@jbrowse/plugin-variants 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/VcfTabixAdapter/VcfFeature.js +1 -1
- package/dist/VcfTabixAdapter/VcfFeature.js.map +1 -1
- package/dist/VcfTabixAdapter/VcfTabixAdapter.js +1 -6
- package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map +1 -1
- package/esm/VcfTabixAdapter/VcfFeature.js +1 -1
- package/esm/VcfTabixAdapter/VcfFeature.js.map +1 -1
- package/esm/VcfTabixAdapter/VcfTabixAdapter.js +1 -7
- package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map +1 -1
- package/package.json +3 -3
- package/src/VcfTabixAdapter/VcfFeature.ts +1 -1
- package/src/VcfTabixAdapter/VcfTabixAdapter.ts +1 -7
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@@ -89,7 +89,7 @@ var VCFFeature = /** @class */ (function () {
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VCFFeature.prototype._getSOTermAndDescription = function (ref, alt) {
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var _this = this;
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// it's just a remark if there are no alternate alleles
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-
if (!alt || alt ===
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92
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+
if (!alt || alt.length === 0) {
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return ['remark', 'no alternative alleles'];
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}
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var soTerms = new Set();
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"VcfFeature.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfFeature.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,iCAAyC;AAyBzC;IAWE,8DAA8D;IAC9D,oBAAY,IAA+C;QACzD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC9C,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAA;IACpB,CAAC;IAED,8DAA8D;IAC9D,wBAAG,GAAH,UAAI,KAAa;QACf,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO;YACtB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC7C,CAAC;IAED,wBAAG,GAAH,cAAa,CAAC;IAEd,2BAAM,GAAN;QACE,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,6BAAQ,GAAR;QACE,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,yBAAI,GAAJ;QACE,IAAM,CAAC,wDACF,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,kBACtB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC;YAC5B,SAAS;iBACV,CAAA;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,uBAAE,GAAF;QACE,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,oCAAe,GAAf,UAAgB,OAOf;QACS,IAAA,GAAG,GAAgC,OAAO,IAAvC,EAAE,GAAG,GAA2B,OAAO,IAAlC,EAAE,GAAG,GAAsB,OAAO,IAA7B,EAAE,KAAK,GAAe,OAAO,MAAtB,EAAE,IAAI,GAAS,OAAO,KAAhB,EAAE,EAAE,GAAK,OAAO,GAAZ,CAAY;QAClD,IAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACf,IAAA,KAAA,OAAyB,IAAI,CAAC,wBAAwB,CAAC,GAAG,EAAE,GAAG,CAAC,IAAA,EAA/D,OAAO,QAAA,EAAE,WAAW,QAA2C,CAAA;QACtE,IAAM,KAAK,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,KAAK,OAAO,EAAb,CAAa,CAAC,CAAA;QAC3C,IAAM,UAAU,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAArB,CAAqB,CAAC,CAAA;QAExD,OAAO;YACL,OAAO,EAAE,KAAK;YACd,KAAK,OAAA;YACL,GAAG,EAAE,UAAU,IAAI,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,MAAM;YACzE,WAAW,aAAA;YACX,IAAI,EAAE,OAAO;YACb,IAAI,EAAE,EAAE,aAAF,EAAE,uBAAF,EAAE,CAAE,IAAI,CAAC,GAAG,CAAC;YACnB,OAAO,EAAE,EAAE,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS;SAC/D,CAAA;IACH,CAAC;IAED;;OAEG;IACH,6CAAwB,GAAxB,UACE,GAAW,EACX,GAAa;QAFf,iBAmDC;QA/CC,uDAAuD;QACvD,IAAI,CAAC,GAAG,IAAI,GAAG,KAAK,
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1
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+
{"version":3,"file":"VcfFeature.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfFeature.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,iCAAyC;AAyBzC;IAWE,8DAA8D;IAC9D,oBAAY,IAA+C;QACzD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC9C,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAA;IACpB,CAAC;IAED,8DAA8D;IAC9D,wBAAG,GAAH,UAAI,KAAa;QACf,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO;YACtB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC7C,CAAC;IAED,wBAAG,GAAH,cAAa,CAAC;IAEd,2BAAM,GAAN;QACE,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,6BAAQ,GAAR;QACE,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,yBAAI,GAAJ;QACE,IAAM,CAAC,wDACF,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,kBACtB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC;YAC5B,SAAS;iBACV,CAAA;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,uBAAE,GAAF;QACE,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,oCAAe,GAAf,UAAgB,OAOf;QACS,IAAA,GAAG,GAAgC,OAAO,IAAvC,EAAE,GAAG,GAA2B,OAAO,IAAlC,EAAE,GAAG,GAAsB,OAAO,IAA7B,EAAE,KAAK,GAAe,OAAO,MAAtB,EAAE,IAAI,GAAS,OAAO,KAAhB,EAAE,EAAE,GAAK,OAAO,GAAZ,CAAY;QAClD,IAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACf,IAAA,KAAA,OAAyB,IAAI,CAAC,wBAAwB,CAAC,GAAG,EAAE,GAAG,CAAC,IAAA,EAA/D,OAAO,QAAA,EAAE,WAAW,QAA2C,CAAA;QACtE,IAAM,KAAK,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,KAAK,OAAO,EAAb,CAAa,CAAC,CAAA;QAC3C,IAAM,UAAU,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAArB,CAAqB,CAAC,CAAA;QAExD,OAAO;YACL,OAAO,EAAE,KAAK;YACd,KAAK,OAAA;YACL,GAAG,EAAE,UAAU,IAAI,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,MAAM;YACzE,WAAW,aAAA;YACX,IAAI,EAAE,OAAO;YACb,IAAI,EAAE,EAAE,aAAF,EAAE,uBAAF,EAAE,CAAE,IAAI,CAAC,GAAG,CAAC;YACnB,OAAO,EAAE,EAAE,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS;SAC/D,CAAA;IACH,CAAC;IAED;;OAEG;IACH,6CAAwB,GAAxB,UACE,GAAW,EACX,GAAa;QAFf,iBAmDC;QA/CC,uDAAuD;QACvD,IAAI,CAAC,GAAG,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;YAC5B,OAAO,CAAC,QAAQ,EAAE,wBAAwB,CAAC,CAAA;SAC5C;QAED,IAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAA;QACjC,IAAI,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;QACpC,GAAG,CAAC,OAAO,CAAC,UAAA,CAAC;;YACP,IAAA,KAAA,OAAwB,KAAI,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,IAAA,EAA5D,MAAM,QAAA,EAAE,WAAW,QAAyC,CAAA;YAEjE,IAAI,CAAC,MAAM,EAAE;gBACX,CAAC;gBAAA,KAAA,OAAwB,KAAI,CAAC,0BAA0B,CAAC,GAAG,EAAE,CAAC,CAAC,IAAA,EAA9D,MAAM,QAAA,EAAE,WAAW,QAAA,CAA2C;aACjE;YACD,IAAI,MAAM,IAAI,WAAW,EAAE;gBACzB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;gBACnB,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,CAAA;aAC9B;QACH,CAAC,CAAC,CAAA;QAEF,6EAA6E;QAC7E,IAAI,YAAY,CAAC,IAAI,GAAG,CAAC,EAAE;YACzB,IAAM,QAAQ,GAAG,IAAI,GAAG,CACtB,yBAAI,YAAY,UAAE,GAAG,CAAC,UAAA,IAAI;gBACxB,IAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;YACrC,CAAC,CAAC,CACH,CAAA;YAED,IAAM,SAAS,GAAG,yBAAI,QAAQ,UAAE,GAAG,CAAC,UAAA,MAAM;gBACxC,IAAM,QAAQ,GAAG,yBAAI,YAAY,UAC9B,GAAG,CAAC,UAAA,IAAI;oBACP,IAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;oBAC9B,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;gBACrD,CAAC,CAAC;qBACD,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,EAAH,CAAG,CAAC,CAAA;gBAEnB,OAAO,QAAQ,CAAC,MAAM;oBACpB,CAAC,CAAC,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC;oBACrC,CAAC,CAAC,yBAAI,YAAY,UAAE,IAAI,CAAC,GAAG,CAAC,CAAA;YACjC,CAAC,CAAC,CAAA;YAEF,YAAY,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,CAAA;SAClC;QACD,IAAI,OAAO,CAAC,IAAI,EAAE;YAChB,OAAO,CAAC,yBAAI,OAAO,UAAE,IAAI,CAAC,GAAG,CAAC,EAAE,yBAAI,YAAY,UAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;SAC7D;QACD,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;IAC/B,CAAC;IAeD,6CAAwB,GAAxB,UACE,GAAW,EACX,GAAW;QAEX,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACnD,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;SAC9B;QAED,iDAAiD;QACjD,IAAI,MAAM,GAAG,UAAU,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;QACzC,gEAAgE;QAChE,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE;YAClD,MAAM,GAAG,kBAAkB,CAAA;SAC5B;QACD,IAAI,MAAM,EAAE;YACV,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;SACrB;QAED,2DAA2D;QAC3D,IAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC7B,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE;YACrB,OAAO,IAAI,CAAC,wBAAwB,CAClC,GAAG,EACH,WAAI,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,MAAG,CACpD,CAAA;SACF;QAED,YAAY;QACZ,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;IAC/B,CAAC;IAED,0EAA0E;IAC1E,yEAAyE;IACzE,OAAO;IACP,+CAA0B,GAA1B,UAA2B,GAAW,EAAE,GAAW;QACjD,IAAM,GAAG,GAAG,IAAA,mBAAa,EAAC,GAAG,CAAC,CAAA;QAC9B,IAAI,GAAG,EAAE;YACP,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;YAC/C,OAAO,CAAC,KAAK,EAAE,IAAI,CAAC,sBAAsB,CAAC,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SAC7D;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,WAAW,EAAE,GAAG,CAAC,CAAA;SAC1B;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,eAAe,EAAE,GAAG,CAAC,CAAA;SAC9B;aAAM,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE;YAC5B,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;SACnB;aAAM,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,CAAC,MAAM,EAAE;YACpC,IAAI,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,GAAG,EAAE;gBAC5C,OAAO,CAAC,WAAW,EAAE,IAAI,CAAC,sBAAsB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;aACzE;YACD,OAAO;gBACL,cAAc;gBACd,IAAI,CAAC,sBAAsB,CAAC,cAAc,EAAE,GAAG,EAAE,GAAG,CAAC;aACtD,CAAA;SACF;aAAM,IAAI,GAAG,CAAC,MAAM,IAAI,GAAG,CAAC,MAAM,EAAE;YACnC,OAAO,CAAC,WAAW,EAAE,IAAI,CAAC,sBAAsB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SACzE;aAAM,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE;YAClC,OAAO,CAAC,UAAU,EAAE,IAAI,CAAC,sBAAsB,CAAC,UAAU,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SACvE;QAED,OAAO,CAAC,OAAO,EAAE,IAAI,CAAC,sBAAsB,CAAC,OAAO,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;IAClE,CAAC;IAED,2CAAsB,GAAtB,UAAuB,MAAc,EAAE,GAAW,EAAE,GAAW;QAC7D,OAAO,UAAG,MAAM,cAAI,GAAG,iBAAO,GAAG,CAAE,CAAA;IACrC,CAAC;IAED,8DAA8D;IAC9D,2BAAM,GAAN;QACE,oCACE,QAAQ,EAAE,IAAI,CAAC,GAAG,IACf,IAAI,CAAC,OAAO,GACZ,IAAI,CAAC,IAAI,KACZ,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,OAAO,IAC9B;IACH,CAAC;IA5FM,uBAAY,GAA0C;QAC3D,GAAG,EAAE,UAAU;QACf,GAAG,EAAE,WAAW;QAChB,GAAG,EAAE,aAAa;QAClB,GAAG,EAAE,WAAW;QAChB,MAAM,EAAE,sBAAsB;QAC9B,GAAG,EAAE,uBAAuB;QAC5B,GAAG,EAAE,eAAe;QACpB,YAAY,EAAE,oBAAoB;QAClC,OAAO,EAAE,kBAAkB;QAC3B,GAAG,EAAE,kBAAkB;KACxB,CAAA;IAkFH,iBAAC;CAAA,AA/ND,IA+NC;kBA/NoB,UAAU"}
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{"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uEAGgD;AAMhD,4CAAoD;AACpD,2CAAoD;AACpD,gDAA0D;AAE1D,qCAA8C;AAC9C,kDAAiC;AAEjC,6DAA4D;AAC5D,4DAAqC;AAGrC;IAA6B,6BAAsB;IAAnD;;
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+
{"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uEAGgD;AAMhD,4CAAoD;AACpD,2CAAoD;AACpD,gDAA0D;AAE1D,qCAA8C;AAC9C,kDAAiC;AAEjC,6DAA4D;AAC5D,4DAAqC;AAGrC;IAA6B,6BAAsB;IAAnD;;IA0HA,CAAC;IAnHe,gCAAY,GAA1B;;;;;;wBACQ,aAAa,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;wBAC5D,QAAQ,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;wBAC7D,SAAS,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;wBAE/D,UAAU,GAAG,IAAA,iBAAY,EAC7B,aAA6B,EAC7B,IAAI,CAAC,aAAa,CACnB,CAAA;wBACK,KAAK,GAAG,SAAS,KAAK,KAAK,CAAA;wBAC3B,GAAG,GAAG,IAAI,wBAAgB,CAAC;4BAC/B,UAAU,YAAA;4BACV,aAAa,EAAE,KAAK;gCAClB,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gCAC5C,CAAC,CAAC,SAAS;4BACb,aAAa,EAAE,CAAC,KAAK;gCACnB,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gCAC5C,CAAC,CAAC,SAAS;4BACb,cAAc,EAAE,EAAE,GAAG,SAAA,CAAC,EAAI,EAAE,CAAA;4BAC5B,cAAc,EAAE,UAAU;yBAC3B,CAAC,CAAA;wBAEa,qBAAM,GAAG,CAAC,SAAS,EAAE,EAAA;;wBAA9B,MAAM,GAAG,SAAqB;wBACpC,sBAAO;gCACL,UAAU,YAAA;gCACV,GAAG,KAAA;gCACH,MAAM,EAAE,IAAI,aAAS,CAAC,EAAE,MAAM,QAAA,EAAE,CAAC;6BAClC,EAAA;;;;KACF;IAEe,6BAAS,GAAzB;;;;gBACE,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;oBACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,UAAA,CAAC;wBAC3C,KAAI,CAAC,UAAU,GAAG,SAAS,CAAA;wBAC3B,MAAM,CAAC,CAAA;oBACT,CAAC,CAAC,CAAA;iBACH;gBACD,sBAAO,IAAI,CAAC,UAAU,EAAA;;;KACvB;IAEY,+BAAW,GAAxB,UAAyB,IAAsB;QAAtB,qBAAA,EAAA,SAAsB;;;;;4BAC7B,qBAAM,IAAI,CAAC,SAAS,EAAE,EAAA;;wBAA9B,GAAG,GAAK,CAAA,SAAsB,CAAA,IAA3B;wBACX,sBAAO,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,EAAA;;;;KAC3C;IAEK,6BAAS,GAAf;;;;;4BACkB,qBAAM,IAAI,CAAC,SAAS,EAAE,EAAA;;wBAA9B,GAAG,GAAK,CAAA,SAAsB,CAAA,IAA3B;wBACX,sBAAO,GAAG,CAAC,SAAS,EAAE,EAAA;;;;KACvB;IAEK,+BAAW,GAAjB;;;;;4BACqB,qBAAM,IAAI,CAAC,SAAS,EAAE,EAAA;;wBAAjC,MAAM,GAAK,CAAA,SAAsB,CAAA,OAA3B;wBACd,sBAAO,MAAM,CAAC,WAAW,EAAE,EAAA;;;;KAC5B;IAEM,+BAAW,GAAlB,UAAmB,KAAuB,EAAE,IAAsB;QAAlE,iBAkBC;QAlB2C,qBAAA,EAAA,SAAsB;QAChE,OAAO,IAAA,uBAAgB,EAAU,UAAM,QAAQ;;;;;;wBACrC,OAAO,GAAiB,KAAK,QAAtB,EAAE,KAAK,GAAU,KAAK,MAAf,EAAE,GAAG,GAAK,KAAK,IAAV,CAAU;wBACb,qBAAM,IAAI,CAAC,SAAS,EAAE,EAAA;;wBAAxC,KAAkB,SAAsB,EAAtC,GAAG,SAAA,EAAE,MAAM,YAAA;wBACnB,qBAAM,GAAG,CAAC,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,aACpC,YAAY,EAAE,UAAC,IAAY,EAAE,UAAkB;oCAC7C,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAU,CAAC;wCACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;wCAC/B,MAAM,QAAA;wCACN,EAAE,EAAE,UAAG,KAAI,CAAC,EAAE,kBAAQ,UAAU,CAAE;qCACnC,CAAC,CACH,CAAA;gCACH,CAAC,IACE,IAAI,EACP,EAAA;;wBAXF,SAWE,CAAA;wBACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;;;;aACpB,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED;;;;;;;;;;;;;OAaG;IACI,gDAA4B,GAAnC,UACE,OAAiB,EACjB,IAAsB;QAFxB,iBAuBC;QArBC,qBAAA,EAAA,SAAsB;QAEtB,OAAO,IAAA,uBAAgB,EAAU,UAAO,QAA2B;;;;4BACjD,qBAAM,IAAI,CAAC,SAAS,EAAE;wBAEtC,aAAa;sBAFyB;;wBAA9B,GAAG,GAAK,CAAA,SAAsB,CAAA,IAA3B;wBAGG,qBAAM,IAAA,sBAAe,EAAC,OAAO,EAAE,GAAG,CAAC,KAAK,CAAC,EAAA;;wBAAjD,KAAK,GAAG,SAAyC;wBAChC,qBAAM,IAAI,CAAC,SAAS,EAAE,EAAA;;wBAArC,UAAU,GAAK,CAAA,SAAsB,CAAA,WAA3B;wBACL,qBAAM,UAAU,CAAC,IAAI,EAAE,EAAA;;wBAA9B,IAAI,GAAG,SAAuB;wBAChC,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,CAAC,CAAA;wBAC/C,IAAI,GAAG,GAAG,GAAG,EAAE;4BACb,yDAAyD;4BACzD,GAAG,GAAG,GAAG,CAAA;yBACV;wBACD,IAAI,GAAG,GAAG,EAAE,EAAE;4BACZ,OAAO,CAAC,IAAI,CACV,gDAAyC,GAAG,gEAA6D,CAC1G,CAAA;yBACF;wBACD,iBAAM,4BAA4B,YAAC,OAAO,EAAE,IAAI,CAAC,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;;;;aACtE,CAAC,CAAA;IACJ,CAAC;IAEM,iCAAa,GAApB,WAAqB,gBAAgB,IAAS,CAAC;IACjD,gBAAC;AAAD,CAAC,AA1HD,CAA6B,oCAAsB,GA0HlD"}
|
|
@@ -52,7 +52,7 @@ export default class VCFFeature {
|
|
|
52
52
|
*/
|
|
53
53
|
_getSOTermAndDescription(ref, alt) {
|
|
54
54
|
// it's just a remark if there are no alternate alleles
|
|
55
|
-
if (!alt || alt ===
|
|
55
|
+
if (!alt || alt.length === 0) {
|
|
56
56
|
return ['remark', 'no alternative alleles'];
|
|
57
57
|
}
|
|
58
58
|
const soTerms = new Set();
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"VcfFeature.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfFeature.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AAyBzC,MAAM,CAAC,OAAO,OAAO,UAAU;IAW7B,8DAA8D;IAC9D,YAAY,IAA+C;QACzD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC9C,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAA;IACpB,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO;YACtB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC7C,CAAC;IAED,GAAG,KAAU,CAAC;IAEd,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI;QACF,MAAM,CAAC,GAAG;YACR,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC;YACzB,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC;YAC5B,SAAS;SACV,CAAA;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,EAAE;QACA,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,eAAe,CAAC,OAOf;QACC,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,OAAO,CAAA;QAClD,MAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACrB,MAAM,CAAC,OAAO,EAAE,WAAW,CAAC,GAAG,IAAI,CAAC,wBAAwB,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QACtE,MAAM,KAAK,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,OAAO,CAAC,CAAA;QAC3C,MAAM,UAAU,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAExD,OAAO;YACL,OAAO,EAAE,KAAK;YACd,KAAK;YACL,GAAG,EAAE,UAAU,IAAI,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,MAAM;YACzE,WAAW;YACX,IAAI,EAAE,OAAO;YACb,IAAI,EAAE,EAAE,aAAF,EAAE,uBAAF,EAAE,CAAE,IAAI,CAAC,GAAG,CAAC;YACnB,OAAO,EAAE,EAAE,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS;SAC/D,CAAA;IACH,CAAC;IAED;;OAEG;IACH,wBAAwB,CACtB,GAAW,EACX,GAAa;QAEb,uDAAuD;QACvD,IAAI,CAAC,GAAG,IAAI,GAAG,KAAK,
|
|
1
|
+
{"version":3,"file":"VcfFeature.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfFeature.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AAyBzC,MAAM,CAAC,OAAO,OAAO,UAAU;IAW7B,8DAA8D;IAC9D,YAAY,IAA+C;QACzD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC9C,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAA;IACpB,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO;YACtB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC7C,CAAC;IAED,GAAG,KAAU,CAAC;IAEd,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI;QACF,MAAM,CAAC,GAAG;YACR,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC;YACzB,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC;YAC5B,SAAS;SACV,CAAA;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,EAAE;QACA,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,eAAe,CAAC,OAOf;QACC,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,OAAO,CAAA;QAClD,MAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACrB,MAAM,CAAC,OAAO,EAAE,WAAW,CAAC,GAAG,IAAI,CAAC,wBAAwB,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QACtE,MAAM,KAAK,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,OAAO,CAAC,CAAA;QAC3C,MAAM,UAAU,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAExD,OAAO;YACL,OAAO,EAAE,KAAK;YACd,KAAK;YACL,GAAG,EAAE,UAAU,IAAI,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,MAAM;YACzE,WAAW;YACX,IAAI,EAAE,OAAO;YACb,IAAI,EAAE,EAAE,aAAF,EAAE,uBAAF,EAAE,CAAE,IAAI,CAAC,GAAG,CAAC;YACnB,OAAO,EAAE,EAAE,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS;SAC/D,CAAA;IACH,CAAC;IAED;;OAEG;IACH,wBAAwB,CACtB,GAAW,EACX,GAAa;QAEb,uDAAuD;QACvD,IAAI,CAAC,GAAG,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;YAC5B,OAAO,CAAC,QAAQ,EAAE,wBAAwB,CAAC,CAAA;SAC5C;QAED,MAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAA;QACjC,IAAI,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;QACpC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACd,IAAI,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,IAAI,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAEjE,IAAI,CAAC,MAAM,EAAE;gBACX,CAAC;gBAAA,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,IAAI,CAAC,0BAA0B,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;aACjE;YACD,IAAI,MAAM,IAAI,WAAW,EAAE;gBACzB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;gBACnB,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,CAAA;aAC9B;QACH,CAAC,CAAC,CAAA;QAEF,6EAA6E;QAC7E,IAAI,YAAY,CAAC,IAAI,GAAG,CAAC,EAAE;YACzB,MAAM,QAAQ,GAAG,IAAI,GAAG,CACtB,CAAC,GAAG,YAAY,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;gBAC3B,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;YACrC,CAAC,CAAC,CACH,CAAA;YAED,MAAM,SAAS,GAAG,CAAC,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;gBAC3C,MAAM,QAAQ,GAAG,CAAC,GAAG,YAAY,CAAC;qBAC/B,GAAG,CAAC,IAAI,CAAC,EAAE;oBACV,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;oBAC9B,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;gBACrD,CAAC,CAAC;qBACD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBAEnB,OAAO,QAAQ,CAAC,MAAM;oBACpB,CAAC,CAAC,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC;oBACrC,CAAC,CAAC,CAAC,GAAG,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YACjC,CAAC,CAAC,CAAA;YAEF,YAAY,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,CAAA;SAClC;QACD,IAAI,OAAO,CAAC,IAAI,EAAE;YAChB,OAAO,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;SAC7D;QACD,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;IAC/B,CAAC;IAeD,wBAAwB,CACtB,GAAW,EACX,GAAW;QAEX,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACnD,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;SAC9B;QAED,iDAAiD;QACjD,IAAI,MAAM,GAAG,UAAU,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;QACzC,gEAAgE;QAChE,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE;YAClD,MAAM,GAAG,kBAAkB,CAAA;SAC5B;QACD,IAAI,MAAM,EAAE;YACV,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;SACrB;QAED,2DAA2D;QAC3D,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC7B,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE;YACrB,OAAO,IAAI,CAAC,wBAAwB,CAClC,GAAG,EACH,IAAI,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CACpD,CAAA;SACF;QAED,YAAY;QACZ,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;IAC/B,CAAC;IAED,0EAA0E;IAC1E,yEAAyE;IACzE,OAAO;IACP,0BAA0B,CAAC,GAAW,EAAE,GAAW;QACjD,MAAM,GAAG,GAAG,aAAa,CAAC,GAAG,CAAC,CAAA;QAC9B,IAAI,GAAG,EAAE;YACP,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;YAC/C,OAAO,CAAC,KAAK,EAAE,IAAI,CAAC,sBAAsB,CAAC,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SAC7D;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,WAAW,EAAE,GAAG,CAAC,CAAA;SAC1B;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,C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@@ -84,9 +84,6 @@ export default class extends BaseFeatureDataAdapter {
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84
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* @returns Observable of Feature objects in the regions
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85
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*/
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86
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|
getFeaturesInMultipleRegions(regions, opts = {}) {
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87
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-
// TODO: restore commented version below once TSDX supports Rollup v2
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88
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-
// xref: https://github.com/rollup/rollup/blob/master/CHANGELOG.md#bug-fixes-45
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-
const superGetFeaturesInMultipleRegions = super.getFeaturesInMultipleRegions;
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|
return ObservableCreate(async (observer) => {
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91
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|
const { vcf } = await this.configure();
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// @ts-ignore
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@@ -101,10 +98,7 @@ export default class extends BaseFeatureDataAdapter {
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101
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if (pct > 60) {
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console.warn(`getFeaturesInMultipleRegions fetching ${pct}% of VCF file, but whole-file streaming not yet implemented`);
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}
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-
.call(this, regions, opts)
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.subscribe(observer);
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-
// super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)
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+
super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer);
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});
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}
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freeResources( /* { region } */) { }
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@@ -1 +1 @@
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1
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-
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|
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1
|
+
{"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAMhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,SAAS,MAAM,WAAW,CAAA;AAEjC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,UAAU,MAAM,cAAc,CAAA;AAGrC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;IAOzC,KAAK,CAAC,YAAY;QACxB,MAAM,aAAa,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAClE,MAAM,QAAQ,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACnE,MAAM,SAAS,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAErE,MAAM,UAAU,GAAG,YAAY,CAC7B,aAA6B,EAC7B,IAAI,CAAC,aAAa,CACnB,CAAA;QACD,MAAM,KAAK,GAAG,SAAS,KAAK,KAAK,CAAA;QACjC,MAAM,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC/B,UAAU;YACV,aAAa,EAAE,KAAK;gBAClB,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACb,aAAa,EAAE,CAAC,KAAK;gBACnB,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACb,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,cAAc,EAAE,UAAU;SAC3B,CAAC,CAAA;QAEF,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,SAAS,EAAE,CAAA;QACpC,OAAO;YACL,UAAU;YACV,GAAG;YACH,MAAM,EAAE,IAAI,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;SAClC,CAAA;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,SAAS,EAAE,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACzC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,MAAM,GAAG,CAAC,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBACtC,YAAY,EAAE,CAAC,IAAY,EAAE,UAAkB,EAAE,EAAE;oBACjD,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;wBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;wBAC/B,MAAM;wBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,QAAQ,UAAU,EAAE;qBACnC,CAAC,CACH,CAAA;gBACH,CAAC;gBACD,GAAG,IAAI;aACR,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED;;;;;;;;;;;;;OAaG;IACI,4BAA4B,CACjC,OAAiB,EACjB,OAAoB,EAAE;QAEtB,OAAO,gBAAgB,CAAU,KAAK,EAAE,QAA2B,EAAE,EAAE;YACrE,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAEtC,aAAa;YACb,MAAM,KAAK,GAAG,MAAM,eAAe,CAAC,OAAO,EAAE,GAAG,CAAC,KAAK,CAAC,CAAA;YACvD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,IAAI,GAAG,MAAM,UAAU,CAAC,IAAI,EAAE,CAAA;YACpC,IAAI,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,CAAC,CAAA;YAC/C,IAAI,GAAG,GAAG,GAAG,EAAE;gBACb,yDAAyD;gBACzD,GAAG,GAAG,GAAG,CAAA;aACV;YACD,IAAI,GAAG,GAAG,EAAE,EAAE;gBACZ,OAAO,CAAC,IAAI,CACV,yCAAyC,GAAG,6DAA6D,CAC1G,CAAA;aACF;YACD,KAAK,CAAC,4BAA4B,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;QACvE,CAAC,CAAC,CAAA;IACJ,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-variants",
|
|
3
|
-
"version": "2.0
|
|
3
|
+
"version": "2.1.0",
|
|
4
4
|
"description": "JBrowse 2 variant adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -44,7 +44,7 @@
|
|
|
44
44
|
"@gmod/vcf": "^5.0.5",
|
|
45
45
|
"@mui/icons-material": "^5.0.2",
|
|
46
46
|
"@mui/x-data-grid": "^5.0.1",
|
|
47
|
-
"generic-filehandle": "^
|
|
47
|
+
"generic-filehandle": "^3.0.0"
|
|
48
48
|
},
|
|
49
49
|
"peerDependencies": {
|
|
50
50
|
"@jbrowse/core": "^2.0.0",
|
|
@@ -66,5 +66,5 @@
|
|
|
66
66
|
"distModule": "esm/index.js",
|
|
67
67
|
"srcModule": "src/index.ts",
|
|
68
68
|
"module": "esm/index.js",
|
|
69
|
-
"gitHead": "
|
|
69
|
+
"gitHead": "0db0462fa1f9f15ab4869da085bcab032b9483c3"
|
|
70
70
|
}
|
|
@@ -106,7 +106,7 @@ export default class VCFFeature implements Feature {
|
|
|
106
106
|
alt: string[],
|
|
107
107
|
): [string, string] | [undefined, undefined] {
|
|
108
108
|
// it's just a remark if there are no alternate alleles
|
|
109
|
-
if (!alt || alt ===
|
|
109
|
+
if (!alt || alt.length === 0) {
|
|
110
110
|
return ['remark', 'no alternative alleles']
|
|
111
111
|
}
|
|
112
112
|
|
|
@@ -118,9 +118,6 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
118
118
|
regions: Region[],
|
|
119
119
|
opts: BaseOptions = {},
|
|
120
120
|
) {
|
|
121
|
-
// TODO: restore commented version below once TSDX supports Rollup v2
|
|
122
|
-
// xref: https://github.com/rollup/rollup/blob/master/CHANGELOG.md#bug-fixes-45
|
|
123
|
-
const superGetFeaturesInMultipleRegions = super.getFeaturesInMultipleRegions
|
|
124
121
|
return ObservableCreate<Feature>(async (observer: Observer<Feature>) => {
|
|
125
122
|
const { vcf } = await this.configure()
|
|
126
123
|
|
|
@@ -138,10 +135,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
138
135
|
`getFeaturesInMultipleRegions fetching ${pct}% of VCF file, but whole-file streaming not yet implemented`,
|
|
139
136
|
)
|
|
140
137
|
}
|
|
141
|
-
|
|
142
|
-
.call(this, regions, opts)
|
|
143
|
-
.subscribe(observer)
|
|
144
|
-
// super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)
|
|
138
|
+
super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)
|
|
145
139
|
})
|
|
146
140
|
}
|
|
147
141
|
|