@jbrowse/plugin-alignments 2.2.1 → 2.2.2
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.
- package/dist/CramAdapter/CramTestAdapters.js +2 -1
- package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
- package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts +3 -1
- package/dist/LinearPileupDisplay/components/ColorByModifications.js +7 -22
- package/dist/LinearPileupDisplay/components/ColorByModifications.js.map +1 -1
- package/dist/LinearPileupDisplay/components/ColorByTag.js +2 -22
- package/dist/LinearPileupDisplay/components/ColorByTag.js.map +1 -1
- package/dist/LinearPileupDisplay/components/FilterByTag.js +2 -15
- package/dist/LinearPileupDisplay/components/FilterByTag.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +2 -19
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js +2 -18
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SortByTag.js +2 -23
- package/dist/LinearPileupDisplay/components/SortByTag.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +13 -9
- package/dist/LinearSNPCoverageDisplay/models/model.js +8 -6
- package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
- package/dist/PileupRenderer/configSchema.js +1 -1
- package/dist/PileupRenderer/configSchema.js.map +1 -1
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +0 -51
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +3 -182
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/dist/SNPCoverageAdapter/generateCoverageBins.d.ts +53 -0
- package/dist/SNPCoverageAdapter/generateCoverageBins.js +185 -0
- package/dist/SNPCoverageAdapter/generateCoverageBins.js.map +1 -0
- package/esm/CramAdapter/CramTestAdapters.js +2 -1
- package/esm/CramAdapter/CramTestAdapters.js.map +1 -1
- package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +3 -1
- package/esm/LinearPileupDisplay/components/ColorByModifications.js +8 -23
- package/esm/LinearPileupDisplay/components/ColorByModifications.js.map +1 -1
- package/esm/LinearPileupDisplay/components/ColorByTag.js +3 -20
- package/esm/LinearPileupDisplay/components/ColorByTag.js.map +1 -1
- package/esm/LinearPileupDisplay/components/FilterByTag.js +3 -13
- package/esm/LinearPileupDisplay/components/FilterByTag.js.map +1 -1
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.js +3 -17
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
- package/esm/LinearPileupDisplay/components/SetMaxHeight.js +3 -16
- package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
- package/esm/LinearPileupDisplay/components/SortByTag.js +3 -21
- package/esm/LinearPileupDisplay/components/SortByTag.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +13 -9
- package/esm/LinearSNPCoverageDisplay/models/model.js +9 -7
- package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
- package/esm/PileupRenderer/configSchema.js +1 -1
- package/esm/PileupRenderer/configSchema.js.map +1 -1
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +0 -51
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +4 -183
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts +53 -0
- package/esm/SNPCoverageAdapter/generateCoverageBins.js +182 -0
- package/esm/SNPCoverageAdapter/generateCoverageBins.js.map +1 -0
- package/package.json +3 -3
- package/src/CramAdapter/CramTestAdapters.ts +1 -0
- package/src/LinearPileupDisplay/components/ColorByModifications.tsx +5 -34
- package/src/LinearPileupDisplay/components/ColorByTag.tsx +2 -29
- package/src/LinearPileupDisplay/components/FilterByTag.tsx +2 -22
- package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +2 -22
- package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +2 -24
- package/src/LinearPileupDisplay/components/SortByTag.tsx +2 -31
- package/src/LinearSNPCoverageDisplay/models/model.ts +12 -8
- package/src/PileupRenderer/configSchema.ts +1 -1
- package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +5 -249
- package/src/SNPCoverageAdapter/generateCoverageBins.ts +245 -0
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{"version":3,"file":"ColorByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByTag.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,
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{"version":3,"file":"ColorByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByTag.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,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,SAAS,aAAa,CAAC,KAGtB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IAEnD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,cAAc;QACrD,oBAAC,aAAa,IAAC,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE;YAC3C,oBAAC,UAAU,kCAAqC;YAChD,oBAAC,UAAU,IAAC,KAAK,EAAC,eAAe,+IAGpB;YAEb,oBAAC,SAAS,IACR,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;oBACV,SAAS,EAAE,CAAC;oBACZ,aAAa,EAAE,sBAAsB;iBACtC,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,EAClE,YAAY,EAAC,KAAK,iBACN,gBAAgB,GAC5B;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC;4BACnB,IAAI,EAAE,KAAK;4BACX,GAAG;yBACJ,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,EACD,QAAQ,EAAE,CAAC,QAAQ,aAGZ;gBACT,oBAAC,MAAM,IAAC,OAAO,EAAC,WAAW,EAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAE,WAAW,aAEzD,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,aAAa,CAAC,CAAA"}
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import React, { useState } from 'react';
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import { observer } from 'mobx-react';
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import { Button,
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import { Button, DialogActions, DialogContent, Link, Paper, TextField, Typography, } from '@mui/material';
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import { Dialog } from '@jbrowse/core/ui';
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import { makeStyles } from 'tss-react/mui';
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import CloseIcon from '@mui/icons-material/Close';
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const useStyles = makeStyles()(theme => ({
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paper: {
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padding: theme.spacing(2),
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margin: theme.spacing(2),
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closeButton: {
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position: 'absolute',
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right: theme.spacing(1),
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top: theme.spacing(1),
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color: theme.palette.grey[500],
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},
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field: {
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},
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@@ -63,11 +57,7 @@ function FilterByTagDlg(props) {
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const [readName, setReadName] = useState((filterBy === null || filterBy === void 0 ? void 0 : filterBy.readName) || '');
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const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
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const site = 'https://broadinstitute.github.io/picard/explain-flags.html';
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return (React.createElement(Dialog, { open: true, onClose: handleClose },
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React.createElement(DialogTitle, null,
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"Filter options",
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React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
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React.createElement(CloseIcon, null))),
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return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Filter options" },
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React.createElement(DialogContent, null,
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React.createElement(Typography, null,
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"Set filter bitmask options. Refer to ",
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{"version":3,"file":"FilterByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/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,
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{"version":3,"file":"FilterByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/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;AAED,SAAS,cAAc,CAAC,KAWvB;;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,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,GAAG,KAAI,EAAE,CAAC,CAAA;IAC9D,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,KAAK,KAAI,EAAE,CAAC,CAAA;IAC1E,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,CAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,QAAQ,KAAI,EAAE,CAAC,CAAA;IAClE,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;wBAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBAC5B,CAAC,EACD,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;wBACV,SAAS,EAAE,CAAC;wBACZ,aAAa,EAAE,sBAAsB;qBACtC,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,iBACtD,gBAAgB,GAC5B;gBACF,oBAAC,SAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACjC,CAAC,EACD,WAAW,EAAC,iBAAiB,EAC7B,UAAU,EAAE;wBACV,aAAa,EAAE,sBAAsB;qBACtC,iBACW,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;wBAChB,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACjC,CAAC,EACD,WAAW,EAAC,iBAAiB,EAC7B,UAAU,EAAE;wBACV,aAAa,EAAE,0BAA0B;qBAC1C,iBACW,oBAAoB,GAChC,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"}
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React.createElement(CloseIcon, null))),
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return (React.createElement(Dialog, { open: true, onClose: handleClose, title: 'Set feature height' },
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{"version":3,"file":"SetFeatureHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetFeatureHeight.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,QAAQ,EACR,
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{"version":3,"file":"SetFeatureHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetFeatureHeight.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,QAAQ,EACR,aAAa,EACb,aAAa,EACb,gBAAgB,EAChB,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,SAAS,mBAAmB,CAAC,KAQ5B;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,oBAAoB,EAAE,SAAS,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,GAAG,oBAAoB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,gBAAgB,CAAC,CAAA;IAE5D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAA;IAElD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,oBAAoB;QAC5D,oBAAC,aAAa;YACZ,oBAAC,UAAU,wKAIE;YACb,oBAAC,SAAS,IACR,KAAK,EAAE,MAAM,EACb,UAAU,EAAC,gBAAgB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC/B,CAAC,GACD;YACF,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,CAAC,CAAC,SAAS,EACpB,QAAQ,EAAE,GAAG,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GACzC,EAEJ,KAAK,EAAC,iDAAiD,GACvD;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,QAAQ,EAAE,CAAC,EAAE,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CACpB,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAC9D,CAAA;wBACD,KAAK,CAAC,YAAY,CAAC,SAAS,CAAC,CAAA;wBAC7B,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,mBAAmB,CAAC,CAAA"}
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import React, { useState } from 'react';
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import { Button,
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import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
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import { Dialog } from '@jbrowse/core/ui';
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import CloseIcon from '@mui/icons-material/Close';
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field: {
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},
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}));
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function SetMaxHeightDlg(props) {
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const { model, handleClose } = props;
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const { classes } = useStyles();
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const { maxHeight = '' } = model;
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const [max, setMax] = useState(`${maxHeight}`);
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"Filter options",
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return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Filter options" },
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React.createElement(DialogContent, { className: classes.root },
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React.createElement(Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
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@@ -1 +1 @@
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{"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetMaxHeight.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,
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+
{"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetMaxHeight.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,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,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,eAAe,CAAC,KAMxB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,SAAS,GAAG,EAAE,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,GAAG,SAAS,EAAE,CAAC,CAAA;IAE9C,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,oBAAC,UAAU,qHAGE;YACb,oBAAC,SAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC5B,CAAC,EACD,WAAW,EAAC,6BAA6B,GACzC;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,YAAY,CAChB,GAAG,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CACrD,CAAA;wBACD,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,eAAe,CAAC,CAAA"}
|
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@@ -1,30 +1,12 @@
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import React, { useState } from 'react';
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import { observer } from 'mobx-react';
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import { Button,
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import {
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import CloseIcon from '@mui/icons-material/Close';
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const useStyles = makeStyles()(theme => ({
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root: {
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margin: 0,
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padding: theme.spacing(2),
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},
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closeButton: {
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position: 'absolute',
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right: theme.spacing(1),
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},
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}));
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import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
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import { Dialog } from '@jbrowse/core/ui';
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function SortByTagDlg(props) {
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const { classes } = useStyles();
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const { model, handleClose } = props;
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const [tag, setTag] = useState('');
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const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
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return (React.createElement(Dialog, { open: true, onClose: handleClose },
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React.createElement(DialogTitle, null,
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"Sort by tag",
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React.createElement(CloseIcon, null))),
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return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Sort by tag" },
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React.createElement(DialogContent, null,
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React.createElement(Typography, null, "Set the tag to sort by"),
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React.createElement(Typography, { color: "textSecondary" }, "Examples: HP for haplotype, RG for read group, etc."),
|
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@@ -1 +1 @@
|
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1
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-
{"version":3,"file":"SortByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SortByTag.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,
|
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1
|
+
{"version":3,"file":"SortByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SortByTag.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,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,SAAS,YAAY,CAAC,KAGrB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IACnD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,aAAa;QACpD,oBAAC,aAAa;YACZ,oBAAC,UAAU,iCAAoC;YAC/C,oBAAC,UAAU,IAAC,KAAK,EAAC,eAAe,0DAEpB;YACb,oBAAC,SAAS,IACR,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;oBACV,SAAS,EAAE,CAAC;oBACZ,aAAa,EAAE,qBAAqB;iBACrC,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,EAClE,YAAY,EAAC,KAAK,iBACN,eAAe,GAC3B;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;wBAC7B,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;AACD,eAAe,QAAQ,CAAC,YAAY,CAAC,CAAA"}
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/// <reference types="react" />
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import { AnyConfigurationSchemaType, AnyConfigurationModel } from '@jbrowse/core/configuration';
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import PluginManager from '@jbrowse/core/PluginManager';
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import { AnyConfigurationSchemaType, AnyConfigurationModel } from '@jbrowse/core/configuration';
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/**
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setStatus(message: string): void;
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setLoading(abortController: AbortController): void;
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setRendered(props: {
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@@ -68,9 +66,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
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fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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* #getter
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*/
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color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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@@ -156,11 +152,16 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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}, {
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rendererTypeName: string;
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error: unknown;
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-
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
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* #getter
|
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+
*/
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}> | null;
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readonly adapterConfig: any;
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readonly parentTrack: any;
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|
renderProps(): any;
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/**
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* #method
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*/
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readonly DisplayMessageComponent: import("react").FC<any> | undefined;
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trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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@@ -343,7 +344,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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overrideHeight: number;
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}): Promise<JSX.Element>;
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} & {
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modificationTagMap:
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modificationTagMap: Record<string, string> | undefined;
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} & {
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/**
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@@ -424,6 +425,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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featureUnderMouse: import("@jbrowse/core/util").Feature;
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};
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height: number;
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+
/**
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* #action
|
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+
*/
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offsetMouseCoord: [number, number];
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clientMouseCoord: [number, number];
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clientRect?: DOMRect | undefined;
|
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@@ -1,5 +1,6 @@
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import { addDisposer, types, cast, getEnv, getSnapshot } from 'mobx-state-tree';
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-
import
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+
import clone from 'clone';
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import { autorun } from 'mobx';
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|
import { getConf, readConfObject, } from '@jbrowse/core/configuration';
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|
import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle';
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|
import { getContainingView } from '@jbrowse/core/util';
|
|
@@ -49,7 +50,7 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
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})),
|
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|
}))
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|
.volatile(() => ({
|
|
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|
-
modificationTagMap:
|
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|
+
modificationTagMap: undefined,
|
|
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|
}))
|
|
54
55
|
.actions(self => ({
|
|
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|
/**
|
|
@@ -76,12 +77,14 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
76
77
|
updateModificationColorMap(uniqueModifications) {
|
|
77
78
|
const colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
|
|
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79
|
let i = 0;
|
|
80
|
+
const newMap = clone(self.modificationTagMap) || {};
|
|
79
81
|
uniqueModifications.forEach(value => {
|
|
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|
-
if (!
|
|
82
|
+
if (!newMap[value]) {
|
|
81
83
|
const newColor = colorPalette[i++];
|
|
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|
-
|
|
84
|
+
newMap[value] = newColor;
|
|
83
85
|
}
|
|
84
86
|
});
|
|
87
|
+
self.modificationTagMap = newMap;
|
|
85
88
|
},
|
|
86
89
|
}))
|
|
87
90
|
.views(self => {
|
|
@@ -127,8 +130,7 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
127
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|
get modificationsReady() {
|
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|
var _a;
|
|
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|
return ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) === 'modifications'
|
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|
-
?
|
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|
-
.length > 0
|
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|
+
? self.modificationTagMap !== undefined
|
|
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134
|
: true;
|
|
133
135
|
},
|
|
134
136
|
/**
|
|
@@ -140,7 +142,7 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
140
142
|
return {
|
|
141
143
|
...superProps,
|
|
142
144
|
notReady: superProps.notReady || !this.modificationsReady,
|
|
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|
-
modificationTagMap:
|
|
145
|
+
modificationTagMap: modificationTagMap,
|
|
144
146
|
// must use getSnapshot because otherwise changes to e.g. just the
|
|
145
147
|
// colorBy.type are not read
|
|
146
148
|
colorBy: colorBy ? getSnapshot(colorBy) : undefined,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/models/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,IAAI,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC/E,OAAO,
|
|
1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/models/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,IAAI,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC/E,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAI9B,OAAO,EACL,OAAO,EACP,cAAc,GAGf,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,+BAA+B,EAAE,MAAM,wBAAwB,CAAA;AAExE,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAEtD,SAAS;AACT,OAAO,OAAO,MAAM,uBAAuB,CAAA;AAC3C,OAAO,EAAE,2BAA2B,EAAE,MAAM,cAAc,CAAA;AAE1D,yCAAyC;AACzC,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,aAAa,EAAE,qBAAqB,CAAC,CAAC,CAAC,CAAA;AAIvE;;;GAGG;AACH,SAAS,iBAAiB,CACxB,aAA4B,EAC5B,YAAwC;IAExC,OAAO,KAAK;SACT,OAAO,CACN,0BAA0B,EAC1B,+BAA+B,CAAC,aAAa,EAAE,YAAY,CAAC,EAC5D,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,0BAA0B,CAAC;QAC/C;;WAEG;QACH,mBAAmB,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC;QAC/C;;WAEG;QACH,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC;QAC1C;;WAEG;QACH,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC;QACpC;;WAEG;QACH,QAAQ,EAAE,KAAK,CAAC,QAAQ,CACtB,KAAK,CAAC,KAAK,CAAC;YACV,WAAW,EAAE,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;YAC5C,WAAW,EAAE,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC;YAC/C,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;YACnC,SAAS,EAAE,KAAK,CAAC,KAAK,CACpB,KAAK,CAAC,KAAK,CAAC,EAAE,GAAG,EAAE,KAAK,CAAC,MAAM,EAAE,KAAK,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CACxD;SACF,CAAC,EACF,EAAE,CACH;QACD;;WAEG;QACH,OAAO,EAAE,KAAK,CAAC,KAAK,CAClB,KAAK,CAAC,KAAK,CAAC;YACV,IAAI,EAAE,KAAK,CAAC,MAAM;YAClB,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;SAC/B,CAAC,CACH;KACF,CAAC,CACH;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,kBAAkB,EAAE,SAA+C;KACpE,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,SAAS,CAAC,aAAoC;YAC5C,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;QACpC,CAAC;QACD;;WAEG;QACH,WAAW,CAAC,MAKX;YACC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,MAAM,CAAC,CAAA;QAC9B,CAAC;QACD;;WAEG;QACH,UAAU,CAAC,OAAwC;YACjD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,CAAA;QAC9B,CAAC;QAED;;WAEG;QACH,0BAA0B,CAAC,mBAA6B;YACtD,MAAM,YAAY,GAAG,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,QAAQ,CAAC,CAAA;YACjE,IAAI,CAAC,GAAG,CAAC,CAAA;YAET,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,IAAI,EAAE,CAAA;YACnD,mBAAmB,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;gBAClC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE;oBAClB,MAAM,QAAQ,GAAG,YAAY,CAAC,CAAC,EAAE,CAAC,CAAA;oBAClC,MAAM,CAAC,KAAK,CAAC,GAAG,QAAQ,CAAA;iBACzB;YACH,CAAC,CAAC,CAAA;YACF,IAAI,CAAC,kBAAkB,GAAG,MAAM,CAAA;QAClC,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EAAE,WAAW,EAAE,gBAAgB,EAAE,GAAG,IAAI,CAAA;QAC9C,OAAO;YACL;;eAEG;YACH,IAAI,cAAc;;gBAChB,MAAM,UAAU,GACd,OAAO,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,IAAI,CAAC,gBAAgB,CAAC,CAAC,IAAI,EAAE,CAAA;gBAE3D,OAAO,IAAI,CAAC,YAAY,CAAC,YAAY,CAAC,MAAM,CAC1C;oBACE,GAAG,UAAU;oBACb,mBAAmB,EACjB,MAAA,IAAI,CAAC,mBAAmB,mCAAI,UAAU,CAAC,mBAAmB;oBAC5D,cAAc,EAAE,MAAA,IAAI,CAAC,cAAc,mCAAI,UAAU,CAAC,cAAc;oBAChE,QAAQ,EAAE,MAAA,IAAI,CAAC,QAAQ,mCAAI,UAAU,CAAC,QAAQ;iBAC/C,EACD,MAAM,CAAC,IAAI,CAAC,CACb,CAAA;YACH,CAAC;YACD;;eAEG;YACH,IAAI,eAAe;;gBACjB,OAAO,CACL,MAAA,IAAI,CAAC,QAAQ,mCAAI,cAAc,CAAC,IAAI,CAAC,cAAc,EAAE,UAAU,CAAC,CACjE,CAAA;YACH,CAAC;YACD;;eAEG;YACH,IAAI,0BAA0B;;gBAC5B,OAAO,CACL,MAAA,IAAI,CAAC,mBAAmB,mCACxB,cAAc,CAAC,IAAI,CAAC,cAAc,EAAE,qBAAqB,CAAC,CAC3D,CAAA;YACH,CAAC;YACD;;eAEG;YACH,IAAI,qBAAqB;;gBACvB,OAAO,CACL,MAAA,IAAI,CAAC,cAAc,mCACnB,cAAc,CAAC,IAAI,CAAC,cAAc,EAAE,gBAAgB,CAAC,CACtD,CAAA;YACH,CAAC;YAED;;eAEG;YACH,IAAI,kBAAkB;;gBACpB,OAAO,CAAA,MAAA,IAAI,CAAC,OAAO,0CAAE,IAAI,MAAK,eAAe;oBAC3C,CAAC,CAAC,IAAI,CAAC,kBAAkB,KAAK,SAAS;oBACvC,CAAC,CAAC,IAAI,CAAA;YACV,CAAC;YAED;;eAEG;YACH,WAAW;gBACT,MAAM,UAAU,GAAG,gBAAgB,EAAE,CAAA;gBACrC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;gBACtD,OAAO;oBACL,GAAG,UAAU;oBACb,QAAQ,EAAE,UAAU,CAAC,QAAQ,IAAI,CAAC,IAAI,CAAC,kBAAkB;oBACzD,kBAAkB,EAAE,kBAAkB;oBAEtC,kEAAkE;oBAClE,4BAA4B;oBAC5B,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,SAAS;oBACnD,QAAQ,EAAE,QAAQ,CAAC,CAAC,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,SAAS;iBACvD,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,oBAAoB;YAClB,IAAI,CAAC,cAAc,GAAG,CAAC,IAAI,CAAC,qBAAqB,CAAA;QACnD,CAAC;QACD;;WAEG;QACH,yBAAyB;YACvB,IAAI,CAAC,mBAAmB,GAAG,CAAC,IAAI,CAAC,0BAA0B,CAAA;QAC7D,CAAC;QACD;;WAEG;QACH,cAAc;YACZ,IAAI,CAAC,QAAQ,GAAG,CAAC,IAAI,CAAC,eAAe,CAAA;QACvC,CAAC;QACD,WAAW;YACT,WAAW,CACT,IAAI,EACJ,OAAO,CACL,KAAK,IAAI,EAAE;gBACT,IAAI;oBACF,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;oBACxB,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;oBAE3C,IACE,CAAC,IAAI,CAAC,WAAW;wBACjB,CAAC,IAAI,CAAC,mBAAmB;wBACzB,IAAI,CAAC,cAAc,EACnB;wBACA,OAAM;qBACP;oBACD,MAAM,EAAE,YAAY,EAAE,GAAG,IAAI,CAAA;oBAC7B,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,EAAE;wBACrC,MAAM,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,WAAW,EAAE,SAAS,CAAC,CAAA;wBACpD,IAAI,CAAC,0BAA0B,CAC7B,MAAM,2BAA2B,CAC/B,IAAI,EACJ,OAAO,EACP,OAAO,EACP,YAAY,CACb,CACF,CAAA;qBACF;iBACF;gBAAC,OAAO,KAAK,EAAE;oBACd,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;oBACpB,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAA;iBACrB;YACH,CAAC,EACD,EAAE,KAAK,EAAE,IAAI,EAAE,CAChB,CACF,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SAEF,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EAAE,cAAc,EAAE,mBAAmB,EAAE,GAAG,IAAI,CAAA;QACpD,OAAO;YACL;;eAEG;YACH,IAAI,gBAAgB;gBAClB,OAAO,OAAO,CAAA;YAChB,CAAC;YAED;;eAEG;YACH,IAAI,aAAa;gBACf,MAAM,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,WAAW,EAAE,SAAS,CAAC,CAAA;gBACvD,OAAO;oBACL,IAAI,EAAE,oBAAoB;oBAC1B,UAAU;iBACX,CAAA;YACH,CAAC;YAED;;eAEG;YACH,IAAI,gBAAgB;gBAClB,OAAO,aAAa,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;YACzC,CAAC;YAED;;eAEG;YACH,IAAI,aAAa;gBACf,OAAO,IAAI,CAAA;YACb,CAAC;YAED;;eAEG;YACH,gBAAgB;gBACd,OAAO,EAAE,CAAA;YACX,CAAC;YAED;;eAEG;YACH,cAAc;gBACZ,OAAO;oBACL,GAAG,mBAAmB,EAAE;oBACxB;wBACE,KAAK,EAAE,oCAAoC;wBAC3C,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,qBAAqB;wBACnC,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,oBAAoB,EAAE;qBAC3C;oBACD;wBACE,KAAK,EAAE,gCAAgC;wBACvC,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,0BAA0B;wBACxC,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,yBAAyB,EAAE;qBAChD;oBACD;wBACE,KAAK,EAAE,WAAW;wBAClB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,eAAe;wBAC7B,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,cAAc,EAAE;qBACrC;iBACF,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC;AAID,eAAe,iBAAiB,CAAA"}
|
|
@@ -22,7 +22,7 @@ const PileupRenderer = ConfigurationSchema('PileupRenderer', {
|
|
|
22
22
|
type: 'stringEnum',
|
|
23
23
|
model: types.enumeration('orientationType', ['fr', 'rf', 'ff']),
|
|
24
24
|
defaultValue: 'fr',
|
|
25
|
-
description: 'read sequencer
|
|
25
|
+
description: 'read sequencer orientation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
|
|
26
26
|
},
|
|
27
27
|
/**
|
|
28
28
|
* #slot
|
|
@@ -1 +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,
|
|
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"}
|
|
@@ -11,57 +11,6 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
|
|
|
11
11
|
estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
|
|
12
12
|
getRefNames(opts?: BaseOptions): Promise<string[]>;
|
|
13
13
|
freeResources(): void;
|
|
14
|
-
generateCoverageBins(features: Feature[], region: Region, opts: {
|
|
15
|
-
bpPerPx?: number;
|
|
16
|
-
colorBy?: {
|
|
17
|
-
type: string;
|
|
18
|
-
tag?: string;
|
|
19
|
-
};
|
|
20
|
-
}): Promise<{
|
|
21
|
-
bins: {
|
|
22
|
-
refbase?: string | undefined;
|
|
23
|
-
total: number;
|
|
24
|
-
all: number;
|
|
25
|
-
ref: number;
|
|
26
|
-
'-1': 0;
|
|
27
|
-
'0': 0;
|
|
28
|
-
'1': 0;
|
|
29
|
-
lowqual: {
|
|
30
|
-
total: number;
|
|
31
|
-
strands: {
|
|
32
|
-
[key: string]: number;
|
|
33
|
-
};
|
|
34
|
-
};
|
|
35
|
-
cov: {
|
|
36
|
-
total: number;
|
|
37
|
-
strands: {
|
|
38
|
-
[key: string]: number;
|
|
39
|
-
};
|
|
40
|
-
};
|
|
41
|
-
delskips: {
|
|
42
|
-
total: number;
|
|
43
|
-
strands: {
|
|
44
|
-
[key: string]: number;
|
|
45
|
-
};
|
|
46
|
-
};
|
|
47
|
-
noncov: {
|
|
48
|
-
total: number;
|
|
49
|
-
strands: {
|
|
50
|
-
[key: string]: number;
|
|
51
|
-
};
|
|
52
|
-
};
|
|
53
|
-
}[];
|
|
54
|
-
skipmap: {
|
|
55
|
-
[key: string]: {
|
|
56
|
-
score: number;
|
|
57
|
-
feature: unknown;
|
|
58
|
-
start: number;
|
|
59
|
-
end: number;
|
|
60
|
-
strand: number;
|
|
61
|
-
xs: string;
|
|
62
|
-
};
|
|
63
|
-
};
|
|
64
|
-
}>;
|
|
65
14
|
}
|
|
66
15
|
declare const capabilities: string[];
|
|
67
16
|
export { capabilities };
|