@jbrowse/plugin-bed 2.4.0 → 2.4.1
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 -2
- package/dist/BedAdapter/BedAdapter.js.map +1 -1
- package/dist/BedpeAdapter/BedpeAdapter.js +2 -4
- package/dist/BedpeAdapter/BedpeAdapter.js.map +1 -1
- package/esm/BedAdapter/BedAdapter.js +1 -2
- package/esm/BedAdapter/BedAdapter.js.map +1 -1
- package/esm/BedpeAdapter/BedpeAdapter.js +2 -4
- package/esm/BedpeAdapter/BedpeAdapter.js.map +1 -1
- package/package.json +3 -3
- package/src/BedAdapter/BedAdapter.ts +1 -2
- package/src/BedTabixAdapter/__snapshots__/BedTabixAdapter.test.ts.snap +71 -71
- package/src/BedpeAdapter/BedpeAdapter.ts +2 -4
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@@ -106,8 +106,7 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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const uniqueId = `${this.id}-${refName}-${i}`;
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return (0, util_1.featureData)(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
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});
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-
for (
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const obj = ret[i];
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+
for (const obj of ret) {
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intervalTree.insert([obj.get('start'), obj.get('end')], obj);
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}
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return intervalTree;
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@@ -1 +1 @@
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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;
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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,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,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,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAzJjC,6BA0JC;AA1Ie,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}
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@@ -147,12 +147,10 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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const uniqueId = `${this.id}-${refName}-${i}`;
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return featureData(f, uniqueId, true, names);
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});
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for (
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const obj = ret1[i];
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for (const obj of ret1) {
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intervalTree.insert([obj.get('start'), obj.get('end')], obj);
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}
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for (
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const obj = ret2[i];
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for (const obj of ret2) {
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intervalTree.insert([obj.get('start'), obj.get('end')], obj);
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}
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return intervalTree;
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@@ -1 +1 @@
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{"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;
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+
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@@ -101,8 +101,7 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
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|
101
101
|
const uniqueId = `${this.id}-${refName}-${i}`;
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102
102
|
return featureData(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
|
|
103
103
|
});
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|
104
|
-
for (
|
|
105
|
-
const obj = ret[i];
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104
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+
for (const obj of ret) {
|
|
106
105
|
intervalTree.insert([obj.get('start'), obj.get('end')], obj);
|
|
107
106
|
}
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|
108
107
|
return intervalTree;
|
|
@@ -1 +1 @@
|
|
|
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,MAAM,CAAC,OAAO,OAAO,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,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,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,uB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@@ -140,12 +140,10 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
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140
140
|
const uniqueId = `${this.id}-${refName}-${i}`;
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|
141
141
|
return featureData(f, uniqueId, true, names);
|
|
142
142
|
});
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143
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-
for (
|
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144
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-
const obj = ret1[i];
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143
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+
for (const obj of ret1) {
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145
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|
intervalTree.insert([obj.get('start'), obj.get('end')], obj);
|
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146
145
|
}
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|
147
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-
for (
|
|
148
|
-
const obj = ret2[i];
|
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146
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+
for (const obj of ret2) {
|
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149
147
|
intervalTree.insert([obj.get('start'), obj.get('end')], obj);
|
|
150
148
|
}
|
|
151
149
|
return intervalTree;
|
|
@@ -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,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,sBAAsB;IAAhE;;QAQY,kBAAa,GAEnB,EAAE,CAAA;
|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-bed",
|
|
3
|
-
"version": "2.4.
|
|
3
|
+
"version": "2.4.1",
|
|
4
4
|
"description": "JBrowse 2 bed adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -41,7 +41,7 @@
|
|
|
41
41
|
"@gmod/bbi": "^3.0.0",
|
|
42
42
|
"@gmod/bed": "^2.1.2",
|
|
43
43
|
"@gmod/bgzf-filehandle": "^1.4.3",
|
|
44
|
-
"@gmod/tabix": "^1.5.
|
|
44
|
+
"@gmod/tabix": "^1.5.6"
|
|
45
45
|
},
|
|
46
46
|
"peerDependencies": {
|
|
47
47
|
"@jbrowse/core": "^2.0.0",
|
|
@@ -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": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
|
|
60
60
|
}
|
|
@@ -140,8 +140,7 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
|
|
|
140
140
|
)
|
|
141
141
|
})
|
|
142
142
|
|
|
143
|
-
for (
|
|
144
|
-
const obj = ret[i]
|
|
143
|
+
for (const obj of ret) {
|
|
145
144
|
intervalTree.insert([obj.get('start'), obj.get('end')], obj)
|
|
146
145
|
}
|
|
147
146
|
return intervalTree
|
|
@@ -7,70 +7,70 @@ exports[`adapter can fetch bed with header 1`] = `
|
|
|
7
7
|
"refName": "contigA",
|
|
8
8
|
"start": 3000,
|
|
9
9
|
"strand": 0,
|
|
10
|
-
"uniqueId": "test-
|
|
10
|
+
"uniqueId": "test-163099",
|
|
11
11
|
},
|
|
12
12
|
{
|
|
13
13
|
"end": 3114,
|
|
14
14
|
"refName": "contigA",
|
|
15
15
|
"start": 3105,
|
|
16
16
|
"strand": 0,
|
|
17
|
-
"uniqueId": "test-
|
|
17
|
+
"uniqueId": "test-163117",
|
|
18
18
|
},
|
|
19
19
|
{
|
|
20
20
|
"end": 3161,
|
|
21
21
|
"refName": "contigA",
|
|
22
22
|
"start": 3152,
|
|
23
23
|
"strand": 0,
|
|
24
|
-
"uniqueId": "test-
|
|
24
|
+
"uniqueId": "test-163135",
|
|
25
25
|
},
|
|
26
26
|
{
|
|
27
27
|
"end": 3180,
|
|
28
28
|
"refName": "contigA",
|
|
29
29
|
"start": 3171,
|
|
30
30
|
"strand": 0,
|
|
31
|
-
"uniqueId": "test-
|
|
31
|
+
"uniqueId": "test-163153",
|
|
32
32
|
},
|
|
33
33
|
{
|
|
34
34
|
"end": 3183,
|
|
35
35
|
"refName": "contigA",
|
|
36
36
|
"start": 3174,
|
|
37
37
|
"strand": 0,
|
|
38
|
-
"uniqueId": "test-
|
|
38
|
+
"uniqueId": "test-163171",
|
|
39
39
|
},
|
|
40
40
|
{
|
|
41
41
|
"end": 3222,
|
|
42
42
|
"refName": "contigA",
|
|
43
43
|
"start": 3213,
|
|
44
44
|
"strand": 0,
|
|
45
|
-
"uniqueId": "test-
|
|
45
|
+
"uniqueId": "test-163189",
|
|
46
46
|
},
|
|
47
47
|
{
|
|
48
48
|
"end": 3474,
|
|
49
49
|
"refName": "contigA",
|
|
50
50
|
"start": 3465,
|
|
51
51
|
"strand": 0,
|
|
52
|
-
"uniqueId": "test-
|
|
52
|
+
"uniqueId": "test-163207",
|
|
53
53
|
},
|
|
54
54
|
{
|
|
55
55
|
"end": 3804,
|
|
56
56
|
"refName": "contigA",
|
|
57
57
|
"start": 3795,
|
|
58
58
|
"strand": 0,
|
|
59
|
-
"uniqueId": "test-
|
|
59
|
+
"uniqueId": "test-163225",
|
|
60
60
|
},
|
|
61
61
|
{
|
|
62
62
|
"end": 4044,
|
|
63
63
|
"refName": "contigA",
|
|
64
64
|
"start": 4035,
|
|
65
65
|
"strand": 0,
|
|
66
|
-
"uniqueId": "test-
|
|
66
|
+
"uniqueId": "test-163243",
|
|
67
67
|
},
|
|
68
68
|
{
|
|
69
69
|
"end": 4082,
|
|
70
70
|
"refName": "contigA",
|
|
71
71
|
"start": 4073,
|
|
72
72
|
"strand": 0,
|
|
73
|
-
"uniqueId": "test-
|
|
73
|
+
"uniqueId": "test-163261",
|
|
74
74
|
},
|
|
75
75
|
]
|
|
76
76
|
`;
|
|
@@ -111,15 +111,15 @@ exports[`adapter can fetch features bed with autosql 1`] = `
|
|
|
111
111
|
"subfeatures": [
|
|
112
112
|
{
|
|
113
113
|
"end": 2,
|
|
114
|
-
"parentId": "test-
|
|
114
|
+
"parentId": "test-52986",
|
|
115
115
|
"start": 1,
|
|
116
116
|
"strand": 0,
|
|
117
117
|
"type": "three_prime_UTR",
|
|
118
|
-
"uniqueId": "test-
|
|
118
|
+
"uniqueId": "test-52986-0",
|
|
119
119
|
},
|
|
120
120
|
],
|
|
121
121
|
"type": "mRNA",
|
|
122
|
-
"uniqueId": "test-
|
|
122
|
+
"uniqueId": "test-52986",
|
|
123
123
|
"weight": "--",
|
|
124
124
|
"years_smoked": "--",
|
|
125
125
|
},
|
|
@@ -133,70 +133,70 @@ exports[`adapter can fetch features from volvox.sort.bed.gz simple bed3 1`] = `
|
|
|
133
133
|
"refName": "contigA",
|
|
134
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|
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|
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`;
|
|
@@ -168,13 +168,11 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
|
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|
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return featureData(f, uniqueId, true, names)
|
|
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|
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for (
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|
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|
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|