@jbrowse/plugin-alignments 2.4.1 → 2.5.0

package/dist/SNPCoverageAdapter/configSchema.d.ts

@@ -1,2 +1,11 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     * normally refers to a BAM or CRAM adapter
+     */
+    subadapter: {
+        type: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/dist/SNPCoverageAdapter/generateCoverageBins.js

@@ -66,21 +66,23 @@ async function generateCoverageBins(features, region, opts, fetchSequence) {
             const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
             const ops = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
             const fend = feature.get('end');
-            (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
-                const mod = `mod_${type}`;
-                for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
-                    const epos = pos + fstart - region.start;
-                    if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
-                        const bin = bins[epos];
-                        if (bin) {
-                            inc(bin, fstrand, 'cov', mod);
-                        }
-                        else {
-                            console.warn('Undefined position in modifications snpcoverage encountered');
+            if (seq) {
+                (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
+                    const mod = `mod_${type}`;
+                    for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
+                        const epos = pos + fstart - region.start;
+                        if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
+                            const bin = bins[epos];
+                            if (bin) {
+                                inc(bin, fstrand, 'cov', mod);
+                            }
+                            else {
+                                console.warn('Undefined position in modifications snpcoverage encountered');
+                            }
                         }
                     }
-                }
-            });
+                });
+            }
         }
         // methylation based coloring takes into account both reference
         // sequence CpG detection and reads
@@ -92,41 +94,43 @@ async function generateCoverageBins(features, region, opts, fetchSequence) {
             const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
             const methBins = new Array(region.end - region.start).fill(0);
             const ops = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-            (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
-                // we are processing methylation
-                if (type === 'm') {
-                    for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
-                        const epos = pos + fstart - region.start;
-                        if (epos >= 0 && epos < methBins.length) {
-                            methBins[epos] = 1;
+            if (seq) {
+                (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
+                    // we are processing methylation
+                    if (type === 'm') {
+                        for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
+                            const epos = pos + fstart - region.start;
+                            if (epos >= 0 && epos < methBins.length) {
+                                methBins[epos] = 1;
+                            }
                         }
                     }
-                }
-            });
-            for (let j = fstart; j < fend; j++) {
-                const i = j - region.start;
-                if (i >= 0 && i < bins.length - 1) {
-                    const l1 = regionSeq[i].toLowerCase();
-                    const l2 = regionSeq[i + 1].toLowerCase();
-                    const bin = bins[i];
-                    const bin1 = bins[i + 1];
-                    // color
-                    if (l1 === 'c' && l2 === 'g') {
-                        if (methBins[i] || methBins[i + 1]) {
-                            inc(bin, fstrand, 'cov', 'meth');
-                            inc(bin1, fstrand, 'cov', 'meth');
-                            bins[i].ref--;
-                            bins[i][fstrand]--;
-                            bins[i + 1].ref--;
-                            bins[i + 1][fstrand]--;
-                        }
-                        else {
-                            inc(bin, fstrand, 'cov', 'unmeth');
-                            inc(bin1, fstrand, 'cov', 'unmeth');
-                            bins[i].ref--;
-                            bins[i][fstrand]--;
-                            bins[i + 1].ref--;
-                            bins[i + 1][fstrand]--;
+                });
+                for (let j = fstart; j < fend; j++) {
+                    const i = j - region.start;
+                    if (i >= 0 && i < bins.length - 1) {
+                        const l1 = regionSeq[i].toLowerCase();
+                        const l2 = regionSeq[i + 1].toLowerCase();
+                        const bin = bins[i];
+                        const bin1 = bins[i + 1];
+                        // color
+                        if (l1 === 'c' && l2 === 'g') {
+                            if (methBins[i] || methBins[i + 1]) {
+                                inc(bin, fstrand, 'cov', 'meth');
+                                inc(bin1, fstrand, 'cov', 'meth');
+                                bins[i].ref--;
+                                bins[i][fstrand]--;
+                                bins[i + 1].ref--;
+                                bins[i + 1][fstrand]--;
+                            }
+                            else {
+                                inc(bin, fstrand, 'cov', 'unmeth');
+                                inc(bin1, fstrand, 'cov', 'unmeth');
+                                bins[i].ref--;
+                                bins[i][fstrand]--;
+                                bins[i + 1].ref--;
+                                bins[i + 1][fstrand]--;
+                            }
                         }
                     }
                 }

package/dist/SNPCoverageAdapter/generateCoverageBins.js.map

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

@@ -85,7 +85,7 @@ class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
             const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
             const score = feature.get('score');
             const snpinfo = feature.get('snpinfo');
-            const w = Math.max(rightPx - leftPx + fudgeFactor, 1);
+            const w = Math.max(rightPx - leftPx, 1);
             const totalScore = snpinfo.total;
             const keys = Object.keys(snpinfo.cov).sort();
             let curr = 0;

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SNPCoverageRenderer.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/SNPCoverageRenderer.ts"],"names":[],"mappings":";;AAAA,yCAAqD;AACrD,6CAAqE;AACrE,+DAA4D;AAE5D,0DAM+B;AA2B/B,MAAM,WAAW,GAAG,GAAG,CAAA;AAEvB,MAAqB,mBAAoB,SAAQ,kCAAkB;IACjE,4EAA4E;IAC5E,kDAAkD;IAClD,KAAK,CAAC,IAAI,CACR,GAA6B,EAC7B,KAAyC;QAEzC,MAAM,EACJ,QAAQ,EACR,OAAO,EACP,OAAO,EACP,mBAAmB,EACnB,kBAAkB,GAAG,EAAE,EACvB,SAAS,EACT,MAAM,EAAE,gBAAgB,EACxB,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,GAAG,EACX,KAAK,GACN,GAAG,KAAK,CAAA;QACT,MAAM,KAAK,GAAG,IAAA,uBAAkB,EAAC,WAAW,CAAC,CAAA;QAC7C,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;QACxB,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QAEnD,yEAAyE;QACzE,oEAAoE;QACpE,iDAAiD;QACjD,MAAM,MAAM,GAAG,sCAAsB,CAAA;QACrC,MAAM,MAAM,GAAG,gBAAgB,GAAG,MAAM,GAAG,CAAC,CAAA;QAE5C,MAAM,EAAE,MAAM,EAAE,GAAG,SAAS,CAAA;QAC5B,IAAI,CAAC,MAAM,EAAE;YACX,OAAM;SACP;QACD,MAAM,IAAI,GAAG,EAAE,GAAG,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,CAAC,EAAE,CAAA;QACjD,MAAM,SAAS,GAAG,IAAA,wBAAQ,EAAC,IAAI,CAAC,CAAA;QAEhC,mEAAmE;QACnE,MAAM,kBAAkB,GAAG,IAAA,wBAAQ,EAAC;YAClC,GAAG,IAAI;YACP,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,GAAG,CAAC,CAAC;YACtB,SAAS,EAAE,QAAQ;SACpB,CAAC,CAAA;QACF,MAAM,OAAO,GAAG,IAAA,yBAAS,EAAC,SAAS,CAAC,SAAS,CAAC,CAAA;QAC9C,MAAM,YAAY,GAAG,IAAA,yBAAS,EAAC,QAAQ,CAAC,CAAA;QAExC,MAAM,kBAAkB,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,oBAAoB,CAAC,CAAA;QACpE,MAAM,mBAAmB,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,qBAAqB,CAAC,CAAA;QACtE,MAAM,QAAQ,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,UAAU,CAAC,CAAA;QAChD,MAAM,cAAc,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,gBAAgB,CAAC,CAAA;QAE5D,sEAAsE;QACtE,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,MAAM,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAChE,MAAM,QAAQ,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;QACrD,kCAAkC;QAClC,MAAM,IAAI,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,MAAM,GAAG,CAAC,kBAAkB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAC1E,MAAM,SAAS,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QAE7D,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,OAAO,CAAA;QAC/B,MAAM,YAAY,GAA8B;YAC9C,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,KAAK,EAAE,WAAW;YAClB,SAAS,EAAE,QAAQ;YACnB,QAAQ,EAAE,MAAM;YAChB,QAAQ,EAAE,KAAK;YACf,IAAI,EAAE,KAAK;YACX,MAAM,EAAE,MAAM;SACf,CAAA;QAED,MAAM,KAAK,GAAG,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;QACpC,MAAM,QAAQ,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAC5D,MAAM,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAEzD,wEAAwE;QACxE,+CAA+C;QAC/C,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,KAAK,CAAA;QAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAA,oBAAa,EAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YACjE,MAAM,CAAC,GAAG,OAAO,GAAG,MAAM,GAAG,WAAW,CAAA;YACxC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAA;SACrD;QAED,0EAA0E;QAC1E,2EAA2E;QAC3E,0EAA0E;QAC1E,0EAA0E;QAC1E,wEAAwE;QACxE,IAAI,SAAS,GAAG,CAAC,CAAA;QAEjB,wEAAwE;QACxE,+DAA+D;QAC/D,MAAM,8BAA8B,GAAG,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAExE,yEAAyE;QACzE,yEAAyE;QACzE,oCAAoC;QAEpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAA,oBAAa,EAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YAEjE,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAY,CAAA;YACjD,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,GAAG,MAAM,EAAE,CAAC,CAAC,CAAA;YACvC,MAAM,UAAU,GAAG,OAAO,CAAC,KAAK,CAAA;YAChC,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAA;YAE5C,IAAI,IAAI,GAAG,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACpC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;gBACpB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;gBACnC,GAAG,CAAC,SAAS;oBACX,YAAY,CAAC,IAAI,CAAC;wBAClB,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;wBAC5C,MAAM,CAAA;gBAER,MAAM,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;gBAC9B,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,MAAM,CAAA;gBAClC,GAAG,CAAC,QAAQ,CACV,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,EAClB,MAAM,GAAG,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,KAAK,CAAC,GAAG,MAAM,EAC1C,CAAC,EACD,CAAC,KAAK,GAAG,KAAK,CAAC,GAAG,MAAM,CACzB,CAAA;gBACD,IAAI,IAAI,KAAK,CAAA;aACd;YAED,MAAM,eAAe,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YACnD,MAAM,eAAe,GAAG,GAAG,CAAA;YAC3B,IAAI,mBAAmB,EAAE;gBACvB,IAAI,IAAI,GAAG,CAAC,CAAA;gBACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/C,MAAM,IAAI,GAAG,eAAe,CAAC,CAAC,CAAC,CAAA;oBAC/B,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;oBACtC,MAAM,CAAC,GAAG,GAAG,CAAA;oBA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package/dist/SNPCoverageRenderer/configSchema.d.ts

@@ -1,2 +1,43 @@
-declare const SNPCoverageRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const SNPCoverageRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    indicatorThreshold: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    drawArcs: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    drawInterbaseCounts: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    drawIndicators: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default SNPCoverageRenderer;

package/dist/shared/FilterByTag.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function FilterByTagDlg(props: {
     model: {
         filterBy?: {

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,6 +1,5 @@
-/// <reference types="react" />
-declare function AlignmentFeatureDetails(props: {
-    model: any;
-}): JSX.Element;
-declare const _default: typeof AlignmentFeatureDetails;
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+declare const _default: (props: {
+    model: IAnyStateTreeNode;
+}) => JSX.Element;
 export default _default;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -1,144 +1,106 @@
 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';
-const useStyles = makeStyles()({
-    compact: {
-        paddingRight: 0,
-        paddingTop: 0,
-        paddingBottom: 0,
-    },
-});
+import { FeatureDetails } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+// 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) {
-    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 (React.createElement(BaseCard, { ...props, title: "Flags" },
-        React.createElement(SimpleValue, { name: 'Flag', value: flags }),
-        React.createElement(FormGroup, null, flagNames.map((name, index) => {
-            const val = flags & (1 << index);
-            const key = `${name}_${val}`;
-            return (React.createElement(FormControlLabel, { key: key, control: React.createElement(Checkbox, { className: classes.compact, checked: Boolean(val), name: name, readOnly: true }), label: name }));
-        }))));
-}
+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 }) {
     const [show, setShow] = useState(false);
     const [copied, setCopied] = useState(false);
     const display = String(value);
-    if (display.length > 100) {
-        return (React.createElement(React.Fragment, null,
-            React.createElement("button", { type: "button", onClick: () => {
-                    copy(display);
-                    setCopied(true);
-                    setTimeout(() => {
-                        setCopied(false);
-                    }, 700);
-                } }, copied ? 'Copied to clipboard' : 'Copy'),
-            React.createElement("button", { type: "button", onClick: () => setShow(val => !val) }, show ? 'Show less' : 'Show more'),
-            React.createElement("div", null, show ? display : `${display.slice(0, 100)}...`)));
-    }
-    return React.createElement("div", null, display);
-}
-// utility function to get length of alignment from cigar
-function getLengthOnRef(cigar) {
-    const cigarOps = parseCigar(cigar);
-    let lengthOnRef = 0;
-    for (let i = 0; i < cigarOps.length; i += 2) {
-        const len = +cigarOps[i];
-        const op = cigarOps[i + 1];
-        if (op !== 'H' && op !== 'S' && op !== 'I') {
-            lengthOnRef += len;
-        }
-    }
-    return lengthOnRef;
+    return display.length > 100 ? (React.createElement(React.Fragment, null,
+        React.createElement("button", { type: "button", onClick: () => {
+                copy(display);
+                setCopied(true);
+                setTimeout(() => setCopied(false), 700);
+            } }, copied ? 'Copied to clipboard' : 'Copy'),
+        React.createElement("button", { type: "button", onClick: () => setShow(val => !val) }, show ? 'Show less' : 'Show more'),
+        React.createElement("div", null, show ? display : `${display.slice(0, 100)}...`))) : (React.createElement("div", null, display));
 }
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function SupplementaryAlignments(props) {
-    const { tag, model } = props;
-    const session = getSession(model);
-    return (React.createElement(BaseCard, { ...props, title: "Supplementary alignments" },
-        React.createElement(Typography, null, "List of supplementary alignment locations"),
-        React.createElement("ul", null, 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} (${saStrand})`;
-            return (React.createElement("li", { key: `${locString}-${index}` },
-                React.createElement(Link, { onClick: async (event) => {
-                        event.preventDefault();
-                        const { view } = model;
-                        try {
-                            if (view) {
-                                await view.navToLocString(locString);
-                            }
-                            else {
-                                throw new Error('No view associated with this view anymore');
-                            }
-                        }
-                        catch (e) {
-                            console.error(e);
-                            session.notify(`${e}`);
-                        }
-                    }, href: "#" }, displayString)));
-        }))));
-}
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function PairLink({ locString, model }) {
-    const session = getSession(model);
-    return (React.createElement(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}`);
-            }
+function PairLink({ locString, model, }) {
+    return (React.createElement(Link, { onClick: event => {
+            event.preventDefault();
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
+            navToLoc(locString, model);
         }, href: "#" }, locString));
 }
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function AlignmentFeatureDetails(props) {
+export default observer(function AlignmentFeatureDetails(props) {
     const { model } = props;
     const feat = clone(model.featureData);
-    const SA = (feat.tags && feat.tags.SA) || feat.SA;
+    const SA = getTag('SA', feat);
     return (React.createElement(Paper, { "data-testid": "alignment-side-drawer" },
-        React.createElement(FeatureDetails, { ...props, omit: omit, feature: feat, formatter: (value, key) => {
-                return key === 'next_segment_position' ? (React.createElement(PairLink, { model: model, locString: value })) : (React.createElement(Formatter, { value: value }));
-            } }),
+        React.createElement(FeatureDetails, { ...props, omit: omit, 
+            // @ts-expect-error
+            descriptions: { ...tags, tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (React.createElement(PairLink, { model: model, locString: value })) : (React.createElement(Formatter, { value: value })) }),
         SA ? React.createElement(SupplementaryAlignments, { model: model, tag: SA }) : null,
         feat.flags !== undefined ? (React.createElement(AlignmentFlags, { feature: feat, ...props })) : null));
-}
-export default observer(AlignmentFeatureDetails);
+});
 //# sourceMappingURL=AlignmentsFeatureDetail.js.map

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map

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package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts

@@ -0,0 +1,5 @@
+export default function AlignmentFlags(props: {
+    feature: {
+        flags: number;
+    };
+}): JSX.Element;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js

@@ -0,0 +1,38 @@
+import React from 'react';
+import { Checkbox, FormControlLabel, FormGroup } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { BaseCard, SimpleValue, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+const useStyles = makeStyles()({
+    compact: {
+        paddingRight: 0,
+        paddingTop: 0,
+        paddingBottom: 0,
+    },
+});
+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',
+];
+export default function AlignmentFlags(props) {
+    const { classes } = useStyles();
+    const { feature } = props;
+    const { flags } = feature;
+    return (React.createElement(BaseCard, { ...props, title: "Flags" },
+        React.createElement(SimpleValue, { name: "Flag", value: flags }),
+        React.createElement(FormGroup, null, flagNames.map((name, idx) => {
+            const val = flags & (1 << idx);
+            const key = `${name}_${val}`;
+            return (React.createElement(FormControlLabel, { key: key, control: React.createElement(Checkbox, { className: classes.compact, checked: Boolean(val), name: name, readOnly: true }), label: name }));
+        }))));
+}
+//# sourceMappingURL=AlignmentsFeatureFlags.js.map

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"AlignmentsFeatureFlags.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACrE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EACL,QAAQ,EACR,WAAW,GACZ,MAAM,mDAAmD,CAAA;AAE1D,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,OAAO,EAAE;QACP,YAAY,EAAE,CAAC;QACf,UAAU,EAAE,CAAC;QACb,aAAa,EAAE,CAAC;KACjB;CACF,CAAC,CAAA;AAEF,MAAM,SAAS,GAAG;IAChB,aAAa;IACb,4BAA4B;IAC5B,eAAe;IACf,eAAe;IACf,qBAAqB;IACrB,qBAAqB;IACrB,eAAe;IACf,gBAAgB;IAChB,uBAAuB;IACvB,2CAA2C;IAC3C,kCAAkC;IAClC,yBAAyB;CAC1B,CAAA;AAED,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,KAAqC;IAC1E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACzB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAA;IAEzB,OAAO,CACL,oBAAC,QAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,OAAO;QAChC,oBAAC,WAAW,IAAC,IAAI,EAAC,MAAM,EAAC,KAAK,EAAE,KAAK,GAAI;QACzC,oBAAC,SAAS,QACP,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,GAAG,EAAE,EAAE;YAC3B,MAAM,GAAG,GAAG,KAAK,GAAG,CAAC,CAAC,IAAI,GAAG,CAAC,CAAA;YAC9B,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,oBAAC,gBAAgB,IACf,GAAG,EAAE,GAAG,EACR,OAAO,EACL,oBAAC,QAAQ,IACP,SAAS,EAAE,OAAO,CAAC,OAAO,EAC1B,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,IAAI,EAAE,IAAI,EACV,QAAQ,SACR,EAEJ,KAAK,EAAE,IAAI,GACX,CACH,CAAA;QACH,CAAC,CAAC,CACQ,CACH,CACZ,CAAA;AACH,CAAC"}

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts

@@ -0,0 +1,5 @@
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+export default function SupplementaryAlignments(props: {
+    tag: string;
+    model: IAnyStateTreeNode;
+}): JSX.Element;