@jbrowse/plugin-bed 2.5.0 → 2.6.1
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/BedAdapter/BedAdapter.js +1 -1
- package/dist/BedAdapter/BedAdapter.js.map +1 -1
- package/dist/BedTabixAdapter/BedTabixAdapter.js +1 -1
- package/dist/BedTabixAdapter/BedTabixAdapter.js.map +1 -1
- package/dist/BedpeAdapter/BedpeAdapter.d.ts +2 -2
- package/dist/BedpeAdapter/BedpeAdapter.js +11 -5
- package/dist/BedpeAdapter/BedpeAdapter.js.map +1 -1
- package/dist/BigBedAdapter/BigBedAdapter.js +2 -2
- package/dist/BigBedAdapter/BigBedAdapter.js.map +1 -1
- package/dist/index.js +8 -0
- package/dist/index.js.map +1 -1
- package/dist/util.js +1 -2
- package/dist/util.js.map +1 -1
- package/esm/BedAdapter/BedAdapter.js +1 -1
- package/esm/BedAdapter/BedAdapter.js.map +1 -1
- package/esm/BedTabixAdapter/BedTabixAdapter.js +1 -1
- package/esm/BedTabixAdapter/BedTabixAdapter.js.map +1 -1
- package/esm/BedpeAdapter/BedpeAdapter.d.ts +2 -2
- package/esm/BedpeAdapter/BedpeAdapter.js +11 -5
- package/esm/BedpeAdapter/BedpeAdapter.js.map +1 -1
- package/esm/BigBedAdapter/BigBedAdapter.js +2 -2
- package/esm/BigBedAdapter/BigBedAdapter.js.map +1 -1
- package/esm/index.js +8 -0
- package/esm/index.js.map +1 -1
- package/esm/util.js +1 -2
- package/esm/util.js.map +1 -1
- package/package.json +3 -3
- package/src/BedAdapter/BedAdapter.ts +1 -1
- package/src/BedTabixAdapter/BedTabixAdapter.ts +1 -1
- package/src/BedpeAdapter/BedpeAdapter.ts +17 -11
- package/src/BigBedAdapter/BigBedAdapter.ts +2 -5
- package/src/index.ts +13 -0
- package/src/util.ts +1 -2
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@@ -86,7 +86,7 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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return columnNames;
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}
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const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
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const defline = defs
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const defline = defs.at(-1);
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return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
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? defline
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.slice(1)
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@@ -1 +1 @@
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-
{"version":3,"file":"BedAdapter.js","sourceRoot":"","sources":["../../src/BedAdapter/BedAdapter.ts"],"names":[],"mappings":";;;;;AAAA,oDAA2B;AAC3B,yEAGgD;AAChD,8CAAoD;AACpD,kDAA0D;AAE1D,kCAAqC;AACrC,8EAAoD;AACpD,2DAA6C;AAE7C,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,oCAAsB;IAA9D;;QAYY,kBAAa,GAEnB,EAAE,CAAA;IA4IR,CAAC;IAxIS,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QAC5C,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC1C,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,MAAM,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACzD,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QACnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QACD,MAAM,IAAI,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACvD,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACxD,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SAC3B;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,EAA8B,CAAA;QAC/C,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC5B,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACrB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YAC9B,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;YAClC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE;gBACtB,QAAQ,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;aACvB;YACD,QAAQ,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAC7B;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAW,CAAA;QACjD,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;QACnC,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAA;QACzC,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QAErC,OAAO;YACL,MAAM;YACN,QAAQ;YACR,MAAM;YACN,WAAW;YACX,WAAW;YACX,MAAM;YACN,QAAQ;YACR,MAAM;SACP,CAAA;IACH,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,OAAoB,EAAE;QAC3C,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAChD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QAED,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC9C,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC5C,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACrD,IAAI,WAAW,CAAC,MAAM,EAAE;YACtB,OAAO,WAAW,CAAA;SACnB;QACD,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,
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{"version":3,"file":"BedAdapter.js","sourceRoot":"","sources":["../../src/BedAdapter/BedAdapter.ts"],"names":[],"mappings":";;;;;AAAA,oDAA2B;AAC3B,yEAGgD;AAChD,8CAAoD;AACpD,kDAA0D;AAE1D,kCAAqC;AACrC,8EAAoD;AACpD,2DAA6C;AAE7C,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,oCAAsB;IAA9D;;QAYY,kBAAa,GAEnB,EAAE,CAAA;IA4IR,CAAC;IAxIS,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QAC5C,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC1C,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,MAAM,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACzD,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QACnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QACD,MAAM,IAAI,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACvD,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACxD,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SAC3B;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,EAA8B,CAAA;QAC/C,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC5B,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACrB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YAC9B,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;YAClC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE;gBACtB,QAAQ,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;aACvB;YACD,QAAQ,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAC7B;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAW,CAAA;QACjD,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;QACnC,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAA;QACzC,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QAErC,OAAO;YACL,MAAM;YACN,QAAQ;YACR,MAAM;YACN,WAAW;YACX,WAAW;YACX,MAAM;YACN,QAAQ;YACR,MAAM;SACP,CAAA;IACH,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,OAAoB,EAAE;QAC3C,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAChD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QAED,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC9C,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC5C,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACrD,IAAI,WAAW,CAAC,MAAM,EAAE;YACtB,OAAO,WAAW,CAAA;SACnB;QACD,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;QAC3B,OAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;YAC5B,CAAC,CAAC,OAAO;iBACJ,KAAK,CAAC,CAAC,CAAC;iBACR,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YAC/B,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAEO,KAAK,CAAC,6BAA6B,CAAC,OAAe;QACzD,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,WAAW,EAAE,GAC/D,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACvB,MAAM,KAAK,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAC/B,IAAI,CAAC,KAAK,EAAE;YACV,OAAO,SAAS,CAAA;SACjB;QACD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAEnC,MAAM,YAAY,GAAG,IAAI,uBAAY,EAAE,CAAA;QACvC,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YAC7B,MAAM,QAAQ,GAAG,GAAG,IAAI,CAAC,EAAE,IAAI,OAAO,IAAI,CAAC,EAAE,CAAA;YAC7C,OAAO,IAAA,kBAAW,EAChB,CAAC,EACD,MAAM,EACN,QAAQ,EACR,MAAM,EACN,WAAW,EACX,MAAM,EACN,QAAQ,EACR,KAAK,CACN,CAAA;QACH,CAAC,CAAC,CAAA;QAEF,KAAK,MAAM,GAAG,IAAI,GAAG,EAAE;YACrB,YAAY,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;SAC7D;QACD,OAAO,YAAY,CAAA;IACrB,CAAC;IAEO,KAAK,CAAC,uBAAuB,CAAC,OAAe;QACnD,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EAAE;YAChC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,IAAI,CAAC,6BAA6B,CAC9D,OAAO,CACR,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACV,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;gBACvC,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;IACpC,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,YAAY,GAAG,MAAM,IAAI,CAAC,uBAAuB,CAAC,OAAO,CAAC,CAAA;YAChE,YAAY,aAAZ,YAAY,uBAAZ,YAAY,CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;YACjE,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,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{"version":3,"file":"BedTabixAdapter.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/BedTabixAdapter.ts"],"names":[],"mappings":";;;;;AAAA,oDAA2B;AAC3B,yEAGgD;AAChD,8CAAoD;AACpD,kDAA0D;AAE1D,uCAA8C;AAC9C,kCAAqC;AAKrC,MAAqB,eAAgB,SAAQ,oCAAsB;IAWjE,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QAC9D,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACjD,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC/C,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;QACvC,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,IAAI,CAAC,GAAG,GAAG,IAAI,wBAAgB,CAAC;YAC9B,UAAU,EAAE,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC;YACtC,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;SAC7B,CAAC,CAAA;QACF,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;IACpC,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAED,KAAK,CAAC,SAAS;QACb,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;YAC3B,OAAO,IAAI,CAAC,WAAW,CAAA;SACxB;QACD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;QACzC,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,
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{"version":3,"file":"BedTabixAdapter.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/BedTabixAdapter.ts"],"names":[],"mappings":";;;;;AAAA,oDAA2B;AAC3B,yEAGgD;AAChD,8CAAoD;AACpD,kDAA0D;AAE1D,uCAA8C;AAC9C,kCAAqC;AAKrC,MAAqB,eAAgB,SAAQ,oCAAsB;IAWjE,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QAC9D,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACjD,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC/C,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;QACvC,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,IAAI,CAAC,GAAG,GAAG,IAAI,wBAAgB,CAAC;YAC9B,UAAU,EAAE,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC;YACtC,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;SAC7B,CAAC,CAAA;QACF,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;IACpC,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAED,KAAK,CAAC,SAAS;QACb,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;YAC3B,OAAO,IAAI,CAAC,WAAW,CAAA;SACxB;QACD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;QACzC,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;QAC3B,OAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;YAC5B,CAAC,CAAC,OAAO;iBACJ,KAAK,CAAC,CAAC,CAAC;iBACR,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;YACvB,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;YACzC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;YAC9B,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;YACpC,MAAM,QAAQ,GAAG,aAAa,CAAC,KAAK,GAAG,CAAC,CAAA;YACxC,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;YACpC,uEAAuE;YACvE,qEAAqE;YACrE,8DAA8D;YAC9D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;YACnC,MAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,EAAE;gBAC7D,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,IAAA,kBAAW,EACT,IAAI,EACJ,MAAM,EACN,QAAQ,EACR,MAAM,EACN,IAAI,CAAC,WAAW,EAChB,IAAI,CAAC,MAAM,EACX,GAAG,IAAI,CAAC,EAAE,IAAI,UAAU,EAAE,EAC1B,KAAK,CACN,CACF,CAAA;gBACH,CAAC;gBACD,MAAM,EAAE,IAAI,CAAC,MAAM;aACpB,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAhFjB,4BAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA;kBATxC,eAAe"}
|
|
@@ -5,8 +5,8 @@ export declare function featureData(line: string, uniqueId: string, flip: boolea
|
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|
5
5
|
export default class BedpeAdapter extends BaseFeatureDataAdapter {
|
|
6
6
|
protected bedpeFeatures?: Promise<{
|
|
7
7
|
header: string;
|
|
8
|
-
feats1: Record<string, string[]>;
|
|
9
|
-
feats2: Record<string, string[]>;
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8
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+
feats1: Record<string, string[] | undefined>;
|
|
9
|
+
feats2: Record<string, string[] | undefined>;
|
|
10
10
|
columnNames: string[];
|
|
11
11
|
}>;
|
|
12
12
|
protected intervalTrees: {
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@@ -91,7 +91,9 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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91
91
|
if (!feats2[r2]) {
|
|
92
92
|
feats2[r2] = [];
|
|
93
93
|
}
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|
94
|
+
// eslint-disable-next-line @typescript-eslint/no-non-null-assertion
|
|
94
95
|
feats1[r1].push(line);
|
|
96
|
+
// eslint-disable-next-line @typescript-eslint/no-non-null-assertion
|
|
95
97
|
feats2[r2].push(line);
|
|
96
98
|
}
|
|
97
99
|
const columnNames = this.getConf('columnNames');
|
|
@@ -125,7 +127,7 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
|
125
127
|
return columnNames;
|
|
126
128
|
}
|
|
127
129
|
const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
|
|
128
|
-
const defline = defs
|
|
130
|
+
const defline = defs.at(-1);
|
|
129
131
|
return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
|
|
130
132
|
? defline
|
|
131
133
|
.slice(1)
|
|
@@ -147,11 +149,15 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
|
147
149
|
const uniqueId = `${this.id}-${refName}-${i}`;
|
|
148
150
|
return featureData(f, uniqueId, true, names);
|
|
149
151
|
});
|
|
150
|
-
|
|
151
|
-
|
|
152
|
+
if (ret1) {
|
|
153
|
+
for (const obj of ret1) {
|
|
154
|
+
intervalTree.insert([obj.get('start'), obj.get('end')], obj);
|
|
155
|
+
}
|
|
152
156
|
}
|
|
153
|
-
|
|
154
|
-
|
|
157
|
+
if (ret2) {
|
|
158
|
+
for (const obj of ret2) {
|
|
159
|
+
intervalTree.insert([obj.get('start'), obj.get('end')], obj);
|
|
160
|
+
}
|
|
155
161
|
}
|
|
156
162
|
return intervalTree;
|
|
157
163
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BedpeAdapter.js","sourceRoot":"","sources":["../../src/BedpeAdapter/BedpeAdapter.ts"],"names":[],"mappings":";;;;;;AAAA,yEAGgD;AAChD,8CAAoD;AACpD,kDAA0D;AAC1D,6CAAmE;AACnE,8EAAoD;AACpD,2DAA6C;AAE7C,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,SAAgB,WAAW,CACzB,IAAY,EACZ,QAAgB,EAChB,IAAa,EACb,KAAgB;IAEhB,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC1B,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC5B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC/B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAChC,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IACjB,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACnB,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,IAAI,GAAG,KAAK;QAChB,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;QACrE,CAAC,CAAC,KAAK,CAAA;IAET,OAAO,IAAI,oBAAa,CAAC;QACvB,KAAK,EAAE,MAAM;QACb,GAAG,EAAE,IAAI;QACT,OAAO,EAAE,IAAI;QACb,MAAM,EAAE,OAAO;QACf,IAAI;QACJ,GAAG,IAAI;QACP,KAAK;QACL,QAAQ;QACR,IAAI,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE;KACnE,CAAC,CAAA;AACJ,CAAC;AAjCD,kCAiCC;AAED,SAAS,WAAW,CAAC,MAAc;IACjC,IAAI,MAAM,KAAK,GAAG,EAAE;QAClB,OAAO,CAAC,CAAA;KACT;SAAM,IAAI,MAAM,KAAK,GAAG,EAAE;QACzB,OAAO,CAAC,CAAC,CAAA;KACV;SAAM,IAAI,MAAM,KAAK,GAAG,EAAE;QACzB,OAAO,CAAC,CAAA;KACT;SAAM;QACL,OAAO,SAAS,CAAA;KACjB;AACH,CAAC;AAED,MAAqB,YAAa,SAAQ,oCAAsB;IAAhE;;QAQY,kBAAa,GAEnB,EAAE,CAAA;
|
|
1
|
+
{"version":3,"file":"BedpeAdapter.js","sourceRoot":"","sources":["../../src/BedpeAdapter/BedpeAdapter.ts"],"names":[],"mappings":";;;;;;AAAA,yEAGgD;AAChD,8CAAoD;AACpD,kDAA0D;AAC1D,6CAAmE;AACnE,8EAAoD;AACpD,2DAA6C;AAE7C,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,SAAgB,WAAW,CACzB,IAAY,EACZ,QAAgB,EAChB,IAAa,EACb,KAAgB;IAEhB,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC1B,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC5B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC/B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAChC,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IACjB,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACnB,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,IAAI,GAAG,KAAK;QAChB,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;QACrE,CAAC,CAAC,KAAK,CAAA;IAET,OAAO,IAAI,oBAAa,CAAC;QACvB,KAAK,EAAE,MAAM;QACb,GAAG,EAAE,IAAI;QACT,OAAO,EAAE,IAAI;QACb,MAAM,EAAE,OAAO;QACf,IAAI;QACJ,GAAG,IAAI;QACP,KAAK;QACL,QAAQ;QACR,IAAI,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE;KACnE,CAAC,CAAA;AACJ,CAAC;AAjCD,kCAiCC;AAED,SAAS,WAAW,CAAC,MAAc;IACjC,IAAI,MAAM,KAAK,GAAG,EAAE;QAClB,OAAO,CAAC,CAAA;KACT;SAAM,IAAI,MAAM,KAAK,GAAG,EAAE;QACzB,OAAO,CAAC,CAAC,CAAA;KACV;SAAM,IAAI,MAAM,KAAK,GAAG,EAAE;QACzB,OAAO,CAAC,CAAA;KACT;SAAM;QACL,OAAO,SAAS,CAAA;KACjB;AACH,CAAC;AAED,MAAqB,YAAa,SAAQ,oCAAsB;IAAhE;;QAQY,kBAAa,GAEnB,EAAE,CAAA;IAwIR,CAAC;IApIS,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QAC5C,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QAC5C,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,MAAM,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACzD,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QACnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QACD,MAAM,IAAI,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACvD,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACxD,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SAC3B;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACrC,MAAM,MAAM,GAAG,EAA0C,CAAA;QACzD,MAAM,MAAM,GAAG,EAA0C,CAAA;QACzD,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC5B,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACrB,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YAClB,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YAClB,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE;gBACf,MAAM,CAAC,EAAE,CAAC,GAAG,EAAE,CAAA;aAChB;YACD,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE;gBACf,MAAM,CAAC,EAAE,CAAC,GAAG,EAAE,CAAA;aAChB;YACD,oEAAoE;YACpE,MAAM,CAAC,EAAE,CAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YACtB,oEAAoE;YACpE,MAAM,CAAC,EAAE,CAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SACvB;QACD,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAE/C,OAAO;YACL,MAAM;YACN,MAAM;YACN,MAAM;YACN,WAAW;SACZ,CAAA;IACH,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,OAAoB,EAAE;QAC3C,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE;YACvB,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAClD,IAAI,CAAC,aAAa,GAAG,SAAS,CAAA;gBAC9B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QAED,OAAO,IAAI,CAAC,aAAa,CAAA;IAC3B,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACpD,OAAO,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;IACvE,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC5C,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACrD,IAAI,WAAW,CAAC,MAAM,EAAE;YACtB,OAAO,WAAW,CAAA;SACnB;QACD,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;QAC3B,OAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;YAC5B,CAAC,CAAC,OAAO;iBACJ,KAAK,CAAC,CAAC,CAAC;iBACR,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,KAAK,C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@@ -11,15 +11,15 @@ const io_1 = require("@jbrowse/core/util/io");
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11
11
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const rxjs_1 = require("@jbrowse/core/util/rxjs");
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const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
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13
13
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const operators_1 = require("rxjs/operators");
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14
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-
const configuration_1 = require("@jbrowse/core/configuration");
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14
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const util_1 = require("../util");
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15
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function isUCSC(f) {
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return f.get('thickStart') && f.get('blockCount') && f.get('strand') !== 0;
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17
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}
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19
18
|
class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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20
19
|
async configurePre(opts) {
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20
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+
const pm = this.pluginManager;
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21
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const bigbed = new bbi_1.BigBed({
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22
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-
filehandle: (0, io_1.openLocation)(
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22
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+
filehandle: (0, io_1.openLocation)(this.getConf('bigBedLocation'), pm),
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23
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});
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24
24
|
const header = await bigbed.getHeader(opts);
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25
25
|
const parser = new bed_1.default({ autoSql: header.autoSql });
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"BigBedAdapter.js","sourceRoot":"","sources":["../../src/BigBedAdapter/BigBedAdapter.ts"],"names":[],"mappings":";;;;;AAAA,uDAAuD;AACvD,mCAAkC;AAClC,oDAA2B;AAC3B,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,qFAAyE;AACzE,8CAA8C;AAC9C
|
|
1
|
+
{"version":3,"file":"BigBedAdapter.js","sourceRoot":"","sources":["../../src/BigBedAdapter/BigBedAdapter.ts"],"names":[],"mappings":";;;;;AAAA,uDAAuD;AACvD,mCAAkC;AAClC,oDAA2B;AAC3B,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,qFAAyE;AACzE,8CAA8C;AAC9C,kCAAiD;AAEjD,SAAS,MAAM,CAAC,CAAU;IACxB,OAAO,CAAC,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAA;AAC5E,CAAC;AAED,MAAqB,aAAc,SAAQ,oCAAsB;IAGxD,KAAK,CAAC,YAAY,CAAC,IAAkB;QAC1C,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,MAAM,GAAG,IAAI,YAAM,CAAC;YACxB,UAAU,EAAE,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,gBAAgB,CAAC,EAAE,EAAE,CAAC;SAC7D,CAAC,CAAA;QACF,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC3C,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,OAAO,EAAE,MAAM,CAAC,OAAO,EAAE,CAAC,CAAA;QACnD,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,CAAA;IACnC,CAAC;IAEM,KAAK,CAAC,SAAS,CAAC,IAAkB;QACvC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC7C,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACvC,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QACrD,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,MAAM,CAAA;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,CAAC,OAAO,CAAA;QAC1C,OAAO;YACL,OAAO;YACP,QAAQ;YACR,OAAO,EAAE,EAAE,GAAG,IAAI,EAAE;YACpB,MAAM,EAAE,MAAM,CAAC,WAAW,CACxB,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CACnD;SACF,CAAA;IACH,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QACvB,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,IAAI;gBACF,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;gBACrD,MAAM,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;oBAC5D,MAAM;oBACN,YAAY,EAAE,GAAG,GAAG,KAAK;iBAC1B,CAAC,CAAA;gBACF,EAAE,CAAC,IAAI,CACL,IAAA,oBAAQ,GAAE,EACV,IAAA,eAAG,EAAC,CAAC,CAAC,EAAE;oBACN,MAAM,IAAI,GAAG,MAAM,CAAC,SAAS,CAC3B,GAAG,OAAO,KAAK,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,IAAI,EAAE,EAC7C;wBACE,QAAQ,EAAE,CAAC,CAAC,QAAkB;qBAC/B,CACF,CAAA;oBAED,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;oBACjE,IAAI,UAAU,EAAE;wBACd,MAAM,MAAM,GAAG,WAAW,IAAI,WAAW,IAAI,EAAE,CAAA;wBAC/C,MAAM,KAAK,GAAG,UAAU,CAAA;wBACxB,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAA;wBAC5B,IAAI,CAAC,WAAW,GAAG,EAAE,CAAA;wBAErB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE;4BACtC,MAAM,IAAI,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,YAAY,CAAA;4BAC5C,MAAM,IAAI,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;4BACnC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC;gCACpB,QAAQ,EAAE,GAAG,CAAC,CAAC,QAAQ,IAAI,CAAC,EAAE;gCAC9B,KAAK,EAAE,IAAI;gCACX,GAAG,EAAE,IAAI;gCACT,IAAI,EAAE,OAAO;6BACd,CAAC,CAAA;yBACH;qBACF;oBACD,IAAI,CAAC,CAAC,QAAQ,KAAK,SAAS,EAAE;wBAC5B,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;qBACvC;oBACD,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,CAAA;oBAErD,MAAM,CAAC,GAAG,IAAI,uBAAa,CAAC;wBAC1B,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,QAAQ,EAAE;wBAC9B,IAAI,EAAE;4BACJ,GAAG,IAAI;4BACP,KAAK,EAAE,CAAC,CAAC,KAAK;4BACd,GAAG,EAAE,CAAC,CAAC,GAAG;4BACV,OAAO;yBACR;qBACF,CAAC,CAAA;oBAEF,4DAA4D;oBAC5D,+DAA+D;oBAC/D,6DAA6D;oBAC7D,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAA,8BAAuB,EAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACnD,CAAC,CAAC,CACH,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;aACtB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;CAChC;AA5GD,gCA4GC"}
|
package/dist/index.js
CHANGED
|
@@ -84,6 +84,14 @@ class BedPlugin extends Plugin_1.default {
|
|
|
84
84
|
return adapterGuesser(file, index, adapterHint);
|
|
85
85
|
};
|
|
86
86
|
});
|
|
87
|
+
pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
|
|
88
|
+
return (adapterName) => {
|
|
89
|
+
if (adapterName === 'BedpeAdapter') {
|
|
90
|
+
return 'VariantTrack';
|
|
91
|
+
}
|
|
92
|
+
return trackTypeGuesser(adapterName);
|
|
93
|
+
};
|
|
94
|
+
});
|
|
87
95
|
}
|
|
88
96
|
}
|
|
89
97
|
exports.default = BedPlugin;
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;AAAA,kEAAyC;AAEzC,oEAA4C;AAC5C,kEAA0C;AAC1C,wEAAgD;AAChD,8DAAsC;AAEtC,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;AAAA,kEAAyC;AAEzC,oEAA4C;AAC5C,kEAA0C;AAC1C,wEAAgD;AAChD,8DAAsC;AAEtC,sDAMkC;AAElC,MAAqB,SAAU,SAAQ,gBAAM;IAA7C;;QACE,SAAI,GAAG,WAAW,CAAA;IAoHpB,CAAC;IAlHC,OAAO,CAAC,aAA4B;QAClC,IAAA,uBAAc,EAAC,aAAa,CAAC,CAAA;QAC7B,IAAA,oBAAW,EAAC,aAAa,CAAC,CAAA;QAC1B,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QAC5B,IAAA,yBAAgB,EAAC,aAAa,CAAC,CAAA;QAC/B,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,iBAAiB,CAAA;gBACpC,MAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,cAAc,EAAE,IAAI;iBACrB,CAAA;gBAED,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,eAAe,CAAA;gBAClC,MAAM,WAAW,GAAG,cAAc,CAAA;gBAClC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,aAAa,EAAE,IAAI;qBACpB,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,eAAe,CAAA;gBAClC,MAAM,WAAW,GAAG,iBAAiB,CAAA;gBACrC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,SAAS,GAAG,KAAK,IAAI,IAAA,oBAAW,EAAC,KAAK,CAAC,CAAA;gBAC7C,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,aAAa,EAAE,IAAI;wBACnB,KAAK,EAAE;4BACL,QAAQ,EAAE,KAAK,IAAI,IAAA,kBAAS,EAAC,IAAI,EAAE,MAAM,CAAC;4BAC1C,SAAS,EAAE,IAAA,sBAAa,EAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;yBAClD;qBACF,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,SAAS,CAAA;gBAC5B,MAAM,WAAW,GAAG,YAAY,CAAA;gBAChC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,WAAW,EAAE,IAAI;qBAClB,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;YACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;gBAC7B,IAAI,WAAW,KAAK,cAAc,EAAE;oBAClC,OAAO,cAAc,CAAA;iBACtB;gBACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;YACtC,CAAC,CAAA;QACH,CAAC,CACF,CAAA;IACH,CAAC;CACF;AArHD,4BAqHC"}
|
package/dist/util.js
CHANGED
|
@@ -104,11 +104,10 @@ function ucscProcessedTranscript(feature) {
|
|
|
104
104
|
delete newData.blockCount;
|
|
105
105
|
delete newData.thickStart;
|
|
106
106
|
delete newData.thickEnd;
|
|
107
|
-
|
|
107
|
+
return new util_1.SimpleFeature({
|
|
108
108
|
data: newData,
|
|
109
109
|
id: feature.id(),
|
|
110
110
|
});
|
|
111
|
-
return newFeature;
|
|
112
111
|
}
|
|
113
112
|
exports.ucscProcessedTranscript = ucscProcessedTranscript;
|
|
114
113
|
function defaultParser(fields, line) {
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;AAAA,6CAA2D;AAG3D,SAAgB,uBAAuB,CAAC,OAAgB;IACtD,MAAM,QAAQ,GAAG,OAAO,CAAC,QAAQ,EAAE,CAAA;IACnC,4CAA4C;IAC5C,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAC5C,MAAM,QAAQ,GAAG,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;IAExC,IAAI,CAAC,UAAU,IAAI,CAAC,QAAQ,EAAE;QAC5B,OAAO,OAAO,CAAA;KACf;IAED,MAAM,MAAM,GAAc,QAAQ;QAChC,CAAC,CAAC,QAAQ;aACL,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,OAAO,CAAC;aAC9C,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;QACpD,CAAC,CAAC,EAAE,CAAA;IAEN,8DAA8D;IAC9D,MAAM,WAAW,GAAwB,EAAE,CAAA;IAC3C,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;QACrB,MAAM,KAAK,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAChC,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC5B,IAAI,UAAU,IAAI,GAAG,EAAE;YACrB,gBAAgB;YAChB,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAA;YAC1D,WAAW,CAAC,IAAI,CAAC;gBACf,IAAI,EAAE,GAAG,KAAK,YAAY;gBAC1B,KAAK;gBACL,GAAG;aACJ,CAAC,CAAA;SACH;aAAM,IAAI,UAAU,GAAG,KAAK,IAAI,UAAU,GAAG,GAAG,IAAI,QAAQ,IAAI,GAAG,EAAE;YACpE,YAAY;YACZ,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAA;YAC1D,WAAW,CAAC,IAAI,CACd;gBACE,IAAI,EAAE,GAAG,KAAK,YAAY;gBAC1B,KAAK;gBACL,GAAG,EAAE,UAAU;aAChB,EACD;gBACE,IAAI,EAAE,KAAK;gBACX,KAAK,EAAE,UAAU;gBACjB,GAAG;aACJ,CACF,CAAA;SACF;aAAM,IAAI,UAAU,IAAI,KAAK,IAAI,QAAQ,IAAI,GAAG,EAAE;YACjD,MAAM;YACN,WAAW,CAAC,IAAI,CAAC;gBACf,IAAI,EAAE,KAAK;gBACX,KAAK;gBACL,GAAG;aACJ,CAAC,CAAA;SACH;aAAM,IAAI,UAAU,GAAG,KAAK,IAAI,UAAU,GAAG,GAAG,IAAI,QAAQ,GAAG,GAAG,EAAE;YACnE,kBAAkB;YAClB,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAA;YAC9D,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;YAC/D,WAAW,CAAC,IAAI,CACd;gBACE,IAAI,EAAE,GAAG,SAAS,YAAY;gBAC9B,KAAK;gBACL,GAAG,EAAE,UAAU;aAChB,EACD;gBACE,IAAI,EAAE,KAAK;gBACX,KAAK,EAAE,UAAU;gBACjB,GAAG,EAAE,QAAQ;aACd,EACD;gBACE,IAAI,EAAE,GAAG,UAAU,YAAY;gBAC/B,KAAK,EAAE,QAAQ;gBACf,GAAG;aACJ,CACF,CAAA;SACF;aAAM,IAAI,UAAU,IAAI,KAAK,IAAI,QAAQ,GAAG,KAAK,IAAI,QAAQ,GAAG,GAAG,EAAE;YACpE,YAAY;YACZ,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;YAC1D,WAAW,CAAC,IAAI,CACd;gBACE,IAAI,EAAE,KAAK;gBACX,KAAK;gBACL,GAAG,EAAE,QAAQ;aACd,EACD;gBACE,IAAI,EAAE,GAAG,KAAK,YAAY;gBAC1B,KAAK,EAAE,QAAQ;gBACf,GAAG;aACJ,CACF,CAAA;SACF;aAAM,IAAI,QAAQ,IAAI,KAAK,EAAE;YAC5B,iBAAiB;YACjB,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;YAC1D,WAAW,CAAC,IAAI,CAAC;gBACf,IAAI,EAAE,GAAG,KAAK,YAAY;gBAC1B,KAAK;gBACL,GAAG;aACJ,CAAC,CAAA;SACH;IACH,CAAC,CAAC,CAAA;IACF,MAAM,OAAO,GAAG,MAAM,CAAC,WAAW,CAChC,OAAO,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CACnD,CAAA;IACD,OAAO,CAAC,WAAW,GAAG,WAAW,CAAA;IACjC,OAAO,CAAC,IAAI,GAAG,MAAM,CAAA;IACrB,OAAO,CAAC,QAAQ,GAAG,OAAO,CAAC,EAAE,EAAE,CAAA;IAC/B,OAAO,OAAO,CAAC,WAAW,CAAA;IAC1B,OAAO,OAAO,CAAC,UAAU,CAAA;IACzB,OAAO,OAAO,CAAC,QAAQ,CAAA;IACvB,OAAO,OAAO,CAAC,KAAK,CAAA;IACpB,OAAO,OAAO,CAAC,WAAW,CAAA;IAC1B,OAAO,OAAO,CAAC,UAAU,CAAA;IACzB,OAAO,OAAO,CAAC,UAAU,CAAA;IACzB,OAAO,OAAO,CAAC,UAAU,CAAA;IACzB,OAAO,OAAO,CAAC,QAAQ,CAAA;IACvB,
|
|
1
|
+
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@@ -81,7 +81,7 @@ class BedAdapter extends BaseFeatureDataAdapter {
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81
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return columnNames;
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}
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83
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const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
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84
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-
const defline = defs
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|
84
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+
const defline = defs.at(-1);
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85
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|
return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
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|
? defline
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87
87
|
.slice(1)
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@@ -1 +1 @@
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1
|
-
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|
|
1
|
+
{"version":3,"file":"BedAdapter.js","sourceRoot":"","sources":["../../src/BedAdapter/BedAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,WAAW,CAAA;AAC3B,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AACrC,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,sBAAsB;IAA9D;;QAYY,kBAAa,GAEnB,EAAE,CAAA;IA4IR,CAAC;IAxIS,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QAC5C,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC1C,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACzD,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QACnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QACD,MAAM,IAAI,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACvD,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACxD,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SAC3B;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,EAA8B,CAAA;QAC/C,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC5B,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACrB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YAC9B,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;YAClC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE;gBACtB,QAAQ,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;aACvB;YACD,QAAQ,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAC7B;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAW,CAAA;QACjD,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;QACnC,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAA;QACzC,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QAErC,OAAO;YACL,MAAM;YACN,QAAQ;YACR,MAAM;YACN,WAAW;YACX,WAAW;YACX,MAAM;YACN,QAAQ;YACR,MAAM;SACP,CAAA;IACH,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,OAAoB,EAAE;QAC3C,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAChD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QAED,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC9C,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC5C,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACrD,IAAI,WAAW,CAAC,MAAM,EAAE;YACtB,OAAO,WAAW,CAAA;SACnB;QACD,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;QAC3B,OAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;YAC5B,CAAC,CAAC,OAAO;iBACJ,KAAK,CAAC,CAAC,CAAC;iBACR,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YAC/B,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAEO,KAAK,CAAC,6BAA6B,CAAC,OAAe;QACzD,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,WAAW,EAAE,GAC/D,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACvB,MAAM,KAAK,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAC/B,IAAI,CAAC,KAAK,EAAE;YACV,OAAO,SAAS,CAAA;SACjB;QACD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAEnC,MAAM,YAAY,GAAG,IAAI,YAAY,EAAE,CAAA;QACvC,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YAC7B,MAAM,QAAQ,GAAG,GAAG,IAAI,CAAC,EAAE,IAAI,OAAO,IAAI,CAAC,EAAE,CAAA;YAC7C,OAAO,WAAW,CAChB,CAAC,EACD,MAAM,EACN,QAAQ,EACR,MAAM,EACN,WAAW,EACX,MAAM,EACN,QAAQ,EACR,KAAK,CACN,CAAA;QACH,CAAC,CAAC,CAAA;QAEF,KAAK,MAAM,GAAG,IAAI,GAAG,EAAE;YACrB,YAAY,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;SAC7D;QACD,OAAO,YAAY,CAAA;IACrB,CAAC;IAEO,KAAK,CAAC,uBAAuB,CAAC,OAAe;QACnD,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EAAE;YAChC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,IAAI,CAAC,6BAA6B,CAC9D,OAAO,CACR,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACV,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;gBACvC,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;IACpC,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,YAAY,GAAG,MAAM,IAAI,CAAC,uBAAuB,CAAC,OAAO,CAAC,CAAA;YAChE,YAAY,aAAZ,YAAY,uBAAZ,YAAY,CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;YACjE,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAzIjB,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,AAAjC,CAAiC;eAhBxC,UAAU"}
|
|
@@ -34,7 +34,7 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
|
|
|
34
34
|
}
|
|
35
35
|
const header = await this.bed.getHeader();
|
|
36
36
|
const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
|
|
37
|
-
const defline = defs
|
|
37
|
+
const defline = defs.at(-1);
|
|
38
38
|
return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
|
|
39
39
|
? defline
|
|
40
40
|
.slice(1)
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BedTabixAdapter.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/BedTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,WAAW,CAAA;AAC3B,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAKrC,MAAqB,eAAgB,SAAQ,sBAAsB;IAWjE,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QAC9D,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACjD,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC/C,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;QACvC,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,IAAI,CAAC,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC9B,UAAU,EAAE,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC;YACtC,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;SAC7B,CAAC,CAAA;QACF,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;IACpC,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAED,KAAK,CAAC,SAAS;QACb,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;YAC3B,OAAO,IAAI,CAAC,WAAW,CAAA;SACxB;QACD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;QACzC,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,
|
|
1
|
+
{"version":3,"file":"BedTabixAdapter.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/BedTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,WAAW,CAAA;AAC3B,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAKrC,MAAqB,eAAgB,SAAQ,sBAAsB;IAWjE,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QAC9D,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACjD,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC/C,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;QACvC,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,IAAI,CAAC,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC9B,UAAU,EAAE,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC;YACtC,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;SAC7B,CAAC,CAAA;QACF,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;IACpC,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAED,KAAK,CAAC,SAAS;QACb,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;YAC3B,OAAO,IAAI,CAAC,WAAW,CAAA;SACxB;QACD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;QACzC,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;QAC3B,OAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;YAC5B,CAAC,CAAC,OAAO;iBACJ,KAAK,CAAC,CAAC,CAAC;iBACR,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;YACvB,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;YACzC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;YAC9B,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;YACpC,MAAM,QAAQ,GAAG,aAAa,CAAC,KAAK,GAAG,CAAC,CAAA;YACxC,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;YACpC,uEAAuE;YACvE,qEAAqE;YACrE,8DAA8D;YAC9D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;YACnC,MAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,EAAE;gBAC7D,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,WAAW,CACT,IAAI,EACJ,MAAM,EACN,QAAQ,EACR,MAAM,EACN,IAAI,CAAC,WAAW,EAChB,IAAI,CAAC,MAAM,EACX,GAAG,IAAI,CAAC,EAAE,IAAI,UAAU,EAAE,EAC1B,KAAK,CACN,CACF,CAAA;gBACH,CAAC;gBACD,MAAM,EAAE,IAAI,CAAC,MAAM;aACpB,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAhFjB,4BAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA;eATxC,eAAe"}
|
|
@@ -5,8 +5,8 @@ export declare function featureData(line: string, uniqueId: string, flip: boolea
|
|
|
5
5
|
export default class BedpeAdapter extends BaseFeatureDataAdapter {
|
|
6
6
|
protected bedpeFeatures?: Promise<{
|
|
7
7
|
header: string;
|
|
8
|
-
feats1: Record<string, string[]>;
|
|
9
|
-
feats2: Record<string, string[]>;
|
|
8
|
+
feats1: Record<string, string[] | undefined>;
|
|
9
|
+
feats2: Record<string, string[] | undefined>;
|
|
10
10
|
columnNames: string[];
|
|
11
11
|
}>;
|
|
12
12
|
protected intervalTrees: {
|
|
@@ -84,7 +84,9 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
|
|
|
84
84
|
if (!feats2[r2]) {
|
|
85
85
|
feats2[r2] = [];
|
|
86
86
|
}
|
|
87
|
+
// eslint-disable-next-line @typescript-eslint/no-non-null-assertion
|
|
87
88
|
feats1[r1].push(line);
|
|
89
|
+
// eslint-disable-next-line @typescript-eslint/no-non-null-assertion
|
|
88
90
|
feats2[r2].push(line);
|
|
89
91
|
}
|
|
90
92
|
const columnNames = this.getConf('columnNames');
|
|
@@ -118,7 +120,7 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
|
|
|
118
120
|
return columnNames;
|
|
119
121
|
}
|
|
120
122
|
const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
|
|
121
|
-
const defline = defs
|
|
123
|
+
const defline = defs.at(-1);
|
|
122
124
|
return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
|
|
123
125
|
? defline
|
|
124
126
|
.slice(1)
|
|
@@ -140,11 +142,15 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
|
|
|
140
142
|
const uniqueId = `${this.id}-${refName}-${i}`;
|
|
141
143
|
return featureData(f, uniqueId, true, names);
|
|
142
144
|
});
|
|
143
|
-
|
|
144
|
-
|
|
145
|
+
if (ret1) {
|
|
146
|
+
for (const obj of ret1) {
|
|
147
|
+
intervalTree.insert([obj.get('start'), obj.get('end')], obj);
|
|
148
|
+
}
|
|
145
149
|
}
|
|
146
|
-
|
|
147
|
-
|
|
150
|
+
if (ret2) {
|
|
151
|
+
for (const obj of ret2) {
|
|
152
|
+
intervalTree.insert([obj.get('start'), obj.get('end')], obj);
|
|
153
|
+
}
|
|
148
154
|
}
|
|
149
155
|
return intervalTree;
|
|
150
156
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BedpeAdapter.js","sourceRoot":"","sources":["../../src/BedpeAdapter/BedpeAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAmB,aAAa,EAAE,MAAM,oBAAoB,CAAA;AACnE,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,UAAU,WAAW,CACzB,IAAY,EACZ,QAAgB,EAChB,IAAa,EACb,KAAgB;IAEhB,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC1B,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC5B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC/B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAChC,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IACjB,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACnB,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,IAAI,GAAG,KAAK;QAChB,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;QACrE,CAAC,CAAC,KAAK,CAAA;IAET,OAAO,IAAI,aAAa,CAAC;QACvB,KAAK,EAAE,MAAM;QACb,GAAG,EAAE,IAAI;QACT,OAAO,EAAE,IAAI;QACb,MAAM,EAAE,OAAO;QACf,IAAI;QACJ,GAAG,IAAI;QACP,KAAK;QACL,QAAQ;QACR,IAAI,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE;KACnE,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,WAAW,CAAC,MAAc;IACjC,IAAI,MAAM,KAAK,GAAG,EAAE;QAClB,OAAO,CAAC,CAAA;KACT;SAAM,IAAI,MAAM,KAAK,GAAG,EAAE;QACzB,OAAO,CAAC,CAAC,CAAA;KACV;SAAM,IAAI,MAAM,KAAK,GAAG,EAAE;QACzB,OAAO,CAAC,CAAA;KACT;SAAM;QACL,OAAO,SAAS,CAAA;KACjB;AACH,CAAC;AAED,MAAqB,YAAa,SAAQ,sBAAsB;IAAhE;;QAQY,kBAAa,GAEnB,EAAE,CAAA;
|
|
1
|
+
{"version":3,"file":"BedpeAdapter.js","sourceRoot":"","sources":["../../src/BedpeAdapter/BedpeAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAmB,aAAa,EAAE,MAAM,oBAAoB,CAAA;AACnE,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,UAAU,WAAW,CACzB,IAAY,EACZ,QAAgB,EAChB,IAAa,EACb,KAAgB;IAEhB,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC1B,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC5B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC/B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAChC,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IACjB,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACnB,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,IAAI,GAAG,KAAK;QAChB,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;QACrE,CAAC,CAAC,KAAK,CAAA;IAET,OAAO,IAAI,aAAa,CAAC;QACvB,KAAK,EAAE,MAAM;QACb,GAAG,EAAE,IAAI;QACT,OAAO,EAAE,IAAI;QACb,MAAM,EAAE,OAAO;QACf,IAAI;QACJ,GAAG,IAAI;QACP,KAAK;QACL,QAAQ;QACR,IAAI,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE;KACnE,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,WAAW,CAAC,MAAc;IACjC,IAAI,MAAM,KAAK,GAAG,EAAE;QAClB,OAAO,CAAC,CAAA;KACT;SAAM,IAAI,MAAM,KAAK,GAAG,EAAE;QACzB,OAAO,CAAC,CAAC,CAAA;KACV;SAAM,IAAI,MAAM,KAAK,GAAG,EAAE;QACzB,OAAO,CAAC,CAAA;KACT;SAAM;QACL,OAAO,SAAS,CAAA;KACjB;AACH,CAAC;AAED,MAAqB,YAAa,SAAQ,sBAAsB;IAAhE;;QAQY,kBAAa,GAEnB,EAAE,CAAA;IAwIR,CAAC;IApIS,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QAC5C,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QAC5C,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACzD,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QACnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QACD,MAAM,IAAI,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACvD,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACxD,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SAC3B;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACrC,MAAM,MAAM,GAAG,EAA0C,CAAA;QACzD,MAAM,MAAM,GAAG,EAA0C,CAAA;QACzD,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC5B,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACrB,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YAClB,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YAClB,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE;gBACf,MAAM,CAAC,EAAE,CAAC,GAAG,EAAE,CAAA;aAChB;YACD,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE;gBACf,MAAM,CAAC,EAAE,CAAC,GAAG,EAAE,CAAA;aAChB;YACD,oEAAoE;YACpE,MAAM,CAAC,EAAE,CAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YACtB,oEAAoE;YACpE,MAAM,CAAC,EAAE,CAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SACvB;QACD,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAE/C,OAAO;YACL,MAAM;YACN,MAAM;YACN,MAAM;YACN,WAAW;SACZ,CAAA;IACH,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,OAAoB,EAAE;QAC3C,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE;YACvB,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAClD,IAAI,CAAC,aAAa,GAAG,SAAS,CAAA;gBAC9B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QAED,OAAO,IAAI,CAAC,aAAa,CAAA;IAC3B,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACpD,OAAO,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;IACvE,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC5C,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACrD,IAAI,WAAW,CAAC,MAAM,EAAE;YACtB,OAAO,WAAW,CAAA;SACnB;QACD,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;QAC3B,OAAO,CAA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|
|
@@ -6,15 +6,15 @@ import { openLocation } from '@jbrowse/core/util/io';
|
|
|
6
6
|
import { ObservableCreate } from '@jbrowse/core/util/rxjs';
|
|
7
7
|
import SimpleFeature from '@jbrowse/core/util/simpleFeature';
|
|
8
8
|
import { map, mergeAll } from 'rxjs/operators';
|
|
9
|
-
import { readConfObject } from '@jbrowse/core/configuration';
|
|
10
9
|
import { ucscProcessedTranscript } from '../util';
|
|
11
10
|
function isUCSC(f) {
|
|
12
11
|
return f.get('thickStart') && f.get('blockCount') && f.get('strand') !== 0;
|
|
13
12
|
}
|
|
14
13
|
export default class BigBedAdapter extends BaseFeatureDataAdapter {
|
|
15
14
|
async configurePre(opts) {
|
|
15
|
+
const pm = this.pluginManager;
|
|
16
16
|
const bigbed = new BigBed({
|
|
17
|
-
filehandle: openLocation(
|
|
17
|
+
filehandle: openLocation(this.getConf('bigBedLocation'), pm),
|
|
18
18
|
});
|
|
19
19
|
const header = await bigbed.getHeader(opts);
|
|
20
20
|
const parser = new BED({ autoSql: header.autoSql });
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BigBedAdapter.js","sourceRoot":"","sources":["../../src/BigBedAdapter/BigBedAdapter.ts"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAA;AAClC,OAAO,GAAG,MAAM,WAAW,CAAA;AAC3B,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAA;AAC9C,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"BigBedAdapter.js","sourceRoot":"","sources":["../../src/BigBedAdapter/BigBedAdapter.ts"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAA;AAClC,OAAO,GAAG,MAAM,WAAW,CAAA;AAC3B,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAA;AAC9C,OAAO,EAAE,uBAAuB,EAAE,MAAM,SAAS,CAAA;AAEjD,SAAS,MAAM,CAAC,CAAU;IACxB,OAAO,CAAC,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAA;AAC5E,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,sBAAsB;IAGxD,KAAK,CAAC,YAAY,CAAC,IAAkB;QAC1C,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,MAAM,GAAG,IAAI,MAAM,CAAC;YACxB,UAAU,EAAE,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,gBAAgB,CAAC,EAAE,EAAE,CAAC;SAC7D,CAAC,CAAA;QACF,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC3C,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,MAAM,CAAC,OAAO,EAAE,CAAC,CAAA;QACnD,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,CAAA;IACnC,CAAC;IAEM,KAAK,CAAC,SAAS,CAAC,IAAkB;QACvC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC7C,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACvC,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QACrD,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,MAAM,CAAA;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,CAAC,OAAO,CAAA;QAC1C,OAAO;YACL,OAAO;YACP,QAAQ;YACR,OAAO,EAAE,EAAE,GAAG,IAAI,EAAE;YACpB,MAAM,EAAE,MAAM,CAAC,WAAW,CACxB,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CACnD;SACF,CAAA;IACH,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QACvB,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,IAAI;gBACF,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;gBACrD,MAAM,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;oBAC5D,MAAM;oBACN,YAAY,EAAE,GAAG,GAAG,KAAK;iBAC1B,CAAC,CAAA;gBACF,EAAE,CAAC,IAAI,CACL,QAAQ,EAAE,EACV,GAAG,CAAC,CAAC,CAAC,EAAE;oBACN,MAAM,IAAI,GAAG,MAAM,CAAC,SAAS,CAC3B,GAAG,OAAO,KAAK,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,IAAI,EAAE,EAC7C;wBACE,QAAQ,EAAE,CAAC,CAAC,QAAkB;qBAC/B,CACF,CAAA;oBAED,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;oBACjE,IAAI,UAAU,EAAE;wBACd,MAAM,MAAM,GAAG,WAAW,IAAI,WAAW,IAAI,EAAE,CAAA;wBAC/C,MAAM,KAAK,GAAG,UAAU,CAAA;wBACxB,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAA;wBAC5B,IAAI,CAAC,WAAW,GAAG,EAAE,CAAA;wBAErB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE;4BACtC,MAAM,IAAI,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,YAAY,CAAA;4BAC5C,MAAM,IAAI,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;4BACnC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC;gCACpB,QAAQ,EAAE,GAAG,CAAC,CAAC,QAAQ,IAAI,CAAC,EAAE;gCAC9B,KAAK,EAAE,IAAI;gCACX,GAAG,EAAE,IAAI;gCACT,IAAI,EAAE,OAAO;6BACd,CAAC,CAAA;yBACH;qBACF;oBACD,IAAI,CAAC,CAAC,QAAQ,KAAK,SAAS,EAAE;wBAC5B,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;qBACvC;oBACD,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,CAAA;oBAErD,MAAM,CAAC,GAAG,IAAI,aAAa,CAAC;wBAC1B,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,QAAQ,EAAE;wBAC9B,IAAI,EAAE;4BACJ,GAAG,IAAI;4BACP,KAAK,EAAE,CAAC,CAAC,KAAK;4BACd,GAAG,EAAE,CAAC,CAAC,GAAG;4BACV,OAAO;yBACR;qBACF,CAAC,CAAA;oBAEF,4DAA4D;oBAC5D,+DAA+D;oBAC/D,6DAA6D;oBAC7D,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,uBAAuB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACnD,CAAC,CAAC,CACH,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;aACtB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;CAChC"}
|
package/esm/index.js
CHANGED
|
@@ -79,6 +79,14 @@ export default class BedPlugin extends Plugin {
|
|
|
79
79
|
return adapterGuesser(file, index, adapterHint);
|
|
80
80
|
};
|
|
81
81
|
});
|
|
82
|
+
pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
|
|
83
|
+
return (adapterName) => {
|
|
84
|
+
if (adapterName === 'BedpeAdapter') {
|
|
85
|
+
return 'VariantTrack';
|
|
86
|
+
}
|
|
87
|
+
return trackTypeGuesser(adapterName);
|
|
88
|
+
};
|
|
89
|
+
});
|
|
82
90
|
}
|
|
83
91
|
}
|
|
84
92
|
//# sourceMappingURL=index.js.map
|
package/esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAC1C,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,WAAW,MAAM,cAAc,CAAA;AAEtC,OAAO,EACL,WAAW,EACX,SAAS,EACT,aAAa,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAC1C,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,WAAW,MAAM,cAAc,CAAA;AAEtC,OAAO,EACL,WAAW,EACX,SAAS,EACT,aAAa,GAGd,MAAM,2BAA2B,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,MAAM;IAA7C;;QACE,SAAI,GAAG,WAAW,CAAA;IAoHpB,CAAC;IAlHC,OAAO,CAAC,aAA4B;QAClC,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,WAAW,CAAC,aAAa,CAAC,CAAA;QAC1B,aAAa,CAAC,aAAa,CAAC,CAAA;QAC5B,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,iBAAiB,CAAA;gBACpC,MAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,cAAc,EAAE,IAAI;iBACrB,CAAA;gBAED,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,eAAe,CAAA;gBAClC,MAAM,WAAW,GAAG,cAAc,CAAA;gBAClC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,aAAa,EAAE,IAAI;qBACpB,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,eAAe,CAAA;gBAClC,MAAM,WAAW,GAAG,iBAAiB,CAAA;gBACrC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,SAAS,GAAG,KAAK,IAAI,WAAW,CAAC,KAAK,CAAC,CAAA;gBAC7C,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,aAAa,EAAE,IAAI;wBACnB,KAAK,EAAE;4BACL,QAAQ,EAAE,KAAK,IAAI,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC;4BAC1C,SAAS,EAAE,aAAa,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;yBAClD;qBACF,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,SAAS,CAAA;gBAC5B,MAAM,WAAW,GAAG,YAAY,CAAA;gBAChC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,WAAW,EAAE,IAAI;qBAClB,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;YACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;gBAC7B,IAAI,WAAW,KAAK,cAAc,EAAE;oBAClC,OAAO,cAAc,CAAA;iBACtB;gBACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;YACtC,CAAC,CAAA;QACH,CAAC,CACF,CAAA;IACH,CAAC;CACF"}
|
package/esm/util.js
CHANGED
|
@@ -101,11 +101,10 @@ export function ucscProcessedTranscript(feature) {
|
|
|
101
101
|
delete newData.blockCount;
|
|
102
102
|
delete newData.thickStart;
|
|
103
103
|
delete newData.thickEnd;
|
|
104
|
-
|
|
104
|
+
return new SimpleFeature({
|
|
105
105
|
data: newData,
|
|
106
106
|
id: feature.id(),
|
|
107
107
|
});
|
|
108
|
-
return newFeature;
|
|
109
108
|
}
|
|
110
109
|
function defaultParser(fields, line) {
|
|
111
110
|
return Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-bed",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.6.1",
|
|
4
4
|
"description": "JBrowse 2 bed adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -38,7 +38,7 @@
|
|
|
38
38
|
},
|
|
39
39
|
"dependencies": {
|
|
40
40
|
"@flatten-js/interval-tree": "^1.0.15",
|
|
41
|
-
"@gmod/bbi": "^
|
|
41
|
+
"@gmod/bbi": "^4.0.0",
|
|
42
42
|
"@gmod/bed": "^2.1.2",
|
|
43
43
|
"@gmod/bgzf-filehandle": "^1.4.3",
|
|
44
44
|
"@gmod/tabix": "^1.5.6"
|
|
@@ -56,5 +56,5 @@
|
|
|
56
56
|
"distModule": "esm/index.js",
|
|
57
57
|
"srcModule": "src/index.ts",
|
|
58
58
|
"module": "esm/index.js",
|
|
59
|
-
"gitHead": "
|
|
59
|
+
"gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
|
|
60
60
|
}
|
|
@@ -107,7 +107,7 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
|
|
|
107
107
|
return columnNames
|
|
108
108
|
}
|
|
109
109
|
const defs = header.split(/\n|\r\n|\r/).filter(f => !!f)
|
|
110
|
-
const defline = defs
|
|
110
|
+
const defline = defs.at(-1)
|
|
111
111
|
return defline?.includes('\t')
|
|
112
112
|
? defline
|
|
113
113
|
.slice(1)
|
|
@@ -60,7 +60,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
|
|
|
60
60
|
}
|
|
61
61
|
const header = await this.bed.getHeader()
|
|
62
62
|
const defs = header.split(/\n|\r\n|\r/).filter(f => !!f)
|
|
63
|
-
const defline = defs
|
|
63
|
+
const defline = defs.at(-1)
|
|
64
64
|
return defline?.includes('\t')
|
|
65
65
|
? defline
|
|
66
66
|
.slice(1)
|
|
@@ -62,8 +62,8 @@ function parseStrand(strand: string) {
|
|
|
62
62
|
export default class BedpeAdapter extends BaseFeatureDataAdapter {
|
|
63
63
|
protected bedpeFeatures?: Promise<{
|
|
64
64
|
header: string
|
|
65
|
-
feats1: Record<string, string[]>
|
|
66
|
-
feats2: Record<string, string[]>
|
|
65
|
+
feats1: Record<string, string[] | undefined>
|
|
66
|
+
feats2: Record<string, string[] | undefined>
|
|
67
67
|
columnNames: string[]
|
|
68
68
|
}>
|
|
69
69
|
|
|
@@ -90,8 +90,8 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
|
|
|
90
90
|
headerLines.push(lines[i])
|
|
91
91
|
}
|
|
92
92
|
const header = headerLines.join('\n')
|
|
93
|
-
const feats1 = {} as Record<string, string[]>
|
|
94
|
-
const feats2 = {} as Record<string, string[]>
|
|
93
|
+
const feats1 = {} as Record<string, string[] | undefined>
|
|
94
|
+
const feats2 = {} as Record<string, string[] | undefined>
|
|
95
95
|
for (; i < lines.length; i++) {
|
|
96
96
|
const line = lines[i]
|
|
97
97
|
const cols = line.split('\t')
|
|
@@ -103,8 +103,10 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
|
|
|
103
103
|
if (!feats2[r2]) {
|
|
104
104
|
feats2[r2] = []
|
|
105
105
|
}
|
|
106
|
-
|
|
107
|
-
|
|
106
|
+
// eslint-disable-next-line @typescript-eslint/no-non-null-assertion
|
|
107
|
+
feats1[r1]!.push(line)
|
|
108
|
+
// eslint-disable-next-line @typescript-eslint/no-non-null-assertion
|
|
109
|
+
feats2[r2]!.push(line)
|
|
108
110
|
}
|
|
109
111
|
const columnNames = this.getConf('columnNames')
|
|
110
112
|
|
|
@@ -143,7 +145,7 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
|
|
|
143
145
|
return columnNames
|
|
144
146
|
}
|
|
145
147
|
const defs = header.split(/\n|\r\n|\r/).filter(f => !!f)
|
|
146
|
-
const defline = defs
|
|
148
|
+
const defline = defs.at(-1)
|
|
147
149
|
return defline?.includes('\t')
|
|
148
150
|
? defline
|
|
149
151
|
.slice(1)
|
|
@@ -168,12 +170,16 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
|
|
|
168
170
|
return featureData(f, uniqueId, true, names)
|
|
169
171
|
})
|
|
170
172
|
|
|
171
|
-
|
|
172
|
-
|
|
173
|
+
if (ret1) {
|
|
174
|
+
for (const obj of ret1) {
|
|
175
|
+
intervalTree.insert([obj.get('start'), obj.get('end')], obj)
|
|
176
|
+
}
|
|
173
177
|
}
|
|
174
178
|
|
|
175
|
-
|
|
176
|
-
|
|
179
|
+
if (ret2) {
|
|
180
|
+
for (const obj of ret2) {
|
|
181
|
+
intervalTree.insert([obj.get('start'), obj.get('end')], obj)
|
|
182
|
+
}
|
|
177
183
|
}
|
|
178
184
|
|
|
179
185
|
return intervalTree
|
|
@@ -10,7 +10,6 @@ import { openLocation } from '@jbrowse/core/util/io'
|
|
|
10
10
|
import { ObservableCreate } from '@jbrowse/core/util/rxjs'
|
|
11
11
|
import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
|
|
12
12
|
import { map, mergeAll } from 'rxjs/operators'
|
|
13
|
-
import { readConfObject } from '@jbrowse/core/configuration'
|
|
14
13
|
import { ucscProcessedTranscript } from '../util'
|
|
15
14
|
|
|
16
15
|
function isUCSC(f: Feature) {
|
|
@@ -21,11 +20,9 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
|
|
|
21
20
|
private cached?: Promise<{ bigbed: BigBed; header: any; parser: BED }>
|
|
22
21
|
|
|
23
22
|
public async configurePre(opts?: BaseOptions) {
|
|
23
|
+
const pm = this.pluginManager
|
|
24
24
|
const bigbed = new BigBed({
|
|
25
|
-
filehandle: openLocation(
|
|
26
|
-
readConfObject(this.config, 'bigBedLocation'),
|
|
27
|
-
this.pluginManager,
|
|
28
|
-
),
|
|
25
|
+
filehandle: openLocation(this.getConf('bigBedLocation'), pm),
|
|
29
26
|
})
|
|
30
27
|
const header = await bigbed.getHeader(opts)
|
|
31
28
|
const parser = new BED({ autoSql: header.autoSql })
|
package/src/index.ts
CHANGED
|
@@ -10,6 +10,7 @@ import {
|
|
|
10
10
|
makeIndex,
|
|
11
11
|
makeIndexType,
|
|
12
12
|
AdapterGuesser,
|
|
13
|
+
TrackTypeGuesser,
|
|
13
14
|
} from '@jbrowse/core/util/tracks'
|
|
14
15
|
|
|
15
16
|
export default class BedPlugin extends Plugin {
|
|
@@ -116,5 +117,17 @@ export default class BedPlugin extends Plugin {
|
|
|
116
117
|
}
|
|
117
118
|
},
|
|
118
119
|
)
|
|
120
|
+
|
|
121
|
+
pluginManager.addToExtensionPoint(
|
|
122
|
+
'Core-guessTrackTypeForLocation',
|
|
123
|
+
(trackTypeGuesser: TrackTypeGuesser) => {
|
|
124
|
+
return (adapterName: string) => {
|
|
125
|
+
if (adapterName === 'BedpeAdapter') {
|
|
126
|
+
return 'VariantTrack'
|
|
127
|
+
}
|
|
128
|
+
return trackTypeGuesser(adapterName)
|
|
129
|
+
}
|
|
130
|
+
},
|
|
131
|
+
)
|
|
119
132
|
}
|
|
120
133
|
}
|
package/src/util.ts
CHANGED
|
@@ -113,11 +113,10 @@ export function ucscProcessedTranscript(feature: Feature) {
|
|
|
113
113
|
delete newData.blockCount
|
|
114
114
|
delete newData.thickStart
|
|
115
115
|
delete newData.thickEnd
|
|
116
|
-
|
|
116
|
+
return new SimpleFeature({
|
|
117
117
|
data: newData,
|
|
118
118
|
id: feature.id(),
|
|
119
119
|
})
|
|
120
|
-
return newFeature
|
|
121
120
|
}
|
|
122
121
|
|
|
123
122
|
function defaultParser(fields: string[], line: string) {
|