_demo.json @@ -4232,7 +4232,7 @@ }, { "type": "AlignmentsTrack", - "name": "Paired-end stranded RNA-seq", + "name": "Paired-end stranded RNA-seq (BAM,XS)", "metadata": { "source": "From sample files listed at https://rseqc.sourceforge.net/" }, @@ -4268,42 +4268,6 @@ }, "assemblyNames": ["hg19"] }, - { - "type": "AlignmentsTrack", - "trackId": "NA12878-DirectRNA.pass.dedup.NoU.fastq.hg38.minimap2.sorted", - "name": "NA12878-DirectRNA.pass.dedup.NoU.fastq.hg38.minimap2.sorted", - "category": ["NA12878"], - "adapter": { - "type": "BamAdapter", - "bamLocation": { - "uri": "https://jbrowse.org/genomes/GRCh38/NA12878/NA12878-DirectRNA.pass.dedup.NoU.fastq.hg38.minimap2.sorted.bam", - "locationType": "UriLocation" - }, - "index": { - "location": { - "uri": "https://jbrowse.org/genomes/GRCh38/NA12878/NA12878-DirectRNA.pass.dedup.NoU.fastq.hg38.minimap2.sorted.bam.bai", - "locationType": "UriLocation" - }, - "indexType": "BAI" - }, - "sequenceAdapter": { - "type": "BgzipFastaAdapter", - "fastaLocation": { - "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz", - "locationType": "UriLocation" - }, - "faiLocation": { - "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai", - "locationType": "UriLocation" - }, - "gziLocation": { - "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi", - "locationType": "UriLocation" - } - } - }, - "assemblyNames": ["hg38"] - }, { "type": "FeatureTrack", "trackId": "ncbi_genes", @@ -4486,6 +4450,177 @@ } }, "assemblyNames": ["hg38"] + }, + { + "type": "AlignmentsTrack", + "trackId": "NA12878-DirectRNA.pass.dedup.NoU.fastq.hg38.minimap2.sorted", + "name": "NA12878-DirectRNA.pass.dedup.NoU.fastq.hg38.minimap2.sorted", + "category": ["NA12878"], + "adapter": { + "type": "BamAdapter", + "bamLocation": { + "uri": "https://jbrowse.org/genomes/GRCh38/NA12878/NA12878-DirectRNA.pass.dedup.NoU.fastq.hg38.minimap2.sorted.bam", + "locationType": "UriLocation" + }, + "index": { + "location": { + "uri": "https://jbrowse.org/genomes/GRCh38/NA12878/NA12878-DirectRNA.pass.dedup.NoU.fastq.hg38.minimap2.sorted.bam.bai", + "locationType": "UriLocation" + }, + "indexType": "BAI" + }, + "sequenceAdapter": { + "type": "BgzipFastaAdapter", + "fastaLocation": { + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz", + "locationType": "UriLocation" + }, + "faiLocation": { + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai", + "locationType": "UriLocation" + }, + "gziLocation": { + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi", + "locationType": "UriLocation" + } + } + }, + "assemblyNames": ["hg38"] + }, + { + "type": "AlignmentsTrack", + "trackId": "NA12878-DirectRNA.pass.dedup.NoU.fastq.hg38.minimap2.sorted.chr1", + "name": "NA12878-DirectRNA.pass.dedup.NoU.fastq.hg38.minimap2.sorted.chr1", + "adapter": { + "type": "CramAdapter", + "cramLocation": { + "uri": "https://jbrowse.org/genomes/GRCh38/NA12878/NA12878-DirectRNA.pass.dedup.NoU.fastq.hg38.minimap2.sorted.chr1.cram", + "locationType": "UriLocation" + }, + "craiLocation": { + "uri": "https://jbrowse.org/genomes/GRCh38/NA12878/NA12878-DirectRNA.pass.dedup.NoU.fastq.hg38.minimap2.sorted.chr1.cram.crai", + "locationType": "UriLocation" + }, + "sequenceAdapter": { + "type": "BgzipFastaAdapter", + "fastaLocation": { + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz", + "locationType": "UriLocation" + }, + "faiLocation": { + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai", + "locationType": "UriLocation" + }, + "gziLocation": { + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi", + "locationType": "UriLocation" + } + } + }, + "category": ["NA12878"], + "assemblyNames": ["hg38"] + }, + { + "type": "AlignmentsTrack", + "trackId": "Pairend_StrandSpecific_51mer_Human_hg19.chr1.cram", + "name": "Paired-end stranded RNA-seq (CRAM,XS)", + "metadata": { + "source": "From sample files listed at https://rseqc.sourceforge.net/" + }, + "adapter": { + "type": "CramAdapter", + "cramLocation": { + "uri": "https://jbrowse.org/genomes/hg19/paired_end-rnaseq/Pairend_StrandSpecific_51mer_Human_hg19.chr1.cram", + "locationType": "UriLocation" + }, + "craiLocation": { + "uri": "https://jbrowse.org/genomes/hg19/paired_end-rnaseq/Pairend_StrandSpecific_51mer_Human_hg19.chr1.cram.crai", + "locationType": "UriLocation" + }, + "sequenceAdapter": { + "type": "BgzipFastaAdapter", + "fastaLocation": { + "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", + "locationType": "UriLocation" + }, + "faiLocation": { + "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai", + "locationType": "UriLocation" + }, + "gziLocation": { + "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi", + "locationType": "UriLocation" + } + } + }, + "assemblyNames": ["hg19"] + }, + { + "type": "AlignmentsTrack", + "trackId": "Pairend_StrandSpecific_51mer_Human_hg19.chr1.TS", + "name": "Paired-end stranded RNA-seq (CRAM,TS)", + "adapter": { + "type": "CramAdapter", + "cramLocation": { + "uri": "https://jbrowse.org/genomes/hg19/paired_end-rnaseq/Pairend_StrandSpecific_51mer_Human_hg19.chr1.TS.cram", + "locationType": "UriLocation" + }, + "craiLocation": { + "uri": "https://jbrowse.org/genomes/hg19/paired_end-rnaseq/Pairend_StrandSpecific_51mer_Human_hg19.chr1.TS.cram.crai", + "locationType": "UriLocation" + }, + "sequenceAdapter": { + "type": "BgzipFastaAdapter", + "fastaLocation": { + "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", + "locationType": "UriLocation" + }, + "faiLocation": { + "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai", + "locationType": "UriLocation" + }, + "gziLocation": { + "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi", + "locationType": "UriLocation" + } + } + }, + "assemblyNames": ["hg19"] + }, + { + "type": "AlignmentsTrack", + "trackId": "Pairend_StrandSpecific_51mer_Human_hg19.chr1.TS.bam", + "name": "Paired-end stranded RNA-seq (BAM,TS)", + "adapter": { + "type": "BamAdapter", + "bamLocation": { + "uri": "https://jbrowse.org/genomes/hg19/paired_end-rnaseq/Pairend_StrandSpecific_51mer_Human_hg19.chr1.TS.bam", + "locationType": "UriLocation" + }, + "index": { + "location": { + "uri": "https://jbrowse.org/genomes/hg19/paired_end-rnaseq/Pairend_StrandSpecific_51mer_Human_hg19.chr1.TS.bam.bai", + "locationType": "UriLocation" + }, + "indexType": "BAI" + }, + "sequenceAdapter": { + 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"@smithy/config-resolver@^3.0.9": +"@smithy/config-resolver@^3.0.10": version "3.0.10" resolved "https://registry.yarnpkg.com/@smithy/config-resolver/-/config-resolver-3.0.10.tgz#d9529d9893e5fae1f14cb1ffd55517feb6d7e50f" integrity sha512-Uh0Sz9gdUuz538nvkPiyv1DZRX9+D15EKDtnQP5rYVAzM/dnYk3P8cg73jcxyOitPgT3mE3OVj7ky7sibzHWkw== @@ -3808,7 +3809,7 @@ "@smithy/util-middleware" "^3.0.8" tslib "^2.6.2" -"@smithy/core@^2.4.8", "@smithy/core@^2.5.1": +"@smithy/core@^2.5.1": version "2.5.1" resolved "https://registry.yarnpkg.com/@smithy/core/-/core-2.5.1.tgz#7f635b76778afca845bcb401d36f22fa37712f15" integrity sha512-DujtuDA7BGEKExJ05W5OdxCoyekcKT3Rhg1ZGeiUWaz2BJIWXjZmsG/DIP4W48GHno7AQwRsaCb8NcBgH3QZpg== @@ -3843,7 +3844,7 @@ "@smithy/util-hex-encoding" "^3.0.0" tslib "^2.6.2" -"@smithy/eventstream-serde-browser@^3.0.10": +"@smithy/eventstream-serde-browser@^3.0.11": version "3.0.11" resolved 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"https://registry.yarnpkg.com/@smithy/hash-stream-node/-/hash-stream-node-3.1.7.tgz#df5c3b7aa8dbe9c389ff7857ce9145694f550b7e" integrity sha512-xMAsvJ3hLG63lsBVi1Hl6BBSfhd8/Qnp8fC06kjOpJvyyCEXdwHITa5Kvdsk6gaAXLhbZMhQMIGvgUbfnJDP6Q== @@ -3929,7 +3919,7 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@smithy/invalid-dependency@^3.0.7": +"@smithy/invalid-dependency@^3.0.8": version "3.0.8" resolved "https://registry.yarnpkg.com/@smithy/invalid-dependency/-/invalid-dependency-3.0.8.tgz#4d381a4c24832371ade79e904a72c173c9851e5f" integrity sha512-7Qynk6NWtTQhnGTTZwks++nJhQ1O54Mzi7fz4PqZOiYXb4Z1Flpb2yRvdALoggTS8xjtohWUM+RygOtB30YL3Q== @@ -3951,7 +3941,7 @@ dependencies: tslib "^2.6.2" -"@smithy/md5-js@^3.0.7": +"@smithy/md5-js@^3.0.8": version "3.0.8" resolved "https://registry.yarnpkg.com/@smithy/md5-js/-/md5-js-3.0.8.tgz#837e54094007e87bf5196e11eca453d1c1e83a26" integrity sha512-LwApfTK0OJ/tCyNUXqnWCKoE2b4rDSr4BJlDAVCkiWYeHESr+y+d5zlAanuLW6fnitVJRD/7d9/kN/ZM9Su4mA== @@ -3960,7 +3950,7 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@smithy/middleware-content-length@^3.0.9": +"@smithy/middleware-content-length@^3.0.10": version "3.0.10" resolved "https://registry.yarnpkg.com/@smithy/middleware-content-length/-/middleware-content-length-3.0.10.tgz#738266f6d81436d7e3a86bea931bc64e04ae7dbf" integrity sha512-T4dIdCs1d/+/qMpwhJ1DzOhxCZjZHbHazEPJWdB4GDi2HjIZllVzeBEcdJUN0fomV8DURsgOyrbEUzg3vzTaOg== @@ -3969,7 +3959,7 @@ "@smithy/types" "^3.6.0" tslib "^2.6.2" -"@smithy/middleware-endpoint@^3.1.4", "@smithy/middleware-endpoint@^3.2.1": +"@smithy/middleware-endpoint@^3.2.1": version "3.2.1" resolved "https://registry.yarnpkg.com/@smithy/middleware-endpoint/-/middleware-endpoint-3.2.1.tgz#b9ee42d29d8f3a266883d293c4d6a586f7b60979" integrity sha512-wWO3xYmFm6WRW8VsEJ5oU6h7aosFXfszlz3Dj176pTij6o21oZnzkCLzShfmRaaCHDkBXWBdO0c4sQAvLFP6zA== @@ -3983,7 +3973,7 @@ "@smithy/util-middleware" "^3.0.8" tslib "^2.6.2" -"@smithy/middleware-retry@^3.0.23": +"@smithy/middleware-retry@^3.0.25": version "3.0.25" resolved "https://registry.yarnpkg.com/@smithy/middleware-retry/-/middleware-retry-3.0.25.tgz#a6b1081fc1a0991ffe1d15e567e76198af01f37c" integrity sha512-m1F70cPaMBML4HiTgCw5I+jFNtjgz5z5UdGnUbG37vw6kh4UvizFYjqJGHvicfgKMkDL6mXwyPp5mhZg02g5sg== @@ -3998,7 +3988,7 @@ tslib "^2.6.2" uuid "^9.0.1" -"@smithy/middleware-serde@^3.0.7", "@smithy/middleware-serde@^3.0.8": +"@smithy/middleware-serde@^3.0.8": version "3.0.8" resolved "https://registry.yarnpkg.com/@smithy/middleware-serde/-/middleware-serde-3.0.8.tgz#a46d10dba3c395be0d28610d55c89ff8c07c0cd3" integrity sha512-Xg2jK9Wc/1g/MBMP/EUn2DLspN8LNt+GMe7cgF+Ty3vl+Zvu+VeZU5nmhveU+H8pxyTsjrAkci8NqY6OuvZnjA== @@ -4006,7 +3996,7 @@ "@smithy/types" "^3.6.0" tslib "^2.6.2" -"@smithy/middleware-stack@^3.0.7", "@smithy/middleware-stack@^3.0.8": +"@smithy/middleware-stack@^3.0.8": version "3.0.8" resolved "https://registry.yarnpkg.com/@smithy/middleware-stack/-/middleware-stack-3.0.8.tgz#f1c7d9c7fe8280c6081141c88f4a76875da1fc43" integrity sha512-d7ZuwvYgp1+3682Nx0MD3D/HtkmZd49N3JUndYWQXfRZrYEnCWYc8BHcNmVsPAp9gKvlurdg/mubE6b/rPS9MA== @@ -4014,7 +4004,7 @@ "@smithy/types" "^3.6.0" tslib "^2.6.2" -"@smithy/node-config-provider@^3.1.8", "@smithy/node-config-provider@^3.1.9": +"@smithy/node-config-provider@^3.1.9": version "3.1.9" resolved "https://registry.yarnpkg.com/@smithy/node-config-provider/-/node-config-provider-3.1.9.tgz#d27ba8e4753f1941c24ed0af824dbc6c492f510a" integrity sha512-qRHoah49QJ71eemjuS/WhUXB+mpNtwHRWQr77J/m40ewBVVwvo52kYAmb7iuaECgGTTcYxHS4Wmewfwy++ueew== @@ -4024,7 +4014,7 @@ "@smithy/types" "^3.6.0" tslib "^2.6.2" -"@smithy/node-http-handler@^3.2.4", "@smithy/node-http-handler@^3.2.5": +"@smithy/node-http-handler@^3.2.5": version "3.2.5" resolved "https://registry.yarnpkg.com/@smithy/node-http-handler/-/node-http-handler-3.2.5.tgz#ad9d9ba1528bf0d4a655135e978ecc14b3df26a2" integrity sha512-PkOwPNeKdvX/jCpn0A8n9/TyoxjGZB8WVoJmm9YzsnAgggTj4CrjpRHlTQw7dlLZ320n1mY1y+nTRUDViKi/3w== @@ -4043,7 +4033,7 @@ "@smithy/types" "^3.6.0" tslib "^2.6.2" -"@smithy/protocol-http@^4.1.4", "@smithy/protocol-http@^4.1.5": +"@smithy/protocol-http@^4.1.5": version "4.1.5" resolved "https://registry.yarnpkg.com/@smithy/protocol-http/-/protocol-http-4.1.5.tgz#a1f397440f299b6a5abeed6866957fecb1bf5013" integrity sha512-hsjtwpIemmCkm3ZV5fd/T0bPIugW1gJXwZ/hpuVubt2hEUApIoUTrf6qIdh9MAWlw0vjMrA1ztJLAwtNaZogvg== @@ -4051,7 +4041,7 @@ "@smithy/types" "^3.6.0" tslib "^2.6.2" -"@smithy/querystring-builder@^3.0.7", "@smithy/querystring-builder@^3.0.8": +"@smithy/querystring-builder@^3.0.8": version "3.0.8" resolved "https://registry.yarnpkg.com/@smithy/querystring-builder/-/querystring-builder-3.0.8.tgz#0d845be53aa624771c518d1412881236ce12ed4f" integrity sha512-btYxGVqFUARbUrN6VhL9c3dnSviIwBYD9Rz1jHuN1hgh28Fpv2xjU1HeCeDJX68xctz7r4l1PBnFhGg1WBBPuA== @@ -4097,7 +4087,7 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@smithy/smithy-client@^3.4.0", "@smithy/smithy-client@^3.4.2": +"@smithy/smithy-client@^3.4.2": version "3.4.2" resolved "https://registry.yarnpkg.com/@smithy/smithy-client/-/smithy-client-3.4.2.tgz#a6e3ed98330ce170cf482e765bd0c21e0fde8ae4" integrity sha512-dxw1BDxJiY9/zI3cBqfVrInij6ShjpV4fmGHesGZZUiP9OSE/EVfdwdRz0PgvkEvrZHpsj2htRaHJfftE8giBA== @@ -4110,14 +4100,14 @@ "@smithy/util-stream" "^3.2.1" tslib "^2.6.2" -"@smithy/types@^3.5.0", "@smithy/types@^3.6.0": +"@smithy/types@^3.6.0": version "3.6.0" resolved "https://registry.yarnpkg.com/@smithy/types/-/types-3.6.0.tgz#03a52bfd62ee4b7b2a1842c8ae3ada7a0a5ff3a4" integrity sha512-8VXK/KzOHefoC65yRgCn5vG1cysPJjHnOVt9d0ybFQSmJgQj152vMn4EkYhGuaOmnnZvCPav/KnYyE6/KsNZ2w== dependencies: tslib "^2.6.2" -"@smithy/url-parser@^3.0.7", "@smithy/url-parser@^3.0.8": +"@smithy/url-parser@^3.0.8": version "3.0.8" resolved "https://registry.yarnpkg.com/@smithy/url-parser/-/url-parser-3.0.8.tgz#8057d91d55ba8df97d74576e000f927b42da9e18" integrity 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-"@smithy/util-endpoints@^2.1.3": +"@smithy/util-endpoints@^2.1.4": version "2.1.4" resolved "https://registry.yarnpkg.com/@smithy/util-endpoints/-/util-endpoints-2.1.4.tgz#a29134c2b1982442c5fc3be18d9b22796e8eb964" integrity sha512-kPt8j4emm7rdMWQyL0F89o92q10gvCUa6sBkBtDJ7nV2+P7wpXczzOfoDJ49CKXe5CCqb8dc1W+ZdLlrKzSAnQ== @@ -4212,7 +4202,7 @@ dependencies: tslib "^2.6.2" -"@smithy/util-middleware@^3.0.7", "@smithy/util-middleware@^3.0.8": +"@smithy/util-middleware@^3.0.8": version "3.0.8" resolved "https://registry.yarnpkg.com/@smithy/util-middleware/-/util-middleware-3.0.8.tgz#372bc7a2845408ad69da039d277fc23c2734d0c6" integrity sha512-p7iYAPaQjoeM+AKABpYWeDdtwQNxasr4aXQEA/OmbOaug9V0odRVDy3Wx4ci8soljE/JXQo+abV0qZpW8NX0yA== @@ -4220,7 +4210,7 @@ "@smithy/types" "^3.6.0" tslib "^2.6.2" -"@smithy/util-retry@^3.0.7", "@smithy/util-retry@^3.0.8": +"@smithy/util-retry@^3.0.8": version "3.0.8" resolved 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