npm - @jbrowse/plugin-alignments - Versions diffs - 2.1.0 → 2.1.2 - Mend

@jbrowse/plugin-alignments 2.1.0 → 2.1.2

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.

Files changed (115) hide show

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +61 -90
package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
package/dist/AlignmentsFeatureDetail/index.js +14 -16
package/dist/AlignmentsFeatureDetail/index.js.map +1 -1
package/dist/AlignmentsTrack/index.js +8 -8
package/dist/AlignmentsTrack/index.js.map +1 -1
package/dist/BamAdapter/BamAdapter.js +157 -336
package/dist/BamAdapter/BamAdapter.js.map +1 -1
package/dist/BamAdapter/BamSlightlyLazyFeature.js +68 -103
package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
package/dist/BamAdapter/MismatchParser.js +96 -162
package/dist/BamAdapter/MismatchParser.js.map +1 -1
package/dist/BamAdapter/configSchema.js +27 -29
package/dist/BamAdapter/configSchema.js.map +1 -1
package/dist/BamAdapter/index.js +9 -11
package/dist/BamAdapter/index.js.map +1 -1
package/dist/CramAdapter/CramAdapter.js +193 -351
package/dist/CramAdapter/CramAdapter.js.map +1 -1
package/dist/CramAdapter/CramSlightlyLazyFeature.js +119 -154
package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
package/dist/CramAdapter/CramTestAdapters.js +51 -148
package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
package/dist/CramAdapter/configSchema.js +23 -25
package/dist/CramAdapter/configSchema.js.map +1 -1
package/dist/CramAdapter/index.js +9 -11
package/dist/CramAdapter/index.js.map +1 -1
package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js +25 -87
package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js.map +1 -1
package/dist/HtsgetBamAdapter/configSchema.js +16 -18
package/dist/HtsgetBamAdapter/configSchema.js.map +1 -1
package/dist/HtsgetBamAdapter/index.js +15 -19
package/dist/HtsgetBamAdapter/index.js.map +1 -1
package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +14 -15
package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
package/dist/LinearAlignmentsDisplay/index.js +7 -7
package/dist/LinearAlignmentsDisplay/index.js.map +1 -1
package/dist/LinearAlignmentsDisplay/models/configSchema.js +5 -5
package/dist/LinearAlignmentsDisplay/models/configSchema.js.map +1 -1
package/dist/LinearAlignmentsDisplay/models/model.js +64 -140
package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
package/dist/LinearPileupDisplay/components/ColorByModifications.js +24 -53
package/dist/LinearPileupDisplay/components/ColorByModifications.js.map +1 -1
package/dist/LinearPileupDisplay/components/ColorByTag.js +14 -30
package/dist/LinearPileupDisplay/components/ColorByTag.js.map +1 -1
package/dist/LinearPileupDisplay/components/FilterByTag.js +33 -49
package/dist/LinearPileupDisplay/components/FilterByTag.js.map +1 -1
package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +7 -7
package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -1
package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +17 -33
package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
package/dist/LinearPileupDisplay/components/SetMaxHeight.js +14 -30
package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
package/dist/LinearPileupDisplay/components/SortByTag.js +14 -30
package/dist/LinearPileupDisplay/components/SortByTag.js.map +1 -1
package/dist/LinearPileupDisplay/configSchema.js +4 -4
package/dist/LinearPileupDisplay/configSchema.js.map +1 -1
package/dist/LinearPileupDisplay/index.js +7 -7
package/dist/LinearPileupDisplay/index.js.map +1 -1
package/dist/LinearPileupDisplay/model.d.ts +2 -2
package/dist/LinearPileupDisplay/model.js +534 -644
package/dist/LinearPileupDisplay/model.js.map +1 -1
package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +30 -78
package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -1
package/dist/LinearSNPCoverageDisplay/index.js +7 -7
package/dist/LinearSNPCoverageDisplay/index.js.map +1 -1
package/dist/LinearSNPCoverageDisplay/models/configSchema.js +4 -4
package/dist/LinearSNPCoverageDisplay/models/configSchema.js.map +1 -1
package/dist/LinearSNPCoverageDisplay/models/model.d.ts +1 -1
package/dist/LinearSNPCoverageDisplay/models/model.js +170 -244
package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
package/dist/NestedFrequencyTable.js +27 -40
package/dist/NestedFrequencyTable.js.map +1 -1
package/dist/PileupRPC/rpcMethods.js +63 -191
package/dist/PileupRPC/rpcMethods.js.map +1 -1
package/dist/PileupRenderer/PileupLayoutSession.js +25 -47
package/dist/PileupRenderer/PileupLayoutSession.js.map +1 -1
package/dist/PileupRenderer/PileupRenderer.js +395 -529
package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
package/dist/PileupRenderer/components/PileupRendering.js +41 -68
package/dist/PileupRenderer/components/PileupRendering.js.map +1 -1
package/dist/PileupRenderer/configSchema.js +2 -2
package/dist/PileupRenderer/configSchema.js.map +1 -1
package/dist/PileupRenderer/index.js +9 -11
package/dist/PileupRenderer/index.js.map +1 -1
package/dist/PileupRenderer/sortUtil.js +36 -40
package/dist/PileupRenderer/sortUtil.js.map +1 -1
package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +229 -415
package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
package/dist/SNPCoverageAdapter/configSchema.js +5 -9
package/dist/SNPCoverageAdapter/configSchema.js.map +1 -1
package/dist/SNPCoverageAdapter/index.js +17 -21
package/dist/SNPCoverageAdapter/index.js.map +1 -1
package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +175 -259
package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
package/dist/SNPCoverageRenderer/configSchema.js +1 -1
package/dist/SNPCoverageRenderer/configSchema.js.map +1 -1
package/dist/SNPCoverageRenderer/index.js +10 -12
package/dist/SNPCoverageRenderer/index.js.map +1 -1
package/dist/index.js +40 -58
package/dist/index.js.map +1 -1
package/dist/shared.js +23 -78
package/dist/shared.js.map +1 -1
package/dist/util.js +13 -66
package/dist/util.js.map +1 -1
package/esm/LinearPileupDisplay/model.d.ts +2 -2
package/esm/LinearSNPCoverageDisplay/models/model.d.ts +1 -1
package/esm/PileupRenderer/PileupRenderer.js +0 -2
package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +0 -1
package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
package/package.json +2 -3
package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +12 -12
package/src/PileupRenderer/PileupRenderer.tsx +0 -2
package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +0 -1

package/esm/PileupRenderer/PileupRenderer.js.map CHANGED Viewed

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package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js CHANGED Viewed

@@ -37,7 +37,6 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
         const toHeight = (n) => toY(originY) - toY(n);
         const indicatorToY = (n) => height - (indicatorViewScale(n) || 0) + offset;
         const indicatorToHeight = (n) => indicatorToY(getOrigin('linear')) - indicatorToY(n);
-        // @ts-ignore
         const { bases } = theme.palette;
         const colorForBase = {
             A: bases.A.main,

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.1.0",
+  "version": "2.1.2",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,7 +37,6 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@babel/runtime": "^7.17.9",
     "@gmod/bam": "^1.1.15",
     "@gmod/cram": "^1.6.4",
     "@mui/icons-material": "^5.0.1",
@@ -65,5 +64,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "0db0462fa1f9f15ab4869da085bcab032b9483c3"
+  "gitHead": "449b17325c9a4a97181f7ddddf48e80219f03b8d"
 }

package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap CHANGED Viewed

@@ -345,7 +345,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -379,7 +379,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -413,7 +413,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -447,7 +447,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -481,7 +481,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -515,7 +515,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -549,7 +549,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -583,7 +583,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -617,7 +617,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -651,7 +651,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -685,7 +685,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -719,7 +719,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"

package/src/PileupRenderer/PileupRenderer.tsx CHANGED Viewed

@@ -63,7 +63,6 @@ function fillRect(
 }
 function getColorBaseMap(theme: Theme) {
-  // @ts-ignore
   const { bases } = theme.palette
   return {
     A: bases.A.main,
@@ -1060,7 +1059,6 @@ export default class PileupRenderer extends BoxRendererType {
     const mismatches: Mismatch[] = feature.get('mismatches')
     const seq = feature.get('seq')
     const { charWidth, charHeight } = this.getCharWidthHeight(ctx)
-    // @ts-ignore
     const { bases } = theme.palette
     const colorForBase: { [key: string]: string } = {
       A: bases.A.main,

package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts CHANGED Viewed

@@ -93,7 +93,6 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     const indicatorToHeight = (n: number) =>
       indicatorToY(getOrigin('linear')) - indicatorToY(n)
-    // @ts-ignore
     const { bases } = theme.palette
     const colorForBase: { [key: string]: string } = {
       A: bases.A.main,