@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":"CramTestAdapters.js","sourceRoot":"","sources":["../../src/CramAdapter/CramTestAdapters.ts"],"names":[],"mappings":";;;;;;AACA,+BAAiC;AACjC,qFAA4D;AAC5D,yEAAgF;AAChF,yFAAqF;AAErF,iCAAiC;AACjC,SAAgB,eAAe,CAAC,IAAY;IAC1C,OAAO,IAAI;SACR,KAAK,CAAC,GAAG,CAAC;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACzB,GAAG,CAAC,SAAS,CAAC,EAAE;QACf,MAAM,CAAC,OAAO,EAAE,GAAG,QAAQ,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;QAC5D,MAAM,CAAC,EAAE,EAAE,GAAG,gBAAgB,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QACpD,MAAM,WAAW,GAAG,gBAAgB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC9C,MAAM,QAAQ,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QACrD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAA;IACtC,CAAC,CAAC,CAAA;AACN,CAAC;AAXD,0CAWC;AAID,MAAa,mBAAmB;IAG9B,YAAY,UAAsB;QAChC,IAAI,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE;YAC9C,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACpC,OAAO,eAAe,CAAC,IAAI,CAAC,CAAA;QAC9B,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,EAAU,EAAE,KAAa,EAAE,GAAW;QAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAA;QAC5B,MAAM,KAAK,GAAG,IAAI,CAAC,EAAE,CAAC,CAAA;QACtB,MAAM,MAAM,GAAG,GAAG,GAAG,KAAK,GAAG,CAAC,CAAA;QAC9B,IAAI,CAAC,KAAK,EAAE;YACV,MAAM,IAAI,KAAK,CAAC,uBAAuB,EAAE,SAAS,CAAC,CAAA;SACpD;QACD,OAAO,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,GAAG,MAAM,CAAC,CAAA;IACpD,CAAC;IAED,KAAK,CAAC,eAAe;QACnB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAA;QAC5B,OAAO,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;IACpC,CAAC;CACF;AAxBD,kDAwBC;AAED,MAAa,eAAgB,SAAQ,oCAAsB;IAKzD,YAAY,UAAsB;QAChC,KAAK,CAAC,IAAA,yCAAmB,EAAC,OAAO,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAA;QAHlD,aAAQ,GAAa,EAAE,CAAA;QAIrB,IAAI,CAAC,KAAK,GAAG,IAAI,mBAAmB,CAAC,UAAU,CAAC,CAAA;IAClD,CAAC;IAED,KAAK,CAAC,WAAW;QACf,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED,WAAW,CAAC,EACV,OAAO,EACP,KAAK,EACL,GAAG,GAKJ;QACC,OAAO,IAAI,iBAAU,CAAC,QAAQ,CAAC,EAAE;YAC/B,IAAI,CAAC,KAAK;iBACP,eAAe,EAAE;iBACjB,IAAI,CAAC,QAAQ,CAAC,EAAE;gBACf,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;YAC1B,CAAC,CAAC;iBACD,IAAI,CAAC,GAAG,EAAE,CACT,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,KAAK,EAAE,GAAG,CAAC,CAC7D;iBACA,IAAI,CAAC,GAAG,CAAC,EAAE;gBACV,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,QAAQ,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,GAAG,EAAE;oBACtC,GAAG,EAAE,GAAG;oBACR,KAAK;oBACL,GAAG;iBACJ,CAAC,CACH,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;YACrB,CAAC,CAAC;iBACD,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;YAChC,OAAO,EAAE,WAAW,EAAE,GAAG,EAAE,GAAE,CAAC,EAAE,CAAA;QAClC,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AAjDD,0CAiDC"}
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const react_1 = __importDefault(require("react"));
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const mobx_react_1 = require("mobx-react");
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const material_1 = require("@mui/material");
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const ui_1 = require("@jbrowse/core/ui");
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const mui_1 = require("tss-react/mui");
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const Close_1 = __importDefault(require("@mui/icons-material/Close"));
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const useStyles = (0, mui_1.makeStyles)()(theme => ({
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} })))))));
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return (react_1.default.createElement(
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react_1.default.createElement(material_1.IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
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react_1.default.createElement(Close_1.default, null))),
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return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Color by modifications" },
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react_1.default.createElement(material_1.Typography, null, "You can choose to color the modifications in the BAM/CRAM MM/ML specification using this dialog. Choosing modifications colors the modified positions and can color multiple modification types. Choosing the methylation setting colors methylated and unmethylated CpG."),
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react_1.default.createElement(material_1.Typography, null, "Note: you can revisit this dialog to see the current mapping of colors to modification type for the modification coloring mode"),
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{"version":3,"file":"ColorByModifications.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByModifications.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AAErC,
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{"version":3,"file":"ColorByModifications.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByModifications.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AAErC,4CAMsB;AACtB,yCAAyC;AACzC,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,MAAM,EAAE,gBAAgB;QACxB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACxB,MAAM,EAAE;YACN,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;SAC1B;KACF;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EACzB,aAAa,GAGd;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,yCAAO,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,6CACG,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CACnC,sCAAI,GAAG,EAAE,GAAG;YACV,0CAAK,GAAG,CAAM;YACd,0CAAK,KAAK,CAAM;YAChB,sCACE,KAAK,EAAE;oBACL,KAAK,EAAE,KAAK;oBACZ,UAAU,EAAE,KAAK;iBAClB,GACD,CACC,CACN,CAAC,CACI,CACF,CACT,CAAA;AACH,CAAC;AAED,SAAS,aAAa,CAAC,KAOtB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAE7C,MAAM,aAAa,GAAG,CAAC,GAAG,kBAAkB,CAAC,OAAO,EAAE,CAAC,CAAA;IAEvD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,wBAAwB;QAC/D,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,oRAKE;YACb,8BAAC,qBAAU,yIAGE;YACb,uCAAK,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE;gBACvB,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,CAAC,CAAC,CAAC,CACnC,2CACG,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC,CACtB;;oBAEE,8BAAC,iBAAiB,IAChB,aAAa,EAAE,CAAC,GAAG,kBAAkB,CAAC,OAAO,EAAE,CAAC,GAChD,CACD,CACJ,CAAC,CAAC,CAAC,CACF;oBACE,8BAAC,qBAAU,4FAGE;oBACb,8BAAC,2BAAgB,IAAC,IAAI,EAAE,EAAE,GAAI,CAC1B,CACP,CACG,CACP,CAAC,CAAC,CAAC,IAAI;gBACP,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,CAAC,CAAC,CAAC,CACjC,8BAAC,iBAAiB,IAChB,aAAa,EAAE;wBACb,CAAC,YAAY,EAAE,KAAK,CAAC;wBACrB,CAAC,cAAc,EAAE,MAAM,CAAC;qBACzB,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACJ;YACN,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,eAAe,EAAE,CAAC,CAAA;wBAC/C,WAAW,EAAE,CAAA;oBACf,CAAC,oBAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,aAAa,EAAE,CAAC,CAAA;wBAC7C,WAAW,EAAE,CAAA;oBACf,CAAC,kBAGM;gBACT,8BAAC,iBAAM,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,kBAAe,IAAA,qBAAQ,EAAC,aAAa,CAAC,CAAA"}
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{"version":3,"file":"ColorByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,yCAAyC;AAEzC,SAAS,aAAa,CAAC,KAGtB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IAEnD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,cAAc;QACrD,8BAAC,wBAAa,IAAC,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE;YAC3C,8BAAC,qBAAU,kCAAqC;YAChD,8BAAC,qBAAU,IAAC,KAAK,EAAC,eAAe,+IAGpB;YAEb,8BAAC,oBAAS,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,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,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,8BAAC,iBAAM,IAAC,OAAO,EAAC,WAAW,EAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAE,WAAW,aAEzD,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,aAAa,CAAC,CAAA"}
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{"version":3,"file":"FilterByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/FilterByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAQsB;AACtB,yCAAyC;AACzC,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,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,8BAAC,oBAAS,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,uCAAK,GAAG,EAAE,GAAG;gBACX,yCACE,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,yCAAO,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,IAAA,gBAAQ,EAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,EAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,GAAG,KAAI,EAAE,CAAC,CAAA;IAC9D,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,KAAK,KAAI,EAAE,CAAC,CAAA;IAC1E,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,EAAC,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,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BAAC,wBAAa;YACZ,8BAAC,qBAAU;;gBAC4B,8BAAC,eAAI,IAAC,IAAI,EAAE,IAAI,IAAG,IAAI,CAAQ;gBAAC,GAAG;8BAE7D;YACb,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,uCAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;oBAC7B;wBACE,8BAAC,qBAAU,yCAA4C;wBACvD,8BAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD;oBACN;wBACE,8BAAC,qBAAU,6CAAgD;wBAC3D,8BAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD,CACF,CACA;YACR,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,8BAAC,qBAAU,kQAKE;gBACb,8BAAC,oBAAS,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,8BAAC,oBAAS,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,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,8BAAC,qBAAU,8BAAiC;gBAC5C,8BAAC,oBAAS,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,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,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,8BAAC,iBAAM,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,kBAAe,IAAA,qBAAQ,EAAC,cAAc,CAAC,CAAA"}
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{"version":3,"file":"SetFeatureHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetFeatureHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAQsB;AACtB,yCAAyC;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,IAAA,gBAAQ,EAAC,GAAG,oBAAoB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,IAAA,gBAAQ,EAAC,gBAAgB,CAAC,CAAA;IAE5D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAA;IAElD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,oBAAoB;QAC5D,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,wKAIE;YACb,8BAAC,oBAAS,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,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,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,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,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,8BAAC,iBAAM,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,kBAAe,IAAA,qBAAQ,EAAC,mBAAmB,CAAC,CAAA"}
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{"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetMaxHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,yCAAyC;AACzC,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,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,IAAA,gBAAQ,EAAC,GAAG,SAAS,EAAE,CAAC,CAAA;IAE9C,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BAAC,wBAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,8BAAC,qBAAU,qHAGE;YACb,8BAAC,oBAAS,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,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,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,8BAAC,iBAAM,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,kBAAe,IAAA,qBAAQ,EAAC,eAAe,CAAC,CAAA"}
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const
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const Close_1 = __importDefault(require("@mui/icons-material/Close"));
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root: {
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const ui_1 = require("@jbrowse/core/ui");
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function SortByTagDlg(props) {
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const { model, handleClose } = props;
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const [tag, setTag] = (0, react_1.useState)('');
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const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
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"Sort by tag",
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react_1.default.createElement(Close_1.default, null))),
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return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Sort by tag" },
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react_1.default.createElement(material_1.DialogContent, null,
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react_1.default.createElement(material_1.Typography, null, "Set the tag to sort by"),
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react_1.default.createElement(material_1.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":"
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+
{"version":3,"file":"SortByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SortByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,yCAAyC;AAEzC,SAAS,YAAY,CAAC,KAGrB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IACnD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,aAAa;QACpD,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,iCAAoC;YAC/C,8BAAC,qBAAU,IAAC,KAAK,EAAC,eAAe,0DAEpB;YACb,8BAAC,oBAAS,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,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,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,8BAAC,iBAAM,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,kBAAe,IAAA,qBAAQ,EAAC,YAAY,CAAC,CAAA"}
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@@ -1,6 +1,6 @@
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1
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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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* #stateModel LinearSNPCoverageDisplay
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* extends `LinearWiggleDisplay`
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@@ -43,9 +43,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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} & {
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setStatus(message: string): void;
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*/
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setStatus(message: string): void;
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setLoading(abortController: AbortController): void;
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setMessage(messageText: string): 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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*/
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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 rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
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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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343
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overrideHeight: number;
|
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344
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}): Promise<JSX.Element>;
|
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345
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} & {
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modificationTagMap:
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modificationTagMap: Record<string, string> | undefined;
|
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347
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} & {
|
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|
/**
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* #action
|
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@@ -424,6 +425,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
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424
425
|
featureUnderMouse: import("@jbrowse/core/util").Feature;
|
|
425
426
|
};
|
|
426
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|
height: number;
|
|
428
|
+
/**
|
|
429
|
+
* #action
|
|
430
|
+
*/
|
|
427
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|
offsetMouseCoord: [number, number];
|
|
428
432
|
clientMouseCoord: [number, number];
|
|
429
433
|
clientRect?: DOMRect | undefined;
|
|
@@ -4,6 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
const mobx_state_tree_1 = require("mobx-state-tree");
|
|
7
|
+
const clone_1 = __importDefault(require("clone"));
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|
7
8
|
const mobx_1 = require("mobx");
|
|
8
9
|
const configuration_1 = require("@jbrowse/core/configuration");
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|
9
10
|
const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
|
|
@@ -54,7 +55,7 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
54
55
|
})),
|
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55
56
|
}))
|
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56
57
|
.volatile(() => ({
|
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57
|
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modificationTagMap:
|
|
58
|
+
modificationTagMap: undefined,
|
|
58
59
|
}))
|
|
59
60
|
.actions(self => ({
|
|
60
61
|
/**
|
|
@@ -81,12 +82,14 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
81
82
|
updateModificationColorMap(uniqueModifications) {
|
|
82
83
|
const colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
|
|
83
84
|
let i = 0;
|
|
85
|
+
const newMap = (0, clone_1.default)(self.modificationTagMap) || {};
|
|
84
86
|
uniqueModifications.forEach(value => {
|
|
85
|
-
if (!
|
|
87
|
+
if (!newMap[value]) {
|
|
86
88
|
const newColor = colorPalette[i++];
|
|
87
|
-
|
|
89
|
+
newMap[value] = newColor;
|
|
88
90
|
}
|
|
89
91
|
});
|
|
92
|
+
self.modificationTagMap = newMap;
|
|
90
93
|
},
|
|
91
94
|
}))
|
|
92
95
|
.views(self => {
|
|
@@ -132,8 +135,7 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
132
135
|
get modificationsReady() {
|
|
133
136
|
var _a;
|
|
134
137
|
return ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) === 'modifications'
|
|
135
|
-
?
|
|
136
|
-
.length > 0
|
|
138
|
+
? self.modificationTagMap !== undefined
|
|
137
139
|
: true;
|
|
138
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|
},
|
|
139
141
|
/**
|
|
@@ -145,7 +147,7 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
145
147
|
return {
|
|
146
148
|
...superProps,
|
|
147
149
|
notReady: superProps.notReady || !this.modificationsReady,
|
|
148
|
-
modificationTagMap:
|
|
150
|
+
modificationTagMap: modificationTagMap,
|
|
149
151
|
// must use getSnapshot because otherwise changes to e.g. just the
|
|
150
152
|
// colorBy.type are not read
|
|
151
153
|
colorBy: colorBy ? (0, mobx_state_tree_1.getSnapshot)(colorBy) : undefined,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/models/model.ts"],"names":[],"mappings":";;;;;AAAA,qDAA+E;AAC/E,+
|
|
1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/models/model.ts"],"names":[],"mappings":";;;;;AAAA,qDAA+E;AAC/E,kDAAyB;AACzB,+BAA8B;AAI9B,+DAKoC;AACpC,0DAAwE;AAExE,6CAAsD;AAEtD,SAAS;AACT,oEAA2C;AAC3C,yCAA0D;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,uBAAK;SACT,OAAO,CACN,0BAA0B,EAC1B,IAAA,+CAA+B,EAAC,aAAa,EAAE,YAAY,CAAC,EAC5D,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,0BAA0B,CAAC;QAC/C;;WAEG;QACH,mBAAmB,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,OAAO,CAAC;QAC/C;;WAEG;QACH,cAAc,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,OAAO,CAAC;QAC1C;;WAEG;QACH,QAAQ,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,OAAO,CAAC;QACpC;;WAEG;QACH,QAAQ,EAAE,uBAAK,CAAC,QAAQ,CACtB,uBAAK,CAAC,KAAK,CAAC;YACV,WAAW,EAAE,uBAAK,CAAC,QAAQ,CAAC,uBAAK,CAAC,MAAM,EAAE,CAAC,CAAC;YAC5C,WAAW,EAAE,uBAAK,CAAC,QAAQ,CAAC,uBAAK,CAAC,MAAM,EAAE,IAAI,CAAC;YAC/C,QAAQ,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;YACnC,SAAS,EAAE,uBAAK,CAAC,KAAK,CACpB,uBAAK,CAAC,KAAK,CAAC,EAAE,GAAG,EAAE,uBAAK,CAAC,MAAM,EAAE,KAAK,EAAE,uBAAK,CAAC,MAAM,EAAE,CAAC,CACxD;SACF,CAAC,EACF,EAAE,CACH;QACD;;WAEG;QACH,OAAO,EAAE,uBAAK,CAAC,KAAK,CAClB,uBAAK,CAAC,KAAK,CAAC;YACV,IAAI,EAAE,uBAAK,CAAC,MAAM;YAClB,GAAG,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,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,IAAA,sBAAI,EAAC,MAAM,CAAC,CAAA;QAC9B,CAAC;QACD;;WAEG;QACH,UAAU,CAAC,OAAwC;YACjD,IAAI,CAAC,OAAO,GAAG,IAAA,sBAAI,EAAC,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,IAAA,eAAK,EAAC,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,IAAA,uBAAO,EAAC,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,IAAA,wBAAM,EAAC,IAAI,CAAC,CACb,CAAA;YACH,CAAC;YACD;;eAEG;YACH,IAAI,eAAe;;gBACjB,OAAO,CACL,MAAA,IAAI,CAAC,QAAQ,mCAAI,IAAA,8BAAc,EAAC,IAAI,CAAC,cAAc,EAAE,UAAU,CAAC,CACjE,CAAA;YACH,CAAC;YACD;;eAEG;YACH,IAAI,0BAA0B;;gBAC5B,OAAO,CACL,MAAA,IAAI,CAAC,mBAAmB,mCACxB,IAAA,8BAAc,EAAC,IAAI,CAAC,cAAc,EAAE,qBAAqB,CAAC,CAC3D,CAAA;YACH,CAAC;YACD;;eAEG;YACH,IAAI,qBAAqB;;gBACvB,OAAO,CACL,MAAA,IAAI,CAAC,cAAc,mCACnB,IAAA,8BAAc,EAAC,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,IAAA,6BAAW,EAAC,OAAO,CAAC,CAAC,CAAC,CAAC,SAAS;oBACnD,QAAQ,EAAE,QAAQ,CAAC,CAAC,CAAC,IAAA,6BAAW,EAAC,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,IAAA,6BAAW,EACT,IAAI,EACJ,IAAA,cAAO,EACL,KAAK,IAAI,EAAE;gBACT,IAAI;oBACF,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;oBACxB,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,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,IAAA,uBAAO,EAAC,IAAI,CAAC,WAAW,EAAE,SAAS,CAAC,CAAA;wBACpD,IAAI,CAAC,0BAA0B,CAC7B,MAAM,IAAA,oCAA2B,EAC/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,iBAAO,CAAA;YAChB,CAAC;YAED;;eAEG;YACH,IAAI,aAAa;gBACf,MAAM,UAAU,GAAG,IAAA,uBAAO,EAAC,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,kBAAe,iBAAiB,CAAA"}
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|
@@ -24,7 +24,7 @@ const PileupRenderer = (0, configuration_1.ConfigurationSchema)('PileupRenderer'
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24
24
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type: 'stringEnum',
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25
25
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model: mobx_state_tree_1.types.enumeration('orientationType', ['fr', 'rf', 'ff']),
|
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defaultValue: 'fr',
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27
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-
description: 'read sequencer
|
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|
+
description: 'read sequencer orientation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
|
|
28
28
|
},
|
|
29
29
|
/**
|
|
30
30
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* #slot
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,qDAAuC;AAEvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,cAAc,GAAG,IAAA,mCAAmB,EACxC,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,uBAAK,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,+DAAiE;AACjE,qDAAuC;AAEvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,cAAc,GAAG,IAAA,mCAAmB,EACxC,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,uBAAK,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,uBAAK,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,kBAAe,cAAc,CAAA"}
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@@ -11,57 +11,6 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
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11
11
|
estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
|
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12
12
|
getRefNames(opts?: BaseOptions): Promise<string[]>;
|
|
13
13
|
freeResources(): void;
|
|
14
|
-
generateCoverageBins(features: Feature[], region: Region, opts: {
|
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15
|
-
bpPerPx?: number;
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|
-
colorBy?: {
|
|
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|
-
type: string;
|
|
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|
-
tag?: string;
|
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|
-
};
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|
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|
-
}): Promise<{
|
|
21
|
-
bins: {
|
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22
|
-
refbase?: string | undefined;
|
|
23
|
-
total: number;
|
|
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|
-
all: number;
|
|
25
|
-
ref: number;
|
|
26
|
-
'-1': 0;
|
|
27
|
-
'0': 0;
|
|
28
|
-
'1': 0;
|
|
29
|
-
lowqual: {
|
|
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-
total: number;
|
|
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|
-
strands: {
|
|
32
|
-
[key: string]: number;
|
|
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|
-
};
|
|
34
|
-
};
|
|
35
|
-
cov: {
|
|
36
|
-
total: number;
|
|
37
|
-
strands: {
|
|
38
|
-
[key: string]: number;
|
|
39
|
-
};
|
|
40
|
-
};
|
|
41
|
-
delskips: {
|
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|
-
total: number;
|
|
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|
-
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 };
|