@jbrowse/plugin-alignments 2.0.1 → 2.1.0
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/BamAdapter/BamAdapter.d.ts +6 -1
- package/dist/BamAdapter/BamAdapter.js.map +1 -1
- package/dist/LinearPileupDisplay/model.d.ts +2 -2
- package/dist/LinearPileupDisplay/model.js +0 -1
- package/dist/LinearPileupDisplay/model.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +4 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +0 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +28 -6
- package/dist/LinearSNPCoverageDisplay/models/model.js +1 -0
- package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
- package/dist/PileupRenderer/PileupRenderer.d.ts +0 -4
- package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +4 -3
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +1 -1
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
- package/esm/BamAdapter/BamAdapter.d.ts +6 -1
- package/esm/BamAdapter/BamAdapter.js.map +1 -1
- package/esm/LinearPileupDisplay/model.d.ts +2 -2
- package/esm/LinearPileupDisplay/model.js +0 -1
- package/esm/LinearPileupDisplay/model.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +4 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +0 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +28 -6
- package/esm/LinearSNPCoverageDisplay/models/model.js +1 -0
- package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
- package/esm/PileupRenderer/PileupRenderer.d.ts +0 -4
- package/esm/PileupRenderer/PileupRenderer.js +1 -1
- package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +4 -3
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +1 -1
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
- package/package.json +3 -3
- package/src/BamAdapter/BamAdapter.ts +1 -1
- package/src/LinearPileupDisplay/model.ts +2 -2
- package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx +3 -4
- package/src/LinearSNPCoverageDisplay/models/model.ts +3 -1
- package/src/PileupRenderer/PileupRenderer.tsx +13 -17
- package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +4 -3
- package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +1 -2
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EACL,MAAM,EACN,SAAS,EACT,aAAa,EACb,4BAA4B,GAC7B,MAAM,SAAS,CAAA;AAChB,OAAO,EACL,UAAU,EACV,aAAa,EACb,wBAAwB,GAEzB,MAAM,8BAA8B,CAAA;AAErC,SAAS,WAAW,CAAC,QAAkB;IACrC,OAAO,CAAC,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;AAC1D,CAAC;AAED,SAAS,WAAW,CAAC,IAAY;IAC/B,OAAO,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,WAAW,CAAA;AAC3E,CAAC;AAED,8DAA8D;AAC9D,SAAS,GAAG,CAAC,GAAQ,EAAE,MAAc,EAAE,IAAY,EAAE,KAAa;IAChE,IAAI,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAA;IAC9B,IAAI,OAAO,KAAK,SAAS,EAAE;QACzB,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,GAAG;YAC3B,KAAK,EAAE,CAAC;YACR,IAAI,EAAE,CAAC;YACP,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;SACP,CAAA;KACF;IACD,OAAO,CAAC,KAAK,EAAE,CAAA;IACf,OAAO,CAAC,MAAM,CAAC,EAAE,CAAA;AACnB,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,sBAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,YAAY,EAAE,iBAAiB,CAAC,CAAC,CAAA;QACpE,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,aAAa,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,UAAU;iBAC3B,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC;iBACzB,IAAI,CAAC,OAAO,EAAE,CAAC;iBACf,SAAS,EAAE,CAAA;YAEd,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,oBAAoB,CACvD,KAAK,EACL,MAAM,EACN,IAAI,CACL,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,
|
|
1
|
+
{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EACL,MAAM,EACN,SAAS,EACT,aAAa,EACb,4BAA4B,GAC7B,MAAM,SAAS,CAAA;AAChB,OAAO,EACL,UAAU,EACV,aAAa,EACb,wBAAwB,GAEzB,MAAM,8BAA8B,CAAA;AAErC,SAAS,WAAW,CAAC,QAAkB;IACrC,OAAO,CAAC,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;AAC1D,CAAC;AAED,SAAS,WAAW,CAAC,IAAY;IAC/B,OAAO,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,WAAW,CAAA;AAC3E,CAAC;AAED,8DAA8D;AAC9D,SAAS,GAAG,CAAC,GAAQ,EAAE,MAAc,EAAE,IAAY,EAAE,KAAa;IAChE,IAAI,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAA;IAC9B,IAAI,OAAO,KAAK,SAAS,EAAE;QACzB,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,GAAG;YAC3B,KAAK,EAAE,CAAC;YACR,IAAI,EAAE,CAAC;YACP,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;SACP,CAAA;KACF;IACD,OAAO,CAAC,KAAK,EAAE,CAAA;IACf,OAAO,CAAC,MAAM,CAAC,EAAE,CAAA;AACnB,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,sBAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,YAAY,EAAE,iBAAiB,CAAC,CAAC,CAAA;QACpE,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,aAAa,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,UAAU;iBAC3B,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC;iBACzB,IAAI,CAAC,OAAO,EAAE,CAAC;iBACf,SAAS,EAAE,CAAA;YAEd,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,oBAAoB,CACvD,KAAK,EACL,MAAM,EACN,IAAI,CACL,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;gBAClC,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,KAAK,EAAE;oBACzB,IAAI,EAAE;wBACJ,KAAK,EAAE,GAAG,CAAC,KAAK;wBAChB,OAAO,EAAE,GAAG;wBACZ,KAAK;wBACL,GAAG,EAAE,KAAK,GAAG,CAAC;wBACd,OAAO,EAAE,MAAM,CAAC,OAAO;qBACxB;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,uCAAuC;YACvC,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE;gBAC9C,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG;oBACP,IAAI,EAAE;wBACJ,IAAI,EAAE,MAAM;wBACZ,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,GAAG,EAAE,IAAI,CAAC,GAAG;wBACb,MAAM,EAAE,IAAI,CAAC,MAAM;wBACnB,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,EAAE,EAAE,IAAI,CAAC,EAAE;qBACZ;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,OAAiB,EAAE,IAAkB;QAC9D,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,oBAAoB,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IACvD,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QACtC,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;IAExC,KAAK,CAAC,oBAAoB,CACxB,QAAmB,EACnB,MAAc,EACd,IAAoE;;QAEpE,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;QACxB,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;QAEnD,MAAM,OAAO,GAAG,EASf,CAAA;QAQD,MAAM,SAAS,GACb,QAAQ,CAAC,MAAM,IAAI,4BAA4B,CAAC,MAAA,IAAI,CAAC,OAAO,0CAAE,IAAI,CAAC;YACjE,CAAC,CAAC,MAAM,IAAI,CAAC,aAAa,CAAC,MAAM,CAAC;YAClC,CAAC,CAAC,SAAS,CAAA;QAEf,MAAM,IAAI,GAAG,EAYV,CAAA;QAEH,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACnC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAC/B,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAe,CAAA;YAEnD,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;gBACtC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;gBAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,MAAM,EAAE;oBACxB,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;wBACzB,IAAI,CAAC,CAAC,CAAC,GAAG;4BACR,KAAK,EAAE,CAAC;4BACR,GAAG,EAAE,CAAC;4BACN,GAAG,EAAE,CAAC;4BACN,IAAI,EAAE,CAAC;4BACP,GAAG,EAAE,CAAC;4BACN,GAAG,EAAE,CAAC;4BACN,OAAO,EAAE,EAAa;4BACtB,GAAG,EAAE,EAAa;4BAClB,QAAQ,EAAE,EAAa;4BACvB,MAAM,EAAE,EAAa;yBACtB,CAAA;qBACF;oBACD,IAAI,CAAC,KAAK,IAAI,EAAE;wBACd,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,EAAE,CAAA;wBACf,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;wBACb,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;wBACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;qBACnB;iBACF;aACF;YAED,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,EAAE;gBACrC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAW,CAAA;gBACxC,MAAM,EAAE,GAAI,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAY,IAAI,EAAE,CAAA;gBAC3D,MAAM,GAAG,GAAG,UAAU,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;gBAC5C,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;gBAE/B,wBAAwB,CAAC,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,CAAC,OAAO,CAChD,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,EAAE,EAAE;oBACtB,MAAM,GAAG,GAAG,OAAO,IAAI,EAAE,CAAA;oBACzB,KAAK,MAAM,GAAG,IAAI,aAAa,CAAC,GAAG,EAAE,SAAS,CAAC,EAAE;wBAC/C,MAAM,IAAI,GAAG,GAAG,GAAG,MAAM,GAAG,MAAM,CAAC,KAAK,CAAA;wBACxC,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,IAAI,CAAC,MAAM,IAAI,GAAG,GAAG,MAAM,GAAG,IAAI,EAAE;4BAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAA;4BACtB,IAAI,GAAG,EAAE;gCACP,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;6BAC9B;iCAAM;gCACL,OAAO,CAAC,IAAI,CACV,6DAA6D,CAC9D,CAAA;6BACF;yBACF;qBACF;gBACH,CAAC,CACF,CAAA;aACF;YAED,+DAA+D;YAC/D,mCAAmC;iBAC9B,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,EAAE;gBACxC,IAAI,CAAC,SAAS,EAAE;oBACd,MAAM,IAAI,KAAK,CACb,iEAAiE,CAClE,CAAA;iBACF;gBACD,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;gBAC9B,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAA;gBAC/C,MAAM,QAAQ,GAAG,IAAI,KAAK,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBAC7D,MAAM,GAAG,GAAG,UAAU,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;gBAE5C,wBAAwB,CAAC,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,CAAC,OAAO,CAChD,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,EAAE,EAAE;oBACtB,gCAAgC;oBAChC,IAAI,IAAI,KAAK,GAAG,EAAE;wBAChB,KAAK,MAAM,GAAG,IAAI,aAAa,CAAC,GAAG,EAAE,SAAS,CAAC,EAAE;4BAC/C,MAAM,IAAI,GAAG,GAAG,GAAG,MAAM,GAAG,MAAM,CAAC,KAAK,CAAA;4BACxC,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,QAAQ,CAAC,MAAM,EAAE;gCACvC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;6BACnB;yBACF;qBACF;gBACH,CAAC,CACF,CAAA;gBAED,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;oBAClC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;oBAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE;wBACjC,MAAM,EAAE,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;wBACrC,MAAM,EAAE,GAAG,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;wBACzC,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;wBACnB,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;wBAExB,QAAQ;wBACR,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;4BAC5B,IAAI,QAAQ,CAAC,CAAC,CAAC,IAAI,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE;gCAClC,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;gCAChC,GAAG,CAAC,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;gCACjC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gCACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;gCAClB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gCACjB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;6BACvB;iCAAM;gCACL,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,QAAQ,CAAC,CAAA;gCAClC,GAAG,CAAC,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,QAAQ,CAAC,CAAA;gCACnC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gCACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;gCAClB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gCACjB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;6BACvB;yBACF;qBACF;iBACF;aACF;YAED,4BAA4B;YAC5B,MAAM,UAAU,GAAI,OAAO,CAAC,GAAG,CAAC,YAAY,CAAgB,IAAI,EAAE,CAAA;YAClE,MAAM,SAAS,GACb,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,CAAA;YAEtE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBAC1C,MAAM,QAAQ,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;gBAC9B,MAAM,MAAM,GAAG,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAA;gBACtC,MAAM,IAAI,GAAG,WAAW,CAAC,QAAQ,CAAC,CAAA;gBAClC,MAAM,IAAI,GAAG,MAAM,GAAG,IAAI,CAAA;gBAC1B,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,MAAM,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;oBAC3C,MAAM,IAAI,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;oBAC7B,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,IAAI,CAAC,MAAM,EAAE;wBACnC,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAA;wBACtB,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,QAAQ,CAAA;wBAC/B,MAAM,SAAS,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;wBACnC,IAAI,CAAC,SAAS,EAAE;4BACd,GAAG,CAAC,GAAG,EAAE,CAAA;4BACT,GAAG,CAAC,OAAO,CAAC,EAAE,CAAA;yBACf;6BAAM;4BACL,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAA;yBAClC;wBAED,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,MAAM,EAAE;4BAC1C,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,UAAU,EAAE,IAAI,CAAC,CAAA;4BACnC,GAAG,CAAC,KAAK,EAAE,CAAA;yBACZ;6BAAM,IAAI,CAAC,SAAS,IAAI,SAAS,EAAE;4BAClC,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;4BAC9B,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,OAAO,CAAA;yBAC/B;qBACF;iBACF;gBAED,IAAI,QAAQ,CAAC,IAAI,KAAK,MAAM,EAAE;oBAC5B,MAAM,IAAI,GAAG,GAAG,MAAM,IAAI,IAAI,IAAI,OAAO,EAAE,CAAA;oBAC3C,IAAI,OAAO,CAAC,IAAI,CAAC,KAAK,SAAS,EAAE;wBAC/B,OAAO,CAAC,IAAI,CAAC,GAAG;4BACd,OAAO,EAAE,OAAO;4BAChB,KAAK,EAAE,MAAM;4BACb,GAAG,EAAE,IAAI;4BACT,MAAM,EAAE,OAAO;4BACf,EAAE,EAAE,MAAM,CAAC,OAAO,EAAE,IAAI,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,IAAI,CAAC;4BAClD,KAAK,EAAE,CAAC;yBACT,CAAA;qBACF;oBACD,OAAO,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,CAAA;iBACtB;aACF;SACF;QAED,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,CAAA;IAC1B,CAAC;CACF;AAED,MAAM,EAAE,YAAY,EAAE,GAAG,kBAAkB,CAAA;AAC3C,OAAO,EAAE,YAAY,EAAE,CAAA"}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { Feature } from '@jbrowse/core/util
|
|
1
|
+
import { Feature } from '@jbrowse/core/util';
|
|
2
2
|
import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
|
|
3
3
|
import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
|
|
4
4
|
export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"SNPCoverageRenderer.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/SNPCoverageRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AACrD,OAAO,EAAE,aAAa,EAAE,QAAQ,
|
|
1
|
+
{"version":3,"file":"SNPCoverageRenderer.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/SNPCoverageRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AACrD,OAAO,EAAE,aAAa,EAAE,QAAQ,EAAW,MAAM,oBAAoB,CAAA;AACrE,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAE5D,OAAO,EACL,SAAS,EACT,QAAQ,EAER,kBAAkB,EAClB,sBAAsB,GACvB,MAAM,wBAAwB,CAAA;AA2B/B,MAAM,CAAC,OAAO,OAAO,mBAAoB,SAAQ,kBAAkB;IACjE,4EAA4E;IAC5E,kDAAkD;IAClD,KAAK,CAAC,IAAI,CACR,GAA6B,EAC7B,KAAyC;QAEzC,MAAM,EACJ,QAAQ,EACR,OAAO,EACP,OAAO,EACP,mBAAmB,EACnB,kBAAkB,GAAG,EAAE,EACvB,SAAS,EACT,MAAM,EAAE,gBAAgB,EACxB,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,GAAG,EACX,KAAK,GACN,GAAG,KAAK,CAAA;QACT,MAAM,KAAK,GAAG,kBAAkB,CAAC,WAAW,CAAC,CAAA;QAC7C,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;QACxB,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QAEnD,yEAAyE;QACzE,oEAAoE;QACpE,iDAAiD;QACjD,MAAM,MAAM,GAAG,sBAAsB,CAAA;QACrC,MAAM,MAAM,GAAG,gBAAgB,GAAG,MAAM,GAAG,CAAC,CAAA;QAE5C,MAAM,EAAE,MAAM,EAAE,GAAG,SAAS,CAAA;QAC5B,IAAI,CAAC,MAAM,EAAE;YACX,OAAM;SACP;QACD,MAAM,IAAI,GAAG,EAAE,GAAG,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,CAAC,EAAE,CAAA;QACjD,MAAM,SAAS,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;QAEhC,mEAAmE;QACnE,MAAM,kBAAkB,GAAG,QAAQ,CAAC;YAClC,GAAG,IAAI;YACP,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,GAAG,CAAC,CAAC;YACtB,SAAS,EAAE,QAAQ;SACpB,CAAC,CAAA;QACF,MAAM,OAAO,GAAG,SAAS,CAAC,SAAS,CAAC,SAAS,CAAC,CAAA;QAE9C,MAAM,kBAAkB,GAAG,cAAc,CAAC,GAAG,EAAE,oBAAoB,CAAC,CAAA;QACpE,MAAM,mBAAmB,GAAG,cAAc,CAAC,GAAG,EAAE,qBAAqB,CAAC,CAAA;QACtE,MAAM,QAAQ,GAAG,cAAc,CAAC,GAAG,EAAE,UAAU,CAAC,CAAA;QAChD,MAAM,cAAc,GAAG,cAAc,CAAC,GAAG,EAAE,gBAAgB,CAAC,CAAA;QAE5D,sEAAsE;QACtE,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,MAAM,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAChE,MAAM,QAAQ,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;QAErD,MAAM,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CACjC,MAAM,GAAG,CAAC,kBAAkB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAChD,MAAM,iBAAiB,GAAG,CAAC,CAAS,EAAE,EAAE,CACtC,YAAY,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAC,GAAG,YAAY,CAAC,CAAC,CAAC,CAAA;QAErD,aAAa;QACb,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,OAAO,CAAA;QAC/B,MAAM,YAAY,GAA8B;YAC9C,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,KAAK,EAAE,WAAW;YAClB,SAAS,EAAE,QAAQ;YACnB,QAAQ,EAAE,MAAM;YAChB,QAAQ,EAAE,KAAK;YACf,IAAI,EAAE,KAAK;YACX,MAAM,EAAE,MAAM;YACd,GAAG,EAAE,WAAW;SACjB,CAAA;QAED,MAAM,KAAK,GAAG,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;QACpC,MAAM,QAAQ,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAC5D,MAAM,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAEzD,wEAAwE;QACxE,+CAA+C;QAC/C,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,KAAK,CAAA;QAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YACjE,MAAM,CAAC,GAAG,OAAO,GAAG,MAAM,GAAG,GAAG,CAAA;YAChC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAA;SACrD;QAED,0EAA0E;QAC1E,2EAA2E;QAC3E,0EAA0E;QAC1E,0EAA0E;QAC1E,wEAAwE;QACxE,IAAI,SAAS,GAAG,CAAC,CAAA;QAEjB,wEAAwE;QACxE,+DAA+D;QAC/D,MAAM,8BAA8B,GAAG,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAExE,yEAAyE;QACzE,yEAAyE;QACzE,oCAAoC;QAEpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YAEjE,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAY,CAAA;YACjD,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,GAAG,MAAM,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;YAC7C,MAAM,UAAU,GAAG,OAAO,CAAC,KAAK,CAAA;YAChC,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAA;YAE5C,IAAI,IAAI,GAAG,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACpC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;gBACpB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;gBACnC,GAAG,CAAC,SAAS;oBACX,YAAY,CAAC,IAAI,CAAC;wBAClB,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;wBAC5C,MAAM,CAAA;gBAER,MAAM,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;gBAC9B,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,MAAM,CAAA;gBAClC,GAAG,CAAC,QAAQ,CACV,MAAM,EACN,MAAM,GAAG,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,KAAK,CAAC,GAAG,MAAM,EAC1C,CAAC,EACD,CAAC,KAAK,GAAG,KAAK,CAAC,GAAG,MAAM,CACzB,CAAA;gBACD,IAAI,IAAI,KAAK,CAAA;aACd;YAED,MAAM,eAAe,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YACnD,MAAM,eAAe,GAAG,GAAG,CAAA;YAC3B,IAAI,mBAAmB,EAAE;gBACvB,IAAI,IAAI,GAAG,CAAC,CAAA;gBACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/C,MAAM,IAAI,GAAG,eAAe,CAAC,CAAC,CAAC,CAAA;oBAC/B,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;oBACtC,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;oBAClC,GAAG,CAAC,QAAQ,CACV,MAAM,GAAG,GAAG,GAAG,8BAA8B,EAC7C,eAAe,GAAG,iBAAiB,CAAC,IAAI,CAAC,EACzC,GAAG,EACH,iBAAiB,CAAC,KAAK,CAAC,CACzB,CAAA;oBACD,IAAI,IAAI,KAAK,CAAA;iBACd;aACF;YAED,IAAI,cAAc,EAAE;gBAClB,IAAI,KAAK,GAAG,CAAC,CAAA;gBACb,IAAI,GAAG,GAAG,CAAC,CAAA;gBACX,IAAI,OAAO,GAAG,EAAE,CAAA;gBAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/C,MAAM,IAAI,GAAG,eAAe,CAAC,CAAC,CAAC,CAAA;oBAC/B,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;oBACtC,KAAK,IAAI,KAAK,CAAA;oBACd,IAAI,KAAK,GAAG,GAAG,EAAE;wBACf,GAAG,GAAG,KAAK,CAAA;wBACX,OAAO,GAAG,IAAI,CAAA;qBACf;iBACF;gBAED,mEAAmE;gBACnE,8DAA8D;gBAC9D,MAAM,wBAAwB,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,EAAE,SAAS,CAAC,CAAA;gBAChE,IACE,KAAK,GAAG,wBAAwB,GAAG,kBAAkB;oBACrD,wBAAwB,GAAG,CAAC,EAC5B;oBACA,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;oBACrC,GAAG,CAAC,SAAS,EAAE,CAAA;oBACf,MAAM,CAAC,GAAG,MAAM,GAAG,8BAA8B,CAAA;oBACjD,GAAG,CAAC,MAAM,CAAC,CAAC,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;oBACtB,GAAG,CAAC,MAAM,CAAC,CAAC,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;oBACtB,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,eAAe,CAAC,CAAA;oBAC9B,GAAG,CAAC,IAAI,EAAE,CAAA;iBACX;aACF;YACD,SAAS,GAAG,UAAU,CAAA;SACvB;QAED,IAAI,QAAQ,EAAE;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACrC,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;gBAClB,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,GAAG,QAAQ,CAC5B,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EACd,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EACZ,MAAM,EACN,OAAO,CACR,CAAA;gBAED,GAAG,CAAC,SAAS,EAAE,CAAA;gBACf,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAW,CAAA;gBACrC,MAAM,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,IAAI,CAAW,CAAA;gBAChC,MAAM,GAAG,GAAG,uBAAuB,CAAA;gBACnC,MAAM,GAAG,GAAG,uBAAuB,CAAA;gBACnC,MAAM,OAAO,GAAG,uBAAuB,CAAA;gBAEvC,IAAI,EAAE,KAAK,GAAG,EAAE;oBACd,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM,IAAI,EAAE,KAAK,GAAG,EAAE;oBACrB,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM,IAAI,GAAG,KAAK,CAAC,EAAE;oBACpB,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM,IAAI,GAAG,KAAK,CAAC,CAAC,EAAE;oBACrB,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM;oBACL,GAAG,CAAC,WAAW,GAAG,OAAO,CAAA;iBAC1B;gBAED,GAAG,CAAC,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAA;gBAC5C,GAAG,CAAC,MAAM,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAC,CAAA;gBACrC,GAAG,CAAC,aAAa,CAAC,IAAI,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAC,CAAA;gBAChE,GAAG,CAAC,MAAM,EAAE,CAAA;aACb;SACF;QAED,IAAI,mBAAmB,EAAE;YACvB,GAAG,CAAC,SAAS,GAAG,CAAC,CAAA;YACjB,GAAG,CAAC,WAAW,GAAG,uBAAuB,CAAA;YACzC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;gBAC1B,GAAG,CAAC,SAAS,EAAE,CAAA;gBACf,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACpC,GAAG,CAAC,MAAM,CAAC,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACxC,GAAG,CAAC,MAAM,EAAE,CAAA;YACd,CAAC,CAAC,CAAA;SACH;IACH,CAAC;CACF"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-alignments",
|
|
3
|
-
"version": "2.0
|
|
3
|
+
"version": "2.1.0",
|
|
4
4
|
"description": "JBrowse 2 alignments adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -44,7 +44,7 @@
|
|
|
44
44
|
"color": "^3.1.2",
|
|
45
45
|
"copy-to-clipboard": "^3.3.1",
|
|
46
46
|
"fast-deep-equal": "^3.1.3",
|
|
47
|
-
"generic-filehandle": "^
|
|
47
|
+
"generic-filehandle": "^3.0.0"
|
|
48
48
|
},
|
|
49
49
|
"peerDependencies": {
|
|
50
50
|
"@jbrowse/core": "^2.0.0",
|
|
@@ -65,5 +65,5 @@
|
|
|
65
65
|
"distModule": "esm/index.js",
|
|
66
66
|
"srcModule": "src/index.ts",
|
|
67
67
|
"module": "esm/index.js",
|
|
68
|
-
"gitHead": "
|
|
68
|
+
"gitHead": "0db0462fa1f9f15ab4869da085bcab032b9483c3"
|
|
69
69
|
}
|
|
@@ -105,7 +105,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
|
|
|
105
105
|
return this.samHeader
|
|
106
106
|
}
|
|
107
107
|
|
|
108
|
-
|
|
108
|
+
async setup(opts?: BaseOptions) {
|
|
109
109
|
if (!this.setupP) {
|
|
110
110
|
this.setupP = this.setupPre(opts).catch(e => {
|
|
111
111
|
this.setupP = undefined
|
|
@@ -34,6 +34,7 @@ import FilterListIcon from '@mui/icons-material/ClearAll'
|
|
|
34
34
|
import { LinearPileupDisplayConfigModel } from './configSchema'
|
|
35
35
|
import LinearPileupDisplayBlurb from './components/LinearPileupDisplayBlurb'
|
|
36
36
|
import { getUniqueTagValues, getUniqueModificationValues } from '../shared'
|
|
37
|
+
import { SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature'
|
|
37
38
|
|
|
38
39
|
// async
|
|
39
40
|
const ColorByTagDlg = lazy(() => import('./components/ColorByTag'))
|
|
@@ -529,10 +530,9 @@ const stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>
|
|
|
529
530
|
layoutId: getContainingView(self).id,
|
|
530
531
|
rendererType: 'PileupRenderer',
|
|
531
532
|
},
|
|
532
|
-
)) as { feature:
|
|
533
|
+
)) as { feature: SimpleFeatureSerialized }
|
|
533
534
|
|
|
534
535
|
if (feature) {
|
|
535
|
-
// @ts-ignore
|
|
536
536
|
self.setContextMenuFeature(new SimpleFeature(feature))
|
|
537
537
|
}
|
|
538
538
|
}
|
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
/* eslint-disable @typescript-eslint/no-explicit-any */
|
|
2
1
|
import React from 'react'
|
|
3
2
|
import { observer } from 'mobx-react'
|
|
4
3
|
import { Feature } from '@jbrowse/core/util/simpleFeature'
|
|
@@ -31,8 +30,8 @@ const en = (n: number) => n.toLocaleString('en-US')
|
|
|
31
30
|
const toP = (s = 0) => +(+s).toFixed(1)
|
|
32
31
|
const pct = (n: number, total: number) => `${toP((n / (total || 1)) * 100)}%`
|
|
33
32
|
|
|
34
|
-
const TooltipContents = React.forwardRef(
|
|
35
|
-
({ feature }
|
|
33
|
+
const TooltipContents = React.forwardRef<HTMLDivElement, { feature: Feature }>(
|
|
34
|
+
({ feature }, reactRef) => {
|
|
36
35
|
const start = feature.get('start')
|
|
37
36
|
const end = feature.get('end')
|
|
38
37
|
const name = feature.get('refName')
|
|
@@ -109,7 +108,7 @@ type Coord = [number, number]
|
|
|
109
108
|
|
|
110
109
|
const SNPCoverageTooltip = observer(
|
|
111
110
|
(props: {
|
|
112
|
-
model:
|
|
111
|
+
model: { featureUnderMouse: Feature }
|
|
113
112
|
height: number
|
|
114
113
|
offsetMouseCoord: Coord
|
|
115
114
|
clientMouseCoord: Coord
|
|
@@ -7,12 +7,14 @@ import {
|
|
|
7
7
|
AnyConfigurationModel,
|
|
8
8
|
} from '@jbrowse/core/configuration'
|
|
9
9
|
import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle'
|
|
10
|
+
import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
|
|
10
11
|
|
|
11
12
|
import PluginManager from '@jbrowse/core/PluginManager'
|
|
12
13
|
import { getContainingView } from '@jbrowse/core/util'
|
|
14
|
+
|
|
15
|
+
// locals
|
|
13
16
|
import Tooltip from '../components/Tooltip'
|
|
14
17
|
import { getUniqueModificationValues } from '../../shared'
|
|
15
|
-
import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
|
|
16
18
|
|
|
17
19
|
// using a map because it preserves order
|
|
18
20
|
const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']])
|
|
@@ -1292,23 +1292,19 @@ export default class PileupRenderer extends BoxRendererType {
|
|
|
1292
1292
|
const width = (end - start) / bpPerPx
|
|
1293
1293
|
const height = Math.max(layout.getTotalHeight(), 1)
|
|
1294
1294
|
const Color = await import('color').then(f => f.default)
|
|
1295
|
-
const res = await renderToAbstractCanvas(
|
|
1296
|
-
|
|
1297
|
-
|
|
1298
|
-
|
|
1299
|
-
|
|
1300
|
-
|
|
1301
|
-
|
|
1302
|
-
|
|
1303
|
-
|
|
1304
|
-
|
|
1305
|
-
|
|
1306
|
-
|
|
1307
|
-
|
|
1308
|
-
regionSequence,
|
|
1309
|
-
Color,
|
|
1310
|
-
},
|
|
1311
|
-
}),
|
|
1295
|
+
const res = await renderToAbstractCanvas(width, height, renderProps, ctx =>
|
|
1296
|
+
this.makeImageData({
|
|
1297
|
+
ctx,
|
|
1298
|
+
layoutRecords,
|
|
1299
|
+
canvasWidth: width,
|
|
1300
|
+
renderArgs: {
|
|
1301
|
+
...renderProps,
|
|
1302
|
+
layout,
|
|
1303
|
+
features,
|
|
1304
|
+
regionSequence,
|
|
1305
|
+
Color,
|
|
1306
|
+
},
|
|
1307
|
+
}),
|
|
1312
1308
|
)
|
|
1313
1309
|
|
|
1314
1310
|
const results = await super.render({
|
|
@@ -88,14 +88,15 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
|
|
|
88
88
|
)
|
|
89
89
|
|
|
90
90
|
bins.forEach((bin, index) => {
|
|
91
|
+
const start = region.start + index
|
|
91
92
|
observer.next(
|
|
92
93
|
new SimpleFeature({
|
|
93
|
-
id: `${this.id}-${
|
|
94
|
+
id: `${this.id}-${start}`,
|
|
94
95
|
data: {
|
|
95
96
|
score: bin.total,
|
|
96
97
|
snpinfo: bin,
|
|
97
|
-
start
|
|
98
|
-
end:
|
|
98
|
+
start,
|
|
99
|
+
end: start + 1,
|
|
99
100
|
refName: region.refName,
|
|
100
101
|
},
|
|
101
102
|
}),
|
|
@@ -1,6 +1,5 @@
|
|
|
1
1
|
import { createJBrowseTheme } from '@jbrowse/core/ui'
|
|
2
|
-
import { featureSpanPx, bpSpanPx } from '@jbrowse/core/util'
|
|
3
|
-
import { Feature } from '@jbrowse/core/util/simpleFeature'
|
|
2
|
+
import { featureSpanPx, bpSpanPx, Feature } from '@jbrowse/core/util'
|
|
4
3
|
import { readConfObject } from '@jbrowse/core/configuration'
|
|
5
4
|
import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'
|
|
6
5
|
import {
|