@jbrowse/plugin-alignments 2.5.0 → 2.6.0

package/esm/shared/FilterByTag.js

@@ -50,11 +50,11 @@ function FilterByTagDlg(props) {
     const { model, handleClose } = props;
     const { classes } = useStyles();
     const { filterBy } = model;
-    const [flagInclude, setFlagInclude] = useState(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagInclude);
-    const [flagExclude, setFlagExclude] = useState(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagExclude);
-    const [tag, setTag] = useState(((_a = filterBy === null || filterBy === void 0 ? void 0 : filterBy.tagFilter) === null || _a === void 0 ? void 0 : _a.tag) || '');
-    const [tagValue, setTagValue] = useState(((_b = filterBy === null || filterBy === void 0 ? void 0 : filterBy.tagFilter) === null || _b === void 0 ? void 0 : _b.value) || '');
-    const [readName, setReadName] = useState((filterBy === null || filterBy === void 0 ? void 0 : filterBy.readName) || '');
+    const [flagInclude, setFlagInclude] = useState(filterBy.flagInclude);
+    const [flagExclude, setFlagExclude] = useState(filterBy.flagExclude);
+    const [tag, setTag] = useState(((_a = filterBy.tagFilter) === null || _a === void 0 ? void 0 : _a.tag) || '');
+    const [tagValue, setTagValue] = useState(((_b = filterBy.tagFilter) === null || _b === void 0 ? void 0 : _b.value) || '');
+    const [readName, setReadName] = useState(filterBy.readName || '');
     const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
     const site = 'https://broadinstitute.github.io/picard/explain-flags.html';
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Filter options" },
@@ -76,16 +76,11 @@ function FilterByTagDlg(props) {
                 React.createElement(Typography, null, "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"),
                 React.createElement(TextField, { className: classes.field, value: tag, onChange: event => setTag(event.target.value), placeholder: "Enter tag name", inputProps: {
                         maxLength: 2,
-                        'data-testid': 'color-tag-name-input',
-                    }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', "data-testid": "color-tag-name" }),
-                React.createElement(TextField, { className: classes.field, value: tagValue, onChange: event => setTagValue(event.target.value), placeholder: "Enter tag value", inputProps: {
-                        'data-testid': 'color-tag-name-input',
-                    }, "data-testid": "color-tag-value" })),
+                    }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '' }),
+                React.createElement(TextField, { className: classes.field, value: tagValue, onChange: event => setTagValue(event.target.value), placeholder: "Enter tag value" })),
             React.createElement(Paper, { className: classes.paper, variant: "outlined" },
                 React.createElement(Typography, null, "Filter by read name"),
-                React.createElement(TextField, { className: classes.field, value: readName, onChange: event => setReadName(event.target.value), placeholder: "Enter read name", inputProps: {
-                        'data-testid': 'color-tag-readname-input',
-                    }, "data-testid": "color-tag-readname" })),
+                React.createElement(TextField, { className: classes.field, value: readName, onChange: event => setReadName(event.target.value), placeholder: "Enter read name" })),
             React.createElement(DialogActions, null,
                 React.createElement(Button, { variant: "contained", color: "primary", autoFocus: true, type: "submit", onClick: () => {
                         model.setFilterBy({

package/esm/shared/FilterByTag.js.map

@@ -1 +1 @@
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+{"version":3,"file":"FilterByTag.js","sourceRoot":"","sources":["../../src/shared/FilterByTag.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,IAAI,EACJ,KAAK,EACL,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACzB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,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,SAAS,OAAO,CAAC,KAA2C;IAC1D,MAAM,EAAE,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACnC,OAAO,CACL;QACE,oBAAC,SAAS,IACR,IAAI,EAAC,QAAQ,EACb,KAAK,EAAE,IAAI,EACX,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,GAC/C;QACD,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE;YAC7B,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAA;YAC/B,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG;gBACX,+BACE,IAAI,EAAC,UAAU,EACf,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,EAAE;4BACxB,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC7B;6BAAM;4BACL,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC9B;oBACH,CAAC,GACD;gBACF,+BAAO,OAAO,EAAE,GAAG,IAAG,IAAI,CAAS,CAC/B,CACP,CAAA;QACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAOD,SAAS,cAAc,CAAC,KAMvB;;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAA;IACpE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAA;IACpE,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,CAAA,MAAA,QAAQ,CAAC,SAAS,0CAAE,GAAG,KAAI,EAAE,CAAC,CAAA;IAC7D,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,CAAA,MAAA,QAAQ,CAAC,SAAS,0CAAE,KAAK,KAAI,EAAE,CAAC,CAAA;IACzE,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,QAAQ,IAAI,EAAE,CAAC,CAAA;IACjE,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IAEnD,MAAM,IAAI,GAAG,4DAA4D,CAAA;IAEzE,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,oBAAC,aAAa;YACZ,oBAAC,UAAU;;gBAC4B,oBAAC,IAAI,IAAC,IAAI,EAAE,IAAI,IAAG,IAAI,CAAQ;gBAAC,GAAG;8BAE7D;YACb,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;oBAC7B;wBACE,oBAAC,UAAU,yCAA4C;wBACvD,oBAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD;oBACN;wBACE,oBAAC,UAAU,6CAAgD;wBAC3D,oBAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD,CACF,CACA;YACR,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,oBAAC,UAAU,kQAKE;gBACb,oBAAC,SAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;wBACV,SAAS,EAAE,CAAC;qBACb,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,GAClE;gBACF,oBAAC,SAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAClD,WAAW,EAAC,iBAAiB,GAC7B,CACI;YACR,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,oBAAC,UAAU,8BAAiC;gBAC5C,oBAAC,SAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAClD,WAAW,EAAC,iBAAiB,GAC7B,CACI;YACR,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,QACT,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC;4BAChB,WAAW;4BACX,WAAW;4BACX,QAAQ;4BACR,SAAS,EACP,GAAG,KAAK,EAAE;gCACR,CAAC,CAAC;oCACE,GAAG;oCACH,KAAK,EAAE,QAAQ;iCAChB;gCACH,CAAC,CAAC,SAAS;yBAChB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,cAAc,CAAC,CAAA"}

package/esm/shared/afterAttach.d.ts

@@ -0,0 +1,2 @@
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+export declare function doAfterAttach<T extends IAnyStateTreeNode>(self: T, cb: (self: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): void;

package/esm/shared/afterAttach.js

@@ -0,0 +1,40 @@
+import { getContainingView } from '@jbrowse/core/util';
+import { createAutorun } from '../util';
+import { fetchChains } from './fetchChains';
+export function doAfterAttach(self, cb) {
+    createAutorun(self, async () => {
+        await fetchChains(self);
+    }, { delay: 1000 });
+    function draw(view) {
+        const canvas = self.ref;
+        if (!canvas) {
+            return;
+        }
+        const ctx = canvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        if (!self.chainData) {
+            return;
+        }
+        ctx.clearRect(0, 0, canvas.width, self.height * 2);
+        ctx.resetTransform();
+        ctx.scale(2, 2);
+        cb(self, ctx, canvas.width, self.height);
+        self.setLastDrawnOffsetPx(view.offsetPx);
+        self.setLastDrawnBpPerPx(view.bpPerPx);
+    }
+    // first autorun instantly draws if bpPerPx changes
+    createAutorun(self, async () => {
+        const view = getContainingView(self);
+        if (view.bpPerPx !== self.lastDrawnBpPerPx) {
+            draw(view);
+        }
+    });
+    // second autorun draws after delay 1000 e.g. if offsetPx changes
+    createAutorun(self, async () => {
+        const view = getContainingView(self);
+        draw(view);
+    }, { delay: 1000 });
+}
+//# sourceMappingURL=afterAttach.js.map

package/esm/shared/afterAttach.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"afterAttach.js","sourceRoot":"","sources":["../../src/shared/afterAttach.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,aAAa,EAAE,MAAM,SAAS,CAAA;AACvC,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAA;AAM3C,MAAM,UAAU,aAAa,CAC3B,IAAO,EACP,EAKS;IAET,aAAa,CACX,IAAI,EACJ,KAAK,IAAI,EAAE;QACT,MAAM,WAAW,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC,EACD,EAAE,KAAK,EAAE,IAAI,EAAE,CAChB,CAAA;IAED,SAAS,IAAI,CAAC,IAAS;QACrB,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAA;QACvB,IAAI,CAAC,MAAM,EAAE;YACX,OAAM;SACP;QAED,MAAM,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QACnC,IAAI,CAAC,GAAG,EAAE;YACR,OAAM;SACP;QAED,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE;YACnB,OAAM;SACP;QAED,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC,KAAK,EAAE,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QAClD,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACf,EAAE,CAAC,IAAI,EAAE,GAAG,EAAE,MAAM,CAAC,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;QACxC,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QACxC,IAAI,CAAC,mBAAmB,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACxC,CAAC;IAED,mDAAmD;IACnD,aAAa,CAAC,IAAI,EAAE,KAAK,IAAI,EAAE;QAC7B,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;QAC3C,IAAI,IAAI,CAAC,OAAO,KAAK,IAAI,CAAC,gBAAgB,EAAE;YAC1C,IAAI,CAAC,IAAI,CAAC,CAAA;SACX;IACH,CAAC,CAAC,CAAA;IAEF,iEAAiE;IACjE,aAAa,CACX,IAAI,EACJ,KAAK,IAAI,EAAE;QACT,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;QAC3C,IAAI,CAAC,IAAI,CAAC,CAAA;IACZ,CAAC,EACD,EAAE,KAAK,EAAE,IAAI,EAAE,CAChB,CAAA;AACH,CAAC"}

package/esm/shared/color.d.ts

@@ -1,17 +1,55 @@
 import { ChainStats } from './fetchChains';
-export declare function getInsertSizeColor(f1: {
+export declare const fillColor: {
+    color_fwd_strand_not_proper: string;
+    color_rev_strand_not_proper: string;
+    color_fwd_strand: string;
+    color_rev_strand: string;
+    color_fwd_missing_mate: string;
+    color_rev_missing_mate: string;
+    color_fwd_diff_chr: string;
+    color_rev_diff_chr: string;
+    color_pair_lr: string;
+    color_pair_rr: string;
+    color_pair_rl: string;
+    color_pair_ll: string;
+    color_nostrand: string;
+    color_interchrom: string;
+    color_longinsert: string;
+    color_shortinsert: string;
+    color_unknown: string;
+};
+export declare const strokeColor: {
+    color_fwd_strand_not_proper: string;
+    color_rev_strand_not_proper: string;
+    color_fwd_strand: string;
+    color_rev_strand: string;
+    color_fwd_missing_mate: string;
+    color_rev_missing_mate: string;
+    color_fwd_diff_chr: string;
+    color_rev_diff_chr: string;
+    color_pair_lr: string;
+    color_pair_rr: string;
+    color_pair_rl: string;
+    color_pair_ll: string;
+    color_nostrand: string;
+    color_interchrom: string;
+    color_longinsert: string;
+    color_shortinsert: string;
+    color_unknown: string;
+};
+export declare function getPairedInsertSizeColor(f1: {
     refName: string;
     tlen?: number;
 }, f2: {
     refName: string;
-}, stats?: ChainStats): "" | "red" | "purple" | "#f0f";
-export declare function getInsertSizeAndOrientationColor(f1: {
+}, stats?: ChainStats): readonly [string, string] | undefined;
+export declare function getPairedInsertSizeAndOrientationColor(f1: {
     refName: string;
     pair_orientation?: string;
     tlen?: number;
 }, f2: {
     refName: string;
-}, stats?: ChainStats): string;
-export declare function getOrientationColor(f: {
+}, stats?: ChainStats): readonly [string, string];
+export declare function getPairedOrientationColor(f: {
     pair_orientation?: string;
-}): string;
+}): readonly [string, string];

package/esm/shared/color.js

@@ -1,37 +1,71 @@
-import { orientationTypes } from '../util';
-const alignmentColoring = {
+import { orientationTypes, pairMap } from '../util';
+export const fillColor = {
+    color_fwd_strand_not_proper: '#ECC8C8',
+    color_rev_strand_not_proper: '#BEBED8',
+    color_fwd_strand: '#EC8B8B',
+    color_rev_strand: '#8F8FD8',
+    color_fwd_missing_mate: '#D11919',
+    color_rev_missing_mate: '#1919D1',
+    color_fwd_diff_chr: '#000',
+    color_rev_diff_chr: '#969696',
     color_pair_lr: '#c8c8c8',
     color_pair_rr: 'navy',
     color_pair_rl: 'teal',
     color_pair_ll: 'green',
+    color_nostrand: '#c8c8c8',
+    color_interchrom: 'purple',
+    color_longinsert: 'red',
+    color_shortinsert: 'pink',
+    color_unknown: 'grey',
 };
-export function getInsertSizeColor(f1, f2, stats) {
+// manually calculated by running
+// const color = require('color')
+// Object.fromEntries(Object.entries(fillColor).map(([key,val])=>{
+//   return [key, color(val).darken('0.3').hex()]
+// }))
+// this avoids (expensive) use of Color module at runtime
+export const strokeColor = {
+    color_fwd_strand_not_proper: '#CA6767',
+    color_rev_strand_not_proper: '#7272AA',
+    color_fwd_strand: '#DC2A2A',
+    color_rev_strand: '#4141BA',
+    color_fwd_missing_mate: '#921111',
+    color_rev_missing_mate: '#111192',
+    color_fwd_diff_chr: '#000000',
+    color_rev_diff_chr: '#696969',
+    color_pair_lr: '#8C8C8C',
+    color_pair_rr: '#00005A',
+    color_pair_rl: '#005A5A',
+    color_pair_ll: '#005A00',
+    color_nostrand: '#8C8C8C',
+    color_interchrom: '#5A005A',
+    color_longinsert: '#B30000',
+    color_shortinsert: '#FF3A5C',
+    color_unknown: 'grey',
+};
+export function getPairedInsertSizeColor(f1, f2, stats) {
     const sameRef = f1.refName === f2.refName;
     const tlen = Math.abs(f1.tlen || 0);
     if (sameRef && tlen > ((stats === null || stats === void 0 ? void 0 : stats.upper) || 0)) {
-        return 'red';
+        return [fillColor.color_longinsert, strokeColor.color_longinsert];
     }
     else if (sameRef && tlen < ((stats === null || stats === void 0 ? void 0 : stats.lower) || 0)) {
-        return '#f0f';
+        return [fillColor.color_shortinsert, strokeColor.color_shortinsert];
     }
     else if (!sameRef) {
-        return 'purple';
+        return [fillColor.color_interchrom, strokeColor.color_interchrom];
     }
-    return '';
+    return undefined;
 }
-export function getInsertSizeAndOrientationColor(f1, f2, stats) {
-    return getInsertSizeColor(f1, f2, stats) || getOrientationColor(f1);
+export function getPairedInsertSizeAndOrientationColor(f1, f2, stats) {
+    return (getPairedInsertSizeColor(f1, f2, stats) || getPairedOrientationColor(f1));
 }
-export function getOrientationColor(f) {
-    const type = orientationTypes['fr'];
-    const orientation = type[f.pair_orientation || ''];
-    const map = {
-        LR: 'color_pair_lr',
-        RR: 'color_pair_rr',
-        RL: 'color_pair_rl',
-        LL: 'color_pair_ll',
-    };
-    const val = map[orientation];
-    return alignmentColoring[val] || 'grey';
+export function getPairedOrientationColor(f) {
+    const type = orientationTypes.fr;
+    const type2 = pairMap[type[f.pair_orientation || '']];
+    return [
+        fillColor[type2] || fillColor.color_unknown,
+        strokeColor[type2] || strokeColor.color_unknown,
+    ];
 }
 //# sourceMappingURL=color.js.map

package/esm/shared/color.js.map

@@ -1 +1 @@
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+{"version":3,"file":"color.js","sourceRoot":"","sources":["../../src/shared/color.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AAGnD,MAAM,CAAC,MAAM,SAAS,GAAG;IACvB,2BAA2B,EAAE,SAAS;IACtC,2BAA2B,EAAE,SAAS;IACtC,gBAAgB,EAAE,SAAS;IAC3B,gBAAgB,EAAE,SAAS;IAC3B,sBAAsB,EAAE,SAAS;IACjC,sBAAsB,EAAE,SAAS;IACjC,kBAAkB,EAAE,MAAM;IAC1B,kBAAkB,EAAE,SAAS;IAC7B,aAAa,EAAE,SAAS;IACxB,aAAa,EAAE,MAAM;IACrB,aAAa,EAAE,MAAM;IACrB,aAAa,EAAE,OAAO;IACtB,cAAc,EAAE,SAAS;IACzB,gBAAgB,EAAE,QAAQ;IAC1B,gBAAgB,EAAE,KAAK;IACvB,iBAAiB,EAAE,MAAM;IACzB,aAAa,EAAE,MAAM;CACtB,CAAA;AAED,iCAAiC;AACjC,iCAAiC;AACjC,kEAAkE;AAClE,iDAAiD;AACjD,MAAM;AACN,yDAAyD;AACzD,MAAM,CAAC,MAAM,WAAW,GAAG;IACzB,2BAA2B,EAAE,SAAS;IACtC,2BAA2B,EAAE,SAAS;IACtC,gBAAgB,EAAE,SAAS;IAC3B,gBAAgB,EAAE,SAAS;IAC3B,sBAAsB,EAAE,SAAS;IACjC,sBAAsB,EAAE,SAAS;IACjC,kBAAkB,EAAE,SAAS;IAC7B,kBAAkB,EAAE,SAAS;IAC7B,aAAa,EAAE,SAAS;IACxB,aAAa,EAAE,SAAS;IACxB,aAAa,EAAE,SAAS;IACxB,aAAa,EAAE,SAAS;IACxB,cAAc,EAAE,SAAS;IACzB,gBAAgB,EAAE,SAAS;IAC3B,gBAAgB,EAAE,SAAS;IAC3B,iBAAiB,EAAE,SAAS;IAC5B,aAAa,EAAE,MAAM;CACtB,CAAA;AAED,MAAM,UAAU,wBAAwB,CACtC,EAAsC,EACtC,EAAuB,EACvB,KAAkB;IAElB,MAAM,OAAO,GAAG,EAAE,CAAC,OAAO,KAAK,EAAE,CAAC,OAAO,CAAA;IACzC,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,IAAI,CAAC,CAAC,CAAA;IACnC,IAAI,OAAO,IAAI,IAAI,GAAG,CAAC,CAAA,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,KAAK,KAAI,CAAC,CAAC,EAAE;QACzC,OAAO,CAAC,SAAS,CAAC,gBAAgB,EAAE,WAAW,CAAC,gBAAgB,CAAU,CAAA;KAC3E;SAAM,IAAI,OAAO,IAAI,IAAI,GAAG,CAAC,CAAA,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,KAAK,KAAI,CAAC,CAAC,EAAE;QAChD,OAAO,CAAC,SAAS,CAAC,iBAAiB,EAAE,WAAW,CAAC,iBAAiB,CAAU,CAAA;KAC7E;SAAM,IAAI,CAAC,OAAO,EAAE;QACnB,OAAO,CAAC,SAAS,CAAC,gBAAgB,EAAE,WAAW,CAAC,gBAAgB,CAAU,CAAA;KAC3E;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAED,MAAM,UAAU,sCAAsC,CACpD,EAAiE,EACjE,EAAuB,EACvB,KAAkB;IAElB,OAAO,CACL,wBAAwB,CAAC,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,yBAAyB,CAAC,EAAE,CAAC,CACzE,CAAA;AACH,CAAC;AAED,MAAM,UAAU,yBAAyB,CAAC,CAAgC;IACxE,MAAM,IAAI,GAAG,gBAAgB,CAAC,EAAE,CAAA;IAChC,MAAM,KAAK,GAAG,OAAO,CACnB,IAAI,CAAC,CAAC,CAAC,gBAAgB,IAAI,EAAE,CAAyB,CAC7B,CAAA;IAC3B,OAAO;QACL,SAAS,CAAC,KAAK,CAAC,IAAI,SAAS,CAAC,aAAa;QAC3C,WAAW,CAAC,KAAK,CAAC,IAAI,WAAW,CAAC,aAAa;KACvC,CAAA;AACZ,CAAC"}

package/esm/shared/fetchChains.d.ts

@@ -1,4 +1,5 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { LinearReadArcsDisplayModel } from '../LinearReadArcsDisplay/model';
+import { LinearReadCloudDisplayModel } from '../LinearReadCloudDisplay/model';
 export interface ReducedFeature {
     name: string;
     strand: number;
@@ -24,4 +25,4 @@ export interface ChainData {
     chains: ReducedFeature[][];
     stats?: ChainStats;
 }
-export declare function fetchChains(self: IAnyStateTreeNode): Promise<void>;
+export declare function fetchChains(self: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel): Promise<void>;

package/esm/shared/fetchChains.js

@@ -1,26 +1,20 @@
 import { getContainingTrack, getContainingView, getSession, } from '@jbrowse/core/util';
 import { getSnapshot } from 'mobx-state-tree';
 export async function fetchChains(self) {
-    try {
-        const { rpcSessionId: sessionId } = getContainingTrack(self);
-        const { rpcManager } = getSession(self);
-        const view = getContainingView(self);
-        if (!view.initialized || self.error) {
-            return;
-        }
-        self.setLoading(true);
-        const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
-            sessionId,
-            regions: view.staticBlocks.contentBlocks,
-            filterBy: getSnapshot(self.filterBy),
-            adapterConfig: self.adapterConfig,
-        }));
-        self.setChainData(ret);
-        self.setLoading(false);
-    }
-    catch (e) {
-        console.error(e);
-        self.setError(e);
+    const { rpcSessionId: sessionId } = getContainingTrack(self);
+    const { rpcManager } = getSession(self);
+    const view = getContainingView(self);
+    if (!view.initialized || self.error || self.regionTooLarge) {
+        return;
     }
+    self.setLoading(true);
+    const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
+        sessionId,
+        regions: view.staticBlocks.contentBlocks,
+        filterBy: getSnapshot(self.filterBy),
+        adapterConfig: self.adapterConfig,
+    }));
+    self.setChainData(ret);
+    self.setLoading(false);
 }
 //# sourceMappingURL=fetchChains.js.map

package/esm/shared/fetchChains.js.map

@@ -1 +1 @@
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+{"version":3,"file":"fetchChains.js","sourceRoot":"","sources":["../../src/shared/fetchChains.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,kBAAkB,EAClB,iBAAiB,EACjB,UAAU,GACX,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAmC7C,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,IAA8D;IAE9D,MAAM,EAAE,YAAY,EAAE,SAAS,EAAE,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;IAC5D,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IACvC,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;IAE3C,IAAI,CAAC,IAAI,CAAC,WAAW,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,cAAc,EAAE;QAC1D,OAAM;KACP;IAED,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;IACrB,MAAM,GAAG,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,0BAA0B,EAAE;QACxE,SAAS;QACT,OAAO,EAAE,IAAI,CAAC,YAAY,CAAC,aAAa;QACxC,QAAQ,EAAE,WAAW,CAAC,IAAI,CAAC,QAAQ,CAAC;QACpC,aAAa,EAAE,IAAI,CAAC,aAAa;KAClC,CAAC,CAAc,CAAA;IAEhB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;IACtB,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;AACxB,CAAC"}

package/esm/shared/renderSvg.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+export declare function renderSvg<T extends {
+    id: string;
+    height: number;
+}>(self: T, opts: {
+    rasterizeLayers?: boolean;
+}, cb: (model: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): Promise<React.JSX.Element | undefined>;

package/esm/shared/renderSvg.js

@@ -0,0 +1,39 @@
+import React from 'react';
+import { getContainingView } from '@jbrowse/core/util';
+// stabilize clipid under test for snapshot
+function getId(id) {
+    const isJest = typeof jest === 'undefined';
+    return `arc-clip-${isJest ? id : 'jest'}`;
+}
+export async function renderSvg(self, opts, cb) {
+    const view = getContainingView(self);
+    const width = view.dynamicBlocks.totalWidthPx;
+    const height = self.height;
+    if (opts.rasterizeLayers) {
+        const canvas = document.createElement('canvas');
+        canvas.width = width * 2;
+        canvas.height = height * 2;
+        const ctx = canvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        ctx.scale(2, 2);
+        cb(self, ctx, width, height);
+        return (React.createElement("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
+    }
+    else {
+        // @ts-ignore
+        const C2S = await import('canvas2svg');
+        const ctx = new C2S.default(width, height);
+        cb(self, ctx, width, height);
+        const clipid = getId(self.id);
+        return (React.createElement(React.Fragment, null,
+            React.createElement("defs", null,
+                React.createElement("clipPath", { id: clipid },
+                    React.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
+            React.createElement("g", { 
+                /* eslint-disable-next-line react/no-danger */
+                dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML }, clipPath: `url(#${clipid})` })));
+    }
+}
+//# sourceMappingURL=renderSvg.js.map

package/esm/shared/renderSvg.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"renderSvg.js","sourceRoot":"","sources":["../../src/shared/renderSvg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAGtD,2CAA2C;AAC3C,SAAS,KAAK,CAAC,EAAU;IACvB,MAAM,MAAM,GAAG,OAAO,IAAI,KAAK,WAAW,CAAA;IAC1C,OAAO,YAAY,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,EAAE,CAAA;AAC3C,CAAC;AAID,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,IAAO,EACP,IAAmC,EACnC,EAKS;IAET,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;IAC3C,MAAM,KAAK,GAAG,IAAI,CAAC,aAAa,CAAC,YAAY,CAAA;IAC7C,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;IAC1B,IAAI,IAAI,CAAC,eAAe,EAAE;QACxB,MAAM,MAAM,GAAG,QAAQ,CAAC,aAAa,CAAC,QAAQ,CAAC,CAAA;QAC/C,MAAM,CAAC,KAAK,GAAG,KAAK,GAAG,CAAC,CAAA;QACxB,MAAM,CAAC,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;QAC1B,MAAM,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QACnC,IAAI,CAAC,GAAG,EAAE;YACR,OAAM;SACP;QACD,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACf,EAAE,CAAC,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;QAC5B,OAAO,CACL,+BACE,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,CAAC,SAAS,CAAC,WAAW,CAAC,GACxC,CACH,CAAA;KACF;SAAM;QACL,aAAa;QACb,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,YAAY,CAAC,CAAA;QACtC,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC1C,EAAE,CAAC,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;QAC5B,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QAC7B,OAAO,CACL;YACE;gBACE,kCAAU,EAAE,EAAE,MAAM;oBAClB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,GAAI,CACzC,CACN;YACP;gBACE,8CAA8C;gBAC9C,uBAAuB,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,EAC3D,QAAQ,EAAE,QAAQ,MAAM,GAAG,GAC3B,CACD,CACJ,CAAA;KACF;AACH,CAAC"}

package/esm/shared/util.d.ts

@@ -0,0 +1,2 @@
+import { ChainData } from './fetchChains';
+export declare function hasPairedReads(features: ChainData): boolean;

package/esm/shared/util.js

@@ -0,0 +1,9 @@
+export function hasPairedReads(features) {
+    for (const f of features.chains.values()) {
+        if (f[0].flags & 1) {
+            return true;
+        }
+    }
+    return false;
+}
+//# sourceMappingURL=util.js.map

package/esm/shared/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/shared/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,cAAc,CAAC,QAAmB;IAChD,KAAK,MAAM,CAAC,IAAI,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE;QACxC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,EAAE;YAClB,OAAO,IAAI,CAAA;SACZ;KACF;IACD,OAAO,KAAK,CAAA;AACd,CAAC"}

package/esm/util.d.ts

@@ -1,6 +1,7 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AugmentedRegion } from '@jbrowse/core/util';
+import { Feature, AugmentedRegion } from '@jbrowse/core/util';
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { IAutorunOptions } from 'mobx';
 export declare function getTag(feature: Feature, tag: string): any;
 export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
 export declare const orientationTypes: {
@@ -14,6 +15,19 @@ export declare const orientationTypes: {
         [key: string]: string;
     };
 };
+export declare const pairMap: {
+    readonly LR: "color_pair_lr";
+    readonly LL: "color_pair_ll";
+    readonly RR: "color_pair_rr";
+    readonly RL: "color_pair_rl";
+};
 export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
 export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
 export declare function shouldFetchReferenceSequence(type?: string): boolean;
+export declare const modificationColors: Record<string, string | undefined>;
+type DisplayModel = IAnyStateTreeNode & {
+    setError: (arg: unknown) => void;
+};
+export declare function createAutorun(self: DisplayModel, cb: () => Promise<void>, opts?: IAutorunOptions): void;
+export declare function randomColor(): string;
+export {};

package/esm/util.js

@@ -1,15 +1,18 @@
 import { toArray } from 'rxjs/operators';
 import { firstValueFrom } from 'rxjs';
+import { addDisposer, isAlive } from 'mobx-state-tree';
+import { autorun } from 'mobx';
 // get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
 // BAM does not
 export function getTag(feature, tag) {
     const tags = feature.get('tags');
-    return tags ? tags[tag] : feature.get(tag);
+    return tags !== undefined ? tags[tag] : feature.get(tag);
 }
 // use fallback alt tag, used in situations where upper case/lower case tags
 // exist e.g. Mm/MM for base modifications
 export function getTagAlt(feature, tag, alt) {
-    return getTag(feature, tag) || getTag(feature, alt);
+    var _a;
+    return (_a = getTag(feature, tag)) !== null && _a !== void 0 ? _a : getTag(feature, alt);
 }
 // orientation definitions from igv.js, see also
 // https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
@@ -45,6 +48,12 @@ export const orientationTypes = {
         F1F2: 'RL',
     },
 };
+export const pairMap = {
+    LR: 'color_pair_lr',
+    LL: 'color_pair_ll',
+    RR: 'color_pair_rr',
+    RL: 'color_pair_rl',
+};
 export function getColorWGBS(strand, base) {
     if (strand === 1) {
         if (base === 'C') {
@@ -64,14 +73,17 @@ export function getColorWGBS(strand, base) {
     }
     return '#888';
 }
+// fetches region sequence augmenting by +/- 1bp for CpG on either side of
+// requested region
 export async function fetchSequence(region, adapter) {
     var _a;
-    const { end, originalRefName, refName } = region;
+    const { start, end, originalRefName, refName } = region;
     const feats = await firstValueFrom(adapter
         .getFeatures({
         ...region,
         refName: originalRefName || refName,
         end: end + 1,
+        start: Math.max(0, start - 1),
     })
         .pipe(toArray()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
@@ -80,4 +92,31 @@ export async function fetchSequence(region, adapter) {
 export function shouldFetchReferenceSequence(type) {
     return type === 'methylation';
 }
+// adapted from IGV
+// https://github.com/igvteam/igv/blob/e803e3af2d8c9ea049961dfd4628146bdde9a574/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java#L27
+export const modificationColors = {
+    m: 'rgb(255,0,0)',
+    h: 'rgb(11, 132, 165)',
+    o: 'rgb(111, 78, 129)',
+    f: 'rgb(246, 200, 95)',
+    c: 'rgb(157, 216, 102)',
+    g: 'rgb(255, 160, 86)',
+    e: 'rgb(141, 221, 208)',
+    b: 'rgb(202, 71, 47)',
+};
+export function createAutorun(self, cb, opts) {
+    addDisposer(self, autorun(async () => {
+        try {
+            await cb();
+        }
+        catch (e) {
+            if (isAlive(self)) {
+                self.setError(e);
+            }
+        }
+    }, opts));
+}
+export function randomColor() {
+    return `hsl(${Math.random() * 200}, 50%, 50%)`;
+}
 //# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AACrC,OAAO,EAAqB,WAAW,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzE,OAAO,EAAmB,OAAO,EAAE,MAAM,MAAM,CAAA;AAE/C,4EAA4E;AAC5E,eAAe;AACf,MAAM,UAAU,MAAM,CAAC,OAAgB,EAAE,GAAW;IAClD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC1D,CAAC;AAED,4EAA4E;AAC5E,0CAA0C;AAC1C,MAAM,UAAU,SAAS,CAAC,OAAgB,EAAE,GAAW,EAAE,GAAW;;IAClE,OAAO,MAAA,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,mCAAI,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;AACrD,CAAC;AAED,gDAAgD;AAChD,kFAAkF;AAClF,MAAM,CAAC,MAAM,gBAAgB,GAAG;IAC9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;CAC/B,CAAA;AAED,MAAM,CAAC,MAAM,OAAO,GAAG;IACrB,EAAE,EAAE,eAAe;IACnB,EAAE,EAAE,eAAe;IACnB,EAAE,EAAE,eAAe;IACnB,EAAE,EAAE,eAAe;CACX,CAAA;AAEV,MAAM,UAAU,YAAY,CAAC,MAAc,EAAE,IAAY;IACvD,IAAI,MAAM,KAAK,CAAC,EAAE;QAChB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;SAAM,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE;QACxB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,0EAA0E;AAC1E,mBAAmB;AACnB,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,MAAuB,EACvB,OAA+B;;IAE/B,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;IAEvD,MAAM,KAAK,GAAG,MAAM,cAAc,CAChC,OAAO;SACJ,WAAW,CAAC;QACX,GAAG,MAAM;QACT,OAAO,EAAE,eAAe,IAAI,OAAO;QACnC,GAAG,EAAE,GAAG,GAAG,CAAC;QACZ,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,CAAC,CAAC;KAC9B,CAAC;SACD,IAAI,CAAC,OAAO,EAAE,CAAC,CACnB,CAAA;IACD,OAAO,MAAA,KAAK,CAAC,CAAC,CAAC,0CAAE,GAAG,CAAC,KAAK,CAAC,CAAA;AAC7B,CAAC;AAED,kEAAkE;AAClE,MAAM,UAAU,4BAA4B,CAAC,IAAa;IACxD,OAAO,IAAI,KAAK,aAAa,CAAA;AAC/B,CAAC;AAED,mBAAmB;AACnB,oJAAoJ;AACpJ,MAAM,CAAC,MAAM,kBAAkB,GAAG;IAChC,CAAC,EAAE,cAAc;IACjB,CAAC,EAAE,mBAAmB;IACtB,CAAC,EAAE,mBAAmB;IACtB,CAAC,EAAE,mBAAmB;IACtB,CAAC,EAAE,oBAAoB;IACvB,CAAC,EAAE,mBAAmB;IACtB,CAAC,EAAE,oBAAoB;IACvB,CAAC,EAAE,kBAAkB;CACgB,CAAA;AAIvC,MAAM,UAAU,aAAa,CAC3B,IAAkB,EAClB,EAAuB,EACvB,IAAsB;IAEtB,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,KAAK,IAAI,EAAE;QACjB,IAAI;YACF,MAAM,EAAE,EAAE,CAAA;SACX;QAAC,OAAO,CAAC,EAAE;YACV,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE;gBACjB,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;aACjB;SACF;IACH,CAAC,EAAE,IAAI,CAAC,CACT,CAAA;AACH,CAAC;AACD,MAAM,UAAU,WAAW;IACzB,OAAO,OAAO,IAAI,CAAC,MAAM,EAAE,GAAG,GAAG,aAAa,CAAA;AAChD,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.5.0",
+  "version": "2.6.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,7 +37,7 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bam": "^1.1.15",
+    "@gmod/bam": "^2.0.0",
     "@gmod/cram": "^1.7.1",
     "@mui/icons-material": "^5.0.1",
     "canvas2svg": "^1.0.16",
@@ -65,5 +65,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
+  "gitHead": "9962c94711dd3386dcb76c16f3646937d9c4751a"
 }

package/src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx

@@ -1,10 +1,8 @@
 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'
+import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
+import SimpleField from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField'
 
 const useStyles = makeStyles()({
   compact: {
@@ -36,7 +34,7 @@ export default function AlignmentFlags(props: { feature: { flags: number } }) {
 
   return (
     <BaseCard {...props} title="Flags">
-      <SimpleValue name="Flag" value={flags} />
+      <SimpleField name="Flag" value={flags} />
       <FormGroup>
         {flagNames.map((name, idx) => {
           const val = flags & (1 << idx)