@jbrowse/plugin-alignments 2.4.0 → 2.4.2

package/esm/PileupRenderer/components/PileupRendering.js

@@ -113,10 +113,10 @@ function PileupRendering(props) {
         }
     }
     function callMouseHandler(handlerName, event) {
-        // @ts-ignore
+        // @ts-expect-error
         // eslint-disable-next-line react/destructuring-assignment
         const featureHandler = props[`onFeature${handlerName}`];
-        // @ts-ignore
+        // @ts-expect-error
         // eslint-disable-next-line react/destructuring-assignment
         const canvasHandler = props[`on${handlerName}`];
         if (featureHandler && featureIdUnderMouse) {

package/esm/PileupRenderer/components/PileupRendering.js.map

@@ -1 +1 @@
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package/esm/PileupRenderer/configSchema.js

@@ -43,7 +43,7 @@ const PileupRenderer = ConfigurationSchema('PileupRenderer', {
     minSubfeatureWidth: {
         type: 'number',
         description: 'the minimum width in px for a pileup mismatch feature. use for increasing/decreasing mismatch marker widths when zoomed out, e.g. 0 or 1',
-        defaultValue: 0.7,
+        defaultValue: 1,
     },
     /**
      * #slot

package/esm/PileupRenderer/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,cAAc,GAAG,mBAAmB,CACxC,gBAAgB,EAChB;IACE;;;OAGG;IACH,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,iDAAiD;QAC9D,YAAY,EAAE,MAAM;QACpB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IAED;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,iBAAiB,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;QAC/D,YAAY,EAAE,IAAI;QAClB,WAAW,EACT,oIAAoI;KACvI;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,aAAa,EAAE;YACtC,QAAQ;YACR,SAAS;YACT,UAAU;SACX,CAAC;QACF,WAAW,EAAE,2BAA2B;QACxC,YAAY,EAAE,QAAQ;KACvB;IACD;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,0IAA0I;QAC5I,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,qDAAqD;QAClE,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,oDAAoD;QACjE,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,kDAAkD;QAC/D,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,iCAAiC;QAC9C,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,4BAA4B,EAAE;QAC5B,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,kEAAkE;QACpE,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,KAAK;QACnB,WAAW,EAAE,6BAA6B;KAC3C;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,cAAc,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,cAAc,GAAG,mBAAmB,CACxC,gBAAgB,EAChB;IACE;;;OAGG;IACH,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,iDAAiD;QAC9D,YAAY,EAAE,MAAM;QACpB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IAED;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,iBAAiB,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;QAC/D,YAAY,EAAE,IAAI;QAClB,WAAW,EACT,oIAAoI;KACvI;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,aAAa,EAAE;YACtC,QAAQ;YACR,SAAS;YACT,UAAU;SACX,CAAC;QACF,WAAW,EAAE,2BAA2B;QACxC,YAAY,EAAE,QAAQ;KACvB;IACD;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,0IAA0I;QAC5I,YAAY,EAAE,CAAC;KAChB;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,qDAAqD;QAClE,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,oDAAoD;QACjE,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,kDAAkD;QAC/D,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,iCAAiC;QAC9C,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,4BAA4B,EAAE;QAC5B,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,kEAAkE;QACpE,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,KAAK;QACnB,WAAW,EAAE,6BAA6B;KAC3C;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,cAAc,CAAA"}

package/esm/PileupRenderer/sortUtil.js

@@ -59,7 +59,7 @@ export const sortFeature = (features, sortedBy) => {
                 const acode = bMismatch && bMismatch.base.toUpperCase();
                 const bcode = aMismatch && aMismatch.base.toUpperCase();
                 if (acode === bcode && acode === '*') {
-                    // @ts-ignore
+                    // @ts-expect-error
                     return aMismatch.length - bMismatch.length;
                 }
                 return ((acode ? acode.charCodeAt(0) : 0) - (bcode ? bcode.charCodeAt(0) : 0));
@@ -72,9 +72,10 @@ export const sortFeature = (features, sortedBy) => {
             break;
         }
     }
-    const sortedMap = new Map(featuresInCenterLine
-        .concat(featuresOutsideCenter)
-        .map(feature => [feature.id(), feature]));
+    const sortedMap = new Map([...featuresInCenterLine, ...featuresOutsideCenter].map(feature => [
+        feature.id(),
+        feature,
+    ]));
     return sortedMap;
 };
 //# sourceMappingURL=sortUtil.js.map

package/esm/PileupRenderer/sortUtil.js.map

@@ -1 +1 @@
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package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -2,6 +2,7 @@ import { createJBrowseTheme } from '@jbrowse/core/ui';
 import { featureSpanPx, bpSpanPx } from '@jbrowse/core/util';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { getOrigin, getScale, WiggleBaseRenderer, YSCALEBAR_LABEL_OFFSET, } from '@jbrowse/plugin-wiggle';
+const fudgeFactor = 0.6;
 export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     // note: the snps are drawn on linear scale even if the data is drawn in log
     // scape hence the two different scales being used
@@ -28,6 +29,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
             scaleType: 'linear',
         });
         const originY = getOrigin(scaleOpts.scaleType);
+        const originLinear = getOrigin('linear');
         const indicatorThreshold = readConfObject(cfg, 'indicatorThreshold');
         const drawInterbaseCounts = readConfObject(cfg, 'drawInterbaseCounts');
         const drawArcs = readConfObject(cfg, 'drawArcs');
@@ -35,8 +37,9 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
         // get the y coordinate that we are plotting at, this can be log scale
         const toY = (n) => height - (viewScale(n) || 0) + offset;
         const toHeight = (n) => toY(originY) - toY(n);
-        const indicatorToY = (n) => height - (indicatorViewScale(n) || 0) + offset;
-        const indicatorToHeight = (n) => indicatorToY(getOrigin('linear')) - indicatorToY(n);
+        // used specifically for indicator
+        const toY2 = (n) => height - (indicatorViewScale(n) || 0) + offset;
+        const toHeight2 = (n) => toY2(originLinear) - toY2(n);
         const { bases } = theme.palette;
         const colorForBase = {
             A: bases.A.main,
@@ -49,7 +52,6 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
             hardclip: 'red',
             meth: 'red',
             unmeth: 'blue',
-            ref: 'lightgrey',
         };
         const feats = [...features.values()];
         const coverage = feats.filter(f => f.get('type') !== 'skip');
@@ -60,7 +62,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
         for (let i = 0; i < coverage.length; i++) {
             const feature = coverage[i];
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-            const w = rightPx - leftPx + 0.3;
+            const w = rightPx - leftPx + fudgeFactor;
             const score = feature.get('score');
             ctx.fillRect(leftPx, toY(score), w, toHeight(score));
         }
@@ -81,7 +83,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
             const score = feature.get('score');
             const snpinfo = feature.get('snpinfo');
-            const w = Math.max(rightPx - leftPx + 0.3, 1);
+            const w = Math.max(rightPx - leftPx, 1);
             const totalScore = snpinfo.total;
             const keys = Object.keys(snpinfo.cov).sort();
             let curr = 0;
@@ -94,7 +96,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
                         '#888';
                 const height = toHeight(score);
                 const bottom = toY(score) + height;
-                ctx.fillRect(leftPx, bottom - ((total + curr) / score) * height, w, (total / score) * height);
+                ctx.fillRect(Math.round(leftPx), bottom - ((total + curr) / score) * height, w, (total / score) * height);
                 curr += total;
             }
             const interbaseEvents = Object.keys(snpinfo.noncov);
@@ -104,8 +106,9 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
                 for (let i = 0; i < interbaseEvents.length; i++) {
                     const base = interbaseEvents[i];
                     const { total } = snpinfo.noncov[base];
+                    const r = 0.6;
                     ctx.fillStyle = colorForBase[base];
-                    ctx.fillRect(leftPx - 0.6 + extraHorizontallyFlippedOffset, indicatorHeight + indicatorToHeight(curr), 1.2, indicatorToHeight(total));
+                    ctx.fillRect(leftPx - r + extraHorizontallyFlippedOffset, indicatorHeight + toHeight2(curr), r * 2, toHeight2(total));
                     curr += total;
                 }
             }

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map

@@ -1 +1 @@
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package/esm/index.d.ts

@@ -1,11 +1,9 @@
 import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory } from './LinearPileupDisplay';
-import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
-import * as MismatchParser from './MismatchParser';
 export default class AlignmentsPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;
 }
-export { linearPileupDisplayConfigSchemaFactory, linearPileupDisplayStateModelFactory, MismatchParser, };
-export type { LinearPileupDisplayModel };
+export { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, } from './LinearPileupDisplay';
+export { type LinearPileupDisplayModel } from './LinearPileupDisplay/model';
+export * as MismatchParser from './MismatchParser';

package/esm/index.js

@@ -13,8 +13,7 @@ import AlignmentsTrackF from './AlignmentsTrack';
 import AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail';
 import PileupRPCMethodsF from './PileupRPC';
 import GuessAlignmentsTypesF from './GuessAlignmentsTypes';
-import LinearPileupDisplayF, { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, } from './LinearPileupDisplay';
-import * as MismatchParser from './MismatchParser';
+import LinearPileupDisplayF from './LinearPileupDisplay';
 export default class AlignmentsPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -41,5 +40,6 @@ export default class AlignmentsPlugin extends Plugin {
         ].map(f => f(pluginManager));
     }
 }
-export { linearPileupDisplayConfigSchemaFactory, linearPileupDisplayStateModelFactory, MismatchParser, };
+export { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, } from './LinearPileupDisplay';
+export * as MismatchParser from './MismatchParser';
 //# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,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,sBAAsB,MAAM,yBAAyB,CAAA;AAC5D,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,wBAAwB,MAAM,2BAA2B,CAAA;AAChE,OAAO,iBAAiB,MAAM,aAAa,CAAA;AAC3C,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AAExD,MAAM,CAAC,OAAO,OAAO,gBAAiB,SAAQ,MAAM;IAApD;;QACE,SAAI,GAAG,kBAAkB,CAAA;IAqB3B,CAAC;IAnBC,OAAO,CAAC,aAA4B;QAClC,CAAC;QAAA;YACC,YAAY;YACZ,WAAW;YACX,oBAAoB;YACpB,yBAAyB;YACzB,gBAAgB;YAChB,mBAAmB;YACnB,iBAAiB;YACjB,eAAe;YACf,iBAAiB;YACjB,oBAAoB;YACpB,sBAAsB;YACtB,uBAAuB;YACvB,wBAAwB;YACxB,wBAAwB;YACxB,qBAAqB;SACtB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAA;IAC9B,CAAC;CACF;AAED,OAAO,EACL,oCAAoC,EACpC,sCAAsC,GACvC,MAAM,uBAAuB,CAAA;AAE9B,OAAO,KAAK,cAAc,MAAM,kBAAkB,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.4.0",
+  "version": "2.4.2",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -65,5 +65,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "78707a2bc3ba8489f26a590ef83f62ede945d048"
+  "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
 }

package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx

@@ -1,196 +1,121 @@
 import React, { useState } from 'react'
-import {
-  Typography,
-  Link,
-  Paper,
-  Checkbox,
-  FormControlLabel,
-  FormGroup,
-} from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
+import { Link, Paper } from '@mui/material'
 import { observer } from 'mobx-react'
-import { getSession } from '@jbrowse/core/util'
 import copy from 'copy-to-clipboard'
 import clone from 'clone'
-import {
-  FeatureDetails,
-  BaseCard,
-  SimpleValue,
-} from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
-import { parseCigar } from '../MismatchParser'
+import { FeatureDetails } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
+import { IAnyStateTreeNode } from 'mobx-state-tree'
 
-const useStyles = makeStyles()({
-  compact: {
-    paddingRight: 0,
-    paddingTop: 0,
-    paddingBottom: 0,
-  },
-})
+// locals
+import { getTag, navToLoc } from './util'
+import SupplementaryAlignments from './AlignmentsFeatureSuppAligns'
+import AlignmentFlags from './AlignmentsFeatureFlags'
 
 const omit = ['clipPos', 'flags']
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function AlignmentFlags(props: { feature: any }) {
-  const { classes } = useStyles()
-  const { feature } = props
-  const { flags } = feature
-  const flagNames = [
-    'read paired',
-    'read mapped in proper pair',
-    'read unmapped',
-    'mate unmapped',
-    'read reverse strand',
-    'mate reverse strand',
-    'first in pair',
-    'second in pair',
-    'not primary alignment',
-    'read fails platform/vendor quality checks',
-    'read is PCR or optical duplicate',
-    'supplementary alignment',
-  ]
-  return (
-    <BaseCard {...props} title="Flags">
-      <SimpleValue name={'Flag'} value={flags} />
-
-      <FormGroup>
-        {flagNames.map((name, index) => {
-          const val = flags & (1 << index)
-          const key = `${name}_${val}`
-          return (
-            <FormControlLabel
-              key={key}
-              control={
-                <Checkbox
-                  className={classes.compact}
-                  checked={Boolean(val)}
-                  name={name}
-                  readOnly
-                />
-              }
-              label={name}
-            />
-          )
-        })}
-      </FormGroup>
-    </BaseCard>
-  )
+const tags = {
+  AM: 'The smallest template-independent mapping quality in the template',
+  AS: 'Alignment score generated by aligner',
+  BC: 'Barcode sequence identifying the sample',
+  BQ: 'Offset to base alignment quality (BAQ)',
+  BZ: 'Phred quality of the unique molecular barcode bases in the {OX} tag',
+  CB: 'Cell identifier',
+  CC: 'Reference name of the next hit',
+  CM: 'Edit distance between the color sequence and the color reference (see also {NM})',
+  CO: 'Free-text comments',
+  CP: 'Leftmost coordinate of the next hit',
+  CQ: 'Color read base qualities',
+  CR: 'Cellular barcode sequence bases (uncorrected)',
+  CS: 'Color read sequence',
+  CT: 'Complete read annotation tag, used for consensus annotation dummy features',
+  CY: 'Phred quality of the cellular barcode sequence in the {CR} tag',
+  E2: 'The 2nd most likely base calls',
+  FI: 'The index of segment in the template',
+  FS: 'Segment suffix',
+  FZ: 'Flow signal intensities',
+  GC: 'Reserved for backwards compatibility reasons',
+  GQ: 'Reserved for backwards compatibility reasons',
+  GS: 'Reserved for backwards compatibility reasons',
+  H0: 'Number of perfect hits',
+  H1: 'Number of 1-difference hits (see also {NM})',
+  H2: 'Number of 2-difference hits',
+  HI: 'Query hit index',
+  IH: 'Query hit total count',
+  LB: 'Library',
+  MC: 'CIGAR string for mate/next segment',
+  MD: 'String encoding mismatched and deleted reference bases',
+  MF: 'Reserved for backwards compatibility reasons',
+  MI: 'Molecular identifier; a string that uniquely identifies the molecule from which the record was derived',
+  ML: 'Base modification probabilities',
+  MM: 'Base modifications / methylation ',
+  MQ: 'Mapping quality of the mate/next segment',
+  NH: 'Number of reported alignments that contain the query in the current record',
+  NM: 'Edit distance to the reference',
+  OA: 'Original alignment',
+  OC: 'Original CIGAR (deprecated; use {OA} instead)',
+  OP: 'Original mapping position (deprecated; use {OA} instead)',
+  OQ: 'Original base quality',
+  OX: 'Original unique molecular barcode bases',
+  PG: 'Program',
+  PQ: 'Phred likelihood of the template',
+  PT: 'Read annotations for parts of the padded read sequence',
+  PU: 'Platform unit',
+  Q2: 'Phred quality of the mate/next segment sequence in the {R2} tag',
+  QT: 'Phred quality of the sample barcode sequence in the {BC} tag',
+  QX: 'Quality score of the unique molecular identifier in the {RX} tag',
+  R2: 'Sequence of the mate/next segment in the template',
+  RG: 'Read group',
+  RT: 'Reserved for backwards compatibility reasons',
+  RX: 'Sequence bases of the (possibly corrected) unique molecular identifier',
+  S2: 'Reserved for backwards compatibility reasons',
+  SA: 'Other canonical alignments in a chimeric alignment',
+  SM: 'Template-independent mapping quality',
+  SQ: 'Reserved for backwards compatibility reasons',
+  TC: 'The number of segments in the template',
+  TS: 'Transcript strand',
+  U2: 'Phred probability of the 2nd call being wrong conditional on the best being wrong',
+  UQ: 'Phred likelihood of the segment, conditional on the mapping being correct',
 }
 
 function Formatter({ value }: { value: unknown }) {
   const [show, setShow] = useState(false)
   const [copied, setCopied] = useState(false)
   const display = String(value)
-  if (display.length > 100) {
-    return (
-      <>
-        <button
-          type="button"
-          onClick={() => {
-            copy(display)
-            setCopied(true)
-            setTimeout(() => {
-              setCopied(false)
-            }, 700)
-          }}
-        >
-          {copied ? 'Copied to clipboard' : 'Copy'}
-        </button>
-        <button type="button" onClick={() => setShow(val => !val)}>
-          {show ? 'Show less' : 'Show more'}
-        </button>
-        <div>{show ? display : `${display.slice(0, 100)}...`}</div>
-      </>
-    )
-  }
-  return <div>{display}</div>
-}
-
-// utility function to get length of alignment from cigar
-function getLengthOnRef(cigar: string) {
-  const cigarOps = parseCigar(cigar)
-  let lengthOnRef = 0
-  for (let i = 0; i < cigarOps.length; i += 2) {
-    const len = +cigarOps[i]
-    const op = cigarOps[i + 1]
-    if (op !== 'H' && op !== 'S' && op !== 'I') {
-      lengthOnRef += len
-    }
-  }
-  return lengthOnRef
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function SupplementaryAlignments(props: { tag: string; model: any }) {
-  const { tag, model } = props
-  const session = getSession(model)
-  return (
-    <BaseCard {...props} title="Supplementary alignments">
-      <Typography>List of supplementary alignment locations</Typography>
-      <ul>
-        {tag
-          .split(';')
-          .filter(SA => !!SA)
-          .map((SA, index) => {
-            const [saRef, saStart, saStrand, saCigar] = SA.split(',')
-            const saLength = getLengthOnRef(saCigar)
-            const extra = Math.floor(saLength / 5)
-            const start = +saStart
-            const end = +saStart + saLength
-            const locString = `${saRef}:${Math.max(1, start - extra)}-${
-              end + extra
-            }`
-            const displayStart = start.toLocaleString('en-US')
-            const displayEnd = end.toLocaleString('en-US')
-            const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand})`
-            return (
-              <li key={`${locString}-${index}`}>
-                <Link
-                  onClick={async event => {
-                    event.preventDefault()
-                    const { view } = model
-                    try {
-                      if (view) {
-                        await view.navToLocString(locString)
-                      } else {
-                        throw new Error(
-                          'No view associated with this view anymore',
-                        )
-                      }
-                    } catch (e) {
-                      console.error(e)
-                      session.notify(`${e}`)
-                    }
-                  }}
-                  href="#"
-                >
-                  {displayString}
-                </Link>
-              </li>
-            )
-          })}
-      </ul>
-    </BaseCard>
+  return display.length > 100 ? (
+    <>
+      <button
+        type="button"
+        onClick={() => {
+          copy(display)
+          setCopied(true)
+          setTimeout(() => setCopied(false), 700)
+        }}
+      >
+        {copied ? 'Copied to clipboard' : 'Copy'}
+      </button>
+      <button type="button" onClick={() => setShow(val => !val)}>
+        {show ? 'Show less' : 'Show more'}
+      </button>
+      <div>{show ? display : `${display.slice(0, 100)}...`}</div>
+    </>
+  ) : (
+    <div>{display}</div>
   )
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function PairLink({ locString, model }: { locString: string; model: any }) {
-  const session = getSession(model)
+function PairLink({
+  locString,
+  model,
+}: {
+  locString: string
+  model: IAnyStateTreeNode
+}) {
   return (
     <Link
-      onClick={async () => {
-        const { view } = model
-        if (!view) {
-          throw new Error(
-            'No view associated with this feature detail panel anymore',
-          )
-        }
-        try {
-          await view.navToLocString(locString)
-        } catch (e) {
-          console.error(e)
-          session.notify(`${e}`)
-        }
+      onClick={event => {
+        event.preventDefault()
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        navToLoc(locString, model)
       }}
       href="#"
     >
@@ -199,24 +124,27 @@ function PairLink({ locString, model }: { locString: string; model: any }) {
   )
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function AlignmentFeatureDetails(props: { model: any }) {
+export default observer(function AlignmentFeatureDetails(props: {
+  model: IAnyStateTreeNode
+}) {
   const { model } = props
   const feat = clone(model.featureData)
-  const SA = (feat.tags && feat.tags.SA) || feat.SA
+  const SA = getTag('SA', feat) as string
   return (
     <Paper data-testid="alignment-side-drawer">
       <FeatureDetails
         {...props}
         omit={omit}
+        // @ts-expect-error
+        descriptions={{ ...tags, tags }}
         feature={feat}
-        formatter={(value, key) => {
-          return key === 'next_segment_position' ? (
+        formatter={(value, key) =>
+          key === 'next_segment_position' ? (
             <PairLink model={model} locString={value as string} />
           ) : (
             <Formatter value={value} />
           )
-        }}
+        }
       />
       {SA ? <SupplementaryAlignments model={model} tag={SA} /> : null}
       {feat.flags !== undefined ? (
@@ -224,6 +152,4 @@ function AlignmentFeatureDetails(props: { model: any }) {
       ) : null}
     </Paper>
   )
-}
-
-export default observer(AlignmentFeatureDetails)
+})