@jbrowse/plugin-alignments 1.7.8 → 1.7.11
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 +13 -3
- package/dist/AlignmentsFeatureDetail/index.d.ts +28 -3
- package/dist/AlignmentsFeatureDetail/index.js +6 -17
- package/dist/BamAdapter/MismatchParser.js +4 -2
- package/dist/LinearPileupDisplay/model.d.ts +7 -4
- package/dist/LinearPileupDisplay/model.js +131 -50
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +35 -14
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +3 -3
- package/dist/PileupRenderer/PileupRenderer.d.ts +66 -9
- package/dist/PileupRenderer/PileupRenderer.js +199 -124
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +2 -0
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +3 -0
- package/dist/SNPCoverageRenderer/configSchema.d.ts +1 -1
- package/package.json +2 -2
- package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +14 -3
- package/src/AlignmentsFeatureDetail/index.ts +7 -17
- package/src/BamAdapter/MismatchParser.ts +4 -2
- package/src/LinearPileupDisplay/model.ts +75 -23
- package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx +44 -30
- package/src/PileupRenderer/PileupRenderer.tsx +366 -180
- package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +5 -0
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@@ -166,7 +166,9 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
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: undefined
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const bins = [] as {
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+
refbase?: string
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total: number
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+
all: number
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ref: number
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'-1': 0
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'0': 0
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@@ -189,6 +191,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
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if (bins[i] === undefined) {
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bins[i] = {
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total: 0,
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+
all: 0,
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ref: 0,
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'-1': 0,
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'0': 0,
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@@ -201,6 +204,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
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}
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if (j !== fend) {
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bins[i].total++
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+
bins[i].all++
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bins[i].ref++
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bins[i][fstrand]++
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}
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@@ -318,6 +322,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
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bin.total--
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} else if (!interbase && colorSNPs) {
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inc(bin, fstrand, 'cov', base)
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+
bin.refbase = mismatch.altbase
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}
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}
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}
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