@jbrowse/plugin-gff3 2.1.4 → 2.1.6
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/Gff3Adapter/Gff3Adapter.js +3 -2
- package/dist/Gff3Adapter/Gff3Adapter.js.map +1 -1
- package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js +2 -1
- package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js.map +1 -1
- package/esm/Gff3Adapter/Gff3Adapter.js +3 -2
- package/esm/Gff3Adapter/Gff3Adapter.js.map +1 -1
- package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js +2 -1
- package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js.map +1 -1
- package/package.json +3 -3
- package/src/Gff3Adapter/Gff3Adapter.ts +3 -2
- package/src/Gff3Adapter/__snapshots__/Gff3Adapter.test.ts.snap +4 -0
- package/src/Gff3TabixAdapter/Gff3TabixAdapter.ts +3 -1
- package/src/Gff3TabixAdapter/__snapshots__/Gff3TabixAdapter.test.ts.snap +4 -0
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@@ -23,7 +23,7 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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throw new Error('Data exceeds maximum string length (512MB)');
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}
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const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
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-
const lines = data.split(
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+
const lines = data.split(/\n|\r\n|\r/);
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const headerLines = [];
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for (let i = 0; i < lines.length && lines[i].startsWith('#'); i++) {
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headerLines.push(lines[i]);
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@@ -34,6 +34,7 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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parseComments: false,
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parseDirectives: false,
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parseSequences: false,
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disableDerivesFromReferences: true,
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});
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const intervalTree = feats
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.flat()
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@@ -141,7 +142,7 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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}
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delete f.child_features;
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delete f.data;
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-
delete f.derived_features
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+
// delete f.derived_features
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delete f.attributes;
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delete f.seq_id;
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return f;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"Gff3Adapter.js","sourceRoot":"","sources":["../../src/Gff3Adapter/Gff3Adapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,8EAAoD;AACpD,qFAAyE;AACzE,2DAA6C;AAE7C,oDAAwD;AAExD,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,eAAqB,SAAQ,oCAAsB;IAMzC,KAAK,CAAC,SAAS;QACrB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAC1E,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,
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1
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+
{"version":3,"file":"Gff3Adapter.js","sourceRoot":"","sources":["../../src/Gff3Adapter/Gff3Adapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,8EAAoD;AACpD,qFAAyE;AACzE,2DAA6C;AAE7C,oDAAwD;AAExD,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,eAAqB,SAAQ,oCAAsB;IAMzC,KAAK,CAAC,SAAS;QACrB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAC1E,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,CAAA;QACtC,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACjE,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SAC3B;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAErC,MAAM,KAAK,GAAG,aAAG,CAAC,eAAe,CAAC,IAAI,EAAE;YACtC,aAAa,EAAE,IAAI;YACnB,aAAa,EAAE,KAAK;YACpB,eAAe,EAAE,KAAK;YACtB,cAAc,EAAE,KAAK;YACrB,4BAA4B,EAAE,IAAI;SACnC,CAAC,CAAA;QAEF,MAAM,YAAY,GAAG,KAAK;aACvB,IAAI,EAAE;aACN,GAAG,CACF,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,IAAI,uBAAa,CAAC;YAChB,IAAI,EAAE,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC;YACzB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,WAAW,CAAC,EAAE;SAC7B,CAAC,CACL;aACA,MAAM,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,GAAG,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;YAC9B,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACb,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,uBAAY,EAAE,CAAA;aAC9B;YACD,GAAG,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;YACxD,OAAO,GAAG,CAAA;QACZ,CAAC,EAAE,EAAkC,CAAC,CAAA;QAExC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEO,KAAK,CAAC,QAAQ;QACpB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,SAAS,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC5C,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,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAC9C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACxC,OAAO,MAAM,CAAA;IACf,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;gBACrC,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;gBAC9C,MAAA,YAAY,CAAC,OAAO,CAAC,0CACjB,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EACpB,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;gBACjC,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEO,WAAW,CAAC,IAA6B;QAC/C,MAAM,CAAC,GAA4B,EAAE,GAAG,IAAI,EAAE,CAC7C;QAAC,CAAC,CAAC,KAAgB,IAAI,CAAC,CAAA,CAAC,uBAAuB;QACjD,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YACvB,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;SACd;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM;YACL,CAAC,CAAC,MAAM,GAAG,SAAS,CAAA;SACrB;QACD,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC5B,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC,MAAM,CAAA;QACvB,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,OAAO,CAAC,CAAC,KAAK,CAAA;SACf;QACD,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,OAAO,CAAC,CAAC,KAAK,CAAA;SACf;QACD,MAAM,aAAa,GAAG;YACpB,OAAO;YACP,KAAK;YACL,QAAQ;YACR,OAAO;YACP,MAAM;YACN,QAAQ;YACR,OAAO;YACP,QAAQ;SACT,CAAA;QACD,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,IAAI,EAAE,CAAA;QAC5C,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACtC,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAA;YACvB,IAAI,aAAa,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE;gBAC7B,gDAAgD;gBAChD,gCAAgC;gBAChC,CAAC,IAAI,GAAG,CAAA;aACT;YACD,IAAI,cAAc,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;gBAC9B,IAAI,IAAI,GAAkC,cAAc,CAAC,CAAC,CAAC,CAAA;gBAC3D,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE;oBAC5C,CAAC;oBAAA,CAAC,IAAI,CAAC,GAAG,IAAI,CAAA;iBACf;gBACD,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;aACZ;QACH,CAAC,CAAC,CAAA;QACF,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,MAAM,CAAA;QAEpB,gFAAgF;QAChF,IAAI,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE;YACrD,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,cAAc;iBAChC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC;iBACvE,IAAI,EAAE,CAAA;SACV;QAED,OAAO,CAAC,CAAC,cAAc,CAAA;QACvB,OAAO,CAAC,CAAC,IAAI,CAAA;QACb,4BAA4B;QAC5B,OAAO,CAAC,CAAC,UAAU,CAAA;QACnB,OAAO,CAAC,CAAC,MAAM,CAAA;QACf,OAAO,CAAC,CAAA;IACV,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAG,CAAC;CAC1C;AAvJD,4BAuJC"}
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@@ -92,6 +92,7 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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parseComments: false,
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parseDirectives: false,
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parseSequences: false,
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disableDerivesFromReferences: true,
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});
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features.forEach(featureLocs => this.formatFeatures(featureLocs).forEach(f => {
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if ((0, range_1.doesIntersect2)(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
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@@ -180,7 +181,7 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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}
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delete f.child_features;
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delete f.derived_features
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// delete f.derived_features
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delete f._linehash;
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delete f.attributes;
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delete f.seq_id;
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@@ -1 +1 @@
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-
{"version":3,"file":"Gff3TabixAdapter.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/Gff3TabixAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yCAAyC;AACzC,yEAGgD;AAChD,oDAAyD;AAEzD,8CAAoD;AACpD,kDAA0D;AAC1D,qFAAyE;AACzE,uCAA8C;AAC9C,oDAAqE;AAErE,+DAGoC;AAWpC,eAAqB,SAAQ,oCAAsB;IAKjD,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,aAAa,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAC7D,MAAM,SAAS,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAChE,MAAM,QAAQ,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC9D,MAAM,cAAc,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,gBAAgB,CAAC,CAAA;QAE/D,IAAI,CAAC,cAAc,GAAG,cAAc,IAAI,CAAC,YAAY,EAAE,QAAQ,EAAE,QAAQ,CAAC,CAAA;QAC1E,IAAI,CAAC,GAAG,GAAG,IAAI,wBAAgB,CAAC;YAC9B,UAAU,EAAE,IAAA,iBAAY,EAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;YAC3D,aAAa,EACX,SAAS,KAAK,KAAK;gBACjB,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACf,aAAa,EACX,SAAS,KAAK,KAAK;gBACjB,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACf,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,aAAa,EAAE,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC;SAChC,CAAC,CAAA;IACJ,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;YAC7C,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAA;QAC/D,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,iBAAiB,CAC7B,KAAa,EACb,OAAoB,EAAE,EACtB,QAA2D,EAC3D,QAA2B,EAC3B,eAAwB,EACxB,aAAa,GAAG,KAAK;QAErB,IAAI;YACF,MAAM,KAAK,GAAkB,EAAE,CAAA;YAE/B,MAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CACrB,KAAK,CAAC,OAAO,EACb,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,GAAG,EACT,CAAC,IAAY,EAAE,UAAkB,EAAE,EAAE;gBACnC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,aAAa,EAAE,IAAI,EAAE,UAAU,CAAC,CAAC,CAAA;YACtE,CAAC,CACF,CAAA;YACD,IAAI,eAAe,IAAI,KAAK,CAAC,MAAM,EAAE;gBACnC,IAAI,QAAQ,GAAG,QAAQ,CAAA;gBACvB,IAAI,MAAM,GAAG,CAAC,QAAQ,CAAA;gBACtB,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;oBACnB,MAAM,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;oBAClC,yEAAyE;oBACzE,6CAA6C;oBAC7C,IAAI,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE;wBAC9C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA,CAAC,iBAAiB;wBAC9C,IAAI,KAAK,GAAG,QAAQ,EAAE;4BACpB,QAAQ,GAAG,KAAK,CAAA;yBACjB;wBACD,IAAI,IAAI,CAAC,GAAG,GAAG,MAAM,EAAE;4BACrB,MAAM,GAAG,IAAI,CAAC,GAAG,CAAA;yBAClB;qBACF;gBACH,CAAC,CAAC,CAAA;gBACF,IAAI,MAAM,GAAG,KAAK,CAAC,GAAG,IAAI,QAAQ,GAAG,KAAK,CAAC,KAAK,EAAE;oBAChD,gEAAgE;oBAChE,8BAA8B;oBAC9B,IAAI,CAAC,iBAAiB,CACpB,EAAE,GAAG,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,EAAE,MAAM,EAAE,EAC1C,IAAI,EACJ,QAAQ,EACR,QAAQ,EACR,KAAK,EACL,KAAK,CACN,CAAA;oBACD,OAAM;iBACP;aACF;YAED,MAAM,IAAI,GAAG,KAAK;iBACf,GAAG,CAAC,CAAC,UAAuB,EAAE,EAAE;gBAC/B,IAAI,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;oBACxD,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE;wBAC/C,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,cAAc,UAAU,CAAC,QAAQ,EAAE,CAAA;qBAC5D;iBACF;qBAAM;oBACL,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,aAAa,UAAU,CAAC,QAAQ,EAAE,CAAA;iBAC1D;gBACD,OAAO,UAAU,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YACrC,CAAC,CAAC;iBACD,IAAI,CAAC,IAAI,CAAC,CAAA;YAEb,MAAM,QAAQ,GAAG,aAAG,CAAC,eAAe,CAAC,IAAI,EAAE;gBACzC,aAAa,EAAE,IAAI;gBACnB,aAAa,EAAE,KAAK;gBACpB,eAAe,EAAE,KAAK;gBACtB,cAAc,EAAE,KAAK;
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+
{"version":3,"file":"Gff3TabixAdapter.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/Gff3TabixAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yCAAyC;AACzC,yEAGgD;AAChD,oDAAyD;AAEzD,8CAAoD;AACpD,kDAA0D;AAC1D,qFAAyE;AACzE,uCAA8C;AAC9C,oDAAqE;AAErE,+DAGoC;AAWpC,eAAqB,SAAQ,oCAAsB;IAKjD,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,aAAa,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAC7D,MAAM,SAAS,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAChE,MAAM,QAAQ,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC9D,MAAM,cAAc,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,gBAAgB,CAAC,CAAA;QAE/D,IAAI,CAAC,cAAc,GAAG,cAAc,IAAI,CAAC,YAAY,EAAE,QAAQ,EAAE,QAAQ,CAAC,CAAA;QAC1E,IAAI,CAAC,GAAG,GAAG,IAAI,wBAAgB,CAAC;YAC9B,UAAU,EAAE,IAAA,iBAAY,EAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;YAC3D,aAAa,EACX,SAAS,KAAK,KAAK;gBACjB,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACf,aAAa,EACX,SAAS,KAAK,KAAK;gBACjB,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACf,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,aAAa,EAAE,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC;SAChC,CAAC,CAAA;IACJ,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;YAC7C,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAA;QAC/D,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,iBAAiB,CAC7B,KAAa,EACb,OAAoB,EAAE,EACtB,QAA2D,EAC3D,QAA2B,EAC3B,eAAwB,EACxB,aAAa,GAAG,KAAK;QAErB,IAAI;YACF,MAAM,KAAK,GAAkB,EAAE,CAAA;YAE/B,MAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CACrB,KAAK,CAAC,OAAO,EACb,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,GAAG,EACT,CAAC,IAAY,EAAE,UAAkB,EAAE,EAAE;gBACnC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,aAAa,EAAE,IAAI,EAAE,UAAU,CAAC,CAAC,CAAA;YACtE,CAAC,CACF,CAAA;YACD,IAAI,eAAe,IAAI,KAAK,CAAC,MAAM,EAAE;gBACnC,IAAI,QAAQ,GAAG,QAAQ,CAAA;gBACvB,IAAI,MAAM,GAAG,CAAC,QAAQ,CAAA;gBACtB,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;oBACnB,MAAM,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;oBAClC,yEAAyE;oBACzE,6CAA6C;oBAC7C,IAAI,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE;wBAC9C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA,CAAC,iBAAiB;wBAC9C,IAAI,KAAK,GAAG,QAAQ,EAAE;4BACpB,QAAQ,GAAG,KAAK,CAAA;yBACjB;wBACD,IAAI,IAAI,CAAC,GAAG,GAAG,MAAM,EAAE;4BACrB,MAAM,GAAG,IAAI,CAAC,GAAG,CAAA;yBAClB;qBACF;gBACH,CAAC,CAAC,CAAA;gBACF,IAAI,MAAM,GAAG,KAAK,CAAC,GAAG,IAAI,QAAQ,GAAG,KAAK,CAAC,KAAK,EAAE;oBAChD,gEAAgE;oBAChE,8BAA8B;oBAC9B,IAAI,CAAC,iBAAiB,CACpB,EAAE,GAAG,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,EAAE,MAAM,EAAE,EAC1C,IAAI,EACJ,QAAQ,EACR,QAAQ,EACR,KAAK,EACL,KAAK,CACN,CAAA;oBACD,OAAM;iBACP;aACF;YAED,MAAM,IAAI,GAAG,KAAK;iBACf,GAAG,CAAC,CAAC,UAAuB,EAAE,EAAE;gBAC/B,IAAI,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;oBACxD,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE;wBAC/C,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,cAAc,UAAU,CAAC,QAAQ,EAAE,CAAA;qBAC5D;iBACF;qBAAM;oBACL,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,aAAa,UAAU,CAAC,QAAQ,EAAE,CAAA;iBAC1D;gBACD,OAAO,UAAU,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YACrC,CAAC,CAAC;iBACD,IAAI,CAAC,IAAI,CAAC,CAAA;YAEb,MAAM,QAAQ,GAAG,aAAG,CAAC,eAAe,CAAC,IAAI,EAAE;gBACzC,aAAa,EAAE,IAAI;gBACnB,aAAa,EAAE,KAAK;gBACpB,eAAe,EAAE,KAAK;gBACtB,cAAc,EAAE,KAAK;gBACrB,4BAA4B,EAAE,IAAI;aACnC,CAAC,CAAA;YAEF,QAAQ,CAAC,OAAO,CAAC,WAAW,CAAC,EAAE,CAC7B,IAAI,CAAC,cAAc,CAAC,WAAW,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;gBAC3C,IACE,IAAA,sBAAc,EACZ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EACd,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EACZ,aAAa,CAAC,KAAK,EACnB,aAAa,CAAC,GAAG,CAClB,EACD;oBACA,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;iBACjB;YACH,CAAC,CAAC,CACH,CAAA;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;SACpB;QAAC,OAAO,CAAC,EAAE;YACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;SAClB;IACH,CAAC;IAEO,SAAS,CACf,aAA6C,EAC7C,IAAY,EACZ,UAAkB;QAElB,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAE/B,yCAAyC;QACzC,OAAO;YACL,KAAK,EAAE,CAAC,MAAM,CAAC,aAAa,CAAC,KAAK,GAAG,CAAC,CAAC;YACvC,GAAG,EAAE,CAAC,MAAM,CAAC,aAAa,CAAC,GAAG,GAAG,CAAC,CAAC;YACnC,QAAQ,EAAE,UAAU;YACpB,MAAM;SACP,CAAA;IACH,CAAC;IAEO,cAAc,CAAC,WAAwB;QAC7C,OAAO,WAAW,CAAC,GAAG,CACpB,UAAU,CAAC,EAAE,CACX,IAAI,uBAAa,CAAC;YAChB,IAAI,EAAE,IAAI,CAAC,WAAW,CAAC,UAAU,CAAC;YAClC,oEAAoE;YACpE,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,WAAW,UAAU,CAAC,UAAW,CAAC,SAAU,CAAC,CAAC,CAAC,EAAE;SAChE,CAAC,CACL,CAAA;IACH,CAAC;IAEO,WAAW,CAAC,IAA6B;QAC/C,MAAM,CAAC,GAA4B,EAAE,GAAG,IAAI,EAAE,CAC7C;QAAC,CAAC,CAAC,KAAgB,IAAI,CAAC,CAAA,CAAC,uBAAuB;QACjD,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YACvB,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;SACd;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM;YACL,CAAC,CAAC,MAAM,GAAG,SAAS,CAAA;SACrB;QACD,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,IAAI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@@ -18,7 +18,7 @@ export default class extends BaseFeatureDataAdapter {
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throw new Error('Data exceeds maximum string length (512MB)');
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}
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const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
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-
const lines = data.split(
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+
const lines = data.split(/\n|\r\n|\r/);
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const headerLines = [];
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for (let i = 0; i < lines.length && lines[i].startsWith('#'); i++) {
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|
headerLines.push(lines[i]);
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@@ -29,6 +29,7 @@ export default class extends BaseFeatureDataAdapter {
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parseComments: false,
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parseDirectives: false,
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parseSequences: false,
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+
disableDerivesFromReferences: true,
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});
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|
const intervalTree = feats
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|
.flat()
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@@ -136,7 +137,7 @@ export default class extends BaseFeatureDataAdapter {
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}
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delete f.child_features;
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delete f.data;
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-
delete f.derived_features
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+
// delete f.derived_features
|
|
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|
delete f.attributes;
|
|
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|
delete f.seq_id;
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|
return f;
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@@ -1 +1 @@
|
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1
|
-
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|
|
1
|
+
{"version":3,"file":"Gff3Adapter.js","sourceRoot":"","sources":["../../src/Gff3Adapter/Gff3Adapter.ts"],"names":[],"mappings":"AAAA,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,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,GAAgC,MAAM,WAAW,CAAA;AAExD,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,MAAO,SAAQ,sBAAsB;IAMzC,KAAK,CAAC,SAAS;QACrB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAC1E,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,CAAA;QACtC,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACjE,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SAC3B;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAErC,MAAM,KAAK,GAAG,GAAG,CAAC,eAAe,CAAC,IAAI,EAAE;YACtC,aAAa,EAAE,IAAI;YACnB,aAAa,EAAE,KAAK;YACpB,eAAe,EAAE,KAAK;YACtB,cAAc,EAAE,KAAK;YACrB,4BAA4B,EAAE,IAAI;SACnC,CAAC,CAAA;QAEF,MAAM,YAAY,GAAG,KAAK;aACvB,IAAI,EAAE;aACN,GAAG,CACF,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,IAAI,aAAa,CAAC;YAChB,IAAI,EAAE,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC;YACzB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,WAAW,CAAC,EAAE;SAC7B,CAAC,CACL;aACA,MAAM,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,GAAG,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;YAC9B,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACb,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,YAAY,EAAE,CAAA;aAC9B;YACD,GAAG,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;YACxD,OAAO,GAAG,CAAA;QACZ,CAAC,EAAE,EAAkC,CAAC,CAAA;QAExC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEO,KAAK,CAAC,QAAQ;QACpB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,SAAS,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC5C,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,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAC9C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACxC,OAAO,MAAM,CAAA;IACf,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;gBACrC,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;gBAC9C,MAAA,YAAY,CAAC,OAAO,CAAC,0CACjB,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EACpB,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;gBACjC,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEO,WAAW,CAAC,IAA6B;QAC/C,MAAM,CAAC,GAA4B,EAAE,GAAG,IAAI,EAAE,CAC7C;QAAC,CAAC,CAAC,KAAgB,IAAI,CAAC,CAAA,CAAC,uBAAuB;QACjD,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YACvB,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;SACd;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM;YACL,CAAC,CAAC,MAAM,GAAG,SAAS,CAAA;SACrB;QACD,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC5B,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC,MAAM,CAAA;QACvB,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,OAAO,CAAC,CAAC,KAAK,CAAA;SACf;QACD,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,OAAO,CAAC,CAAC,KAAK,CAAA;SACf;QACD,MAAM,aAAa,GAAG;YACpB,OAAO;YACP,KAAK;YACL,QAAQ;YACR,OAAO;YACP,MAAM;YACN,QAAQ;YACR,OAAO;YACP,QAAQ;SACT,CAAA;QACD,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,IAAI,EAAE,CAAA;QAC5C,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACtC,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAA;YACvB,IAAI,aAAa,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE;gBAC7B,gDAAgD;gBAChD,gCAAgC;gBAChC,CAAC,IAAI,GAAG,CAAA;aACT;YACD,IAAI,cAAc,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;gBAC9B,IAAI,IAAI,GAAkC,cAAc,CAAC,CAAC,CAAC,CAAA;gBAC3D,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE;oBAC5C,CAAC;oBAAA,CAAC,IAAI,CAAC,GAAG,IAAI,CAAA;iBACf;gBACD,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;aACZ;QACH,CAAC,CAAC,CAAA;QACF,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,MAAM,CAAA;QAEpB,gFAAgF;QAChF,IAAI,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE;YACrD,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,cAAc;iBAChC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC;iBACvE,IAAI,EAAE,CAAA;SACV;QAED,OAAO,CAAC,CAAC,cAAc,CAAA;QACvB,OAAO,CAAC,CAAC,IAAI,CAAA;QACb,4BAA4B;QAC5B,OAAO,CAAC,CAAC,UAAU,CAAA;QACnB,OAAO,CAAC,CAAC,MAAM,CAAA;QACf,OAAO,CAAC,CAAA;IACV,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAG,CAAC;CAC1C"}
|
|
@@ -87,6 +87,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
87
87
|
parseComments: false,
|
|
88
88
|
parseDirectives: false,
|
|
89
89
|
parseSequences: false,
|
|
90
|
+
disableDerivesFromReferences: true,
|
|
90
91
|
});
|
|
91
92
|
features.forEach(featureLocs => this.formatFeatures(featureLocs).forEach(f => {
|
|
92
93
|
if (doesIntersect2(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
|
|
@@ -175,7 +176,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
175
176
|
}
|
|
176
177
|
delete f.child_features;
|
|
177
178
|
delete f.data;
|
|
178
|
-
delete f.derived_features
|
|
179
|
+
// delete f.derived_features
|
|
179
180
|
delete f._linehash;
|
|
180
181
|
delete f.attributes;
|
|
181
182
|
delete f.seq_id;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"Gff3TabixAdapter.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/Gff3TabixAdapter.ts"],"names":[],"mappings":"AAAA,yCAAyC;AACzC,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAA;AAEzD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,GAA6C,MAAM,WAAW,CAAA;AAErE,OAAO,EACL,cAAc,GAEf,MAAM,6BAA6B,CAAA;AAWpC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;IAKjD,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,aAAa,GAAG,cAAc,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAC7D,MAAM,SAAS,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAChE,MAAM,QAAQ,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC9D,MAAM,cAAc,GAAG,cAAc,CAAC,MAAM,EAAE,gBAAgB,CAAC,CAAA;QAE/D,IAAI,CAAC,cAAc,GAAG,cAAc,IAAI,CAAC,YAAY,EAAE,QAAQ,EAAE,QAAQ,CAAC,CAAA;QAC1E,IAAI,CAAC,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC9B,UAAU,EAAE,YAAY,CAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;YAC3D,aAAa,EACX,SAAS,KAAK,KAAK;gBACjB,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACf,aAAa,EACX,SAAS,KAAK,KAAK;gBACjB,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACf,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,aAAa,EAAE,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC;SAChC,CAAC,CAAA;IACJ,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;YAC7C,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAA;QAC/D,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,iBAAiB,CAC7B,KAAa,EACb,OAAoB,EAAE,EACtB,QAA2D,EAC3D,QAA2B,EAC3B,eAAwB,EACxB,aAAa,GAAG,KAAK;QAErB,IAAI;YACF,MAAM,KAAK,GAAkB,EAAE,CAAA;YAE/B,MAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CACrB,KAAK,CAAC,OAAO,EACb,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,GAAG,EACT,CAAC,IAAY,EAAE,UAAkB,EAAE,EAAE;gBACnC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,aAAa,EAAE,IAAI,EAAE,UAAU,CAAC,CAAC,CAAA;YACtE,CAAC,CACF,CAAA;YACD,IAAI,eAAe,IAAI,KAAK,CAAC,MAAM,EAAE;gBACnC,IAAI,QAAQ,GAAG,QAAQ,CAAA;gBACvB,IAAI,MAAM,GAAG,CAAC,QAAQ,CAAA;gBACtB,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;oBACnB,MAAM,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;oBAClC,yEAAyE;oBACzE,6CAA6C;oBAC7C,IAAI,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE;wBAC9C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA,CAAC,iBAAiB;wBAC9C,IAAI,KAAK,GAAG,QAAQ,EAAE;4BACpB,QAAQ,GAAG,KAAK,CAAA;yBACjB;wBACD,IAAI,IAAI,CAAC,GAAG,GAAG,MAAM,EAAE;4BACrB,MAAM,GAAG,IAAI,CAAC,GAAG,CAAA;yBAClB;qBACF;gBACH,CAAC,CAAC,CAAA;gBACF,IAAI,MAAM,GAAG,KAAK,CAAC,GAAG,IAAI,QAAQ,GAAG,KAAK,CAAC,KAAK,EAAE;oBAChD,gEAAgE;oBAChE,8BAA8B;oBAC9B,IAAI,CAAC,iBAAiB,CACpB,EAAE,GAAG,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,EAAE,MAAM,EAAE,EAC1C,IAAI,EACJ,QAAQ,EACR,QAAQ,EACR,KAAK,EACL,KAAK,CACN,CAAA;oBACD,OAAM;iBACP;aACF;YAED,MAAM,IAAI,GAAG,KAAK;iBACf,GAAG,CAAC,CAAC,UAAuB,EAAE,EAAE;gBAC/B,IAAI,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;oBACxD,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE;wBAC/C,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,cAAc,UAAU,CAAC,QAAQ,EAAE,CAAA;qBAC5D;iBACF;qBAAM;oBACL,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,aAAa,UAAU,CAAC,QAAQ,EAAE,CAAA;iBAC1D;gBACD,OAAO,UAAU,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YACrC,CAAC,CAAC;iBACD,IAAI,CAAC,IAAI,CAAC,CAAA;YAEb,MAAM,QAAQ,GAAG,GAAG,CAAC,eAAe,CAAC,IAAI,EAAE;gBACzC,aAAa,EAAE,IAAI;gBACnB,aAAa,EAAE,KAAK;gBACpB,eAAe,EAAE,KAAK;gBACtB,cAAc,EAAE,KAAK;
|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-gff3",
|
|
3
|
-
"version": "2.1.
|
|
3
|
+
"version": "2.1.6",
|
|
4
4
|
"description": "JBrowse 2 gff3.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -39,7 +39,7 @@
|
|
|
39
39
|
"dependencies": {
|
|
40
40
|
"@flatten-js/interval-tree": "^1.0.15",
|
|
41
41
|
"@gmod/bgzf-filehandle": "^1.4.3",
|
|
42
|
-
"@gmod/gff": "^1.2.
|
|
42
|
+
"@gmod/gff": "^1.2.3",
|
|
43
43
|
"@gmod/tabix": "^1.5.2"
|
|
44
44
|
},
|
|
45
45
|
"peerDependencies": {
|
|
@@ -59,5 +59,5 @@
|
|
|
59
59
|
"distModule": "esm/index.js",
|
|
60
60
|
"srcModule": "src/index.ts",
|
|
61
61
|
"module": "esm/index.js",
|
|
62
|
-
"gitHead": "
|
|
62
|
+
"gitHead": "df810d2a4f057adcd8f5345d54972508fba007a7"
|
|
63
63
|
}
|
|
@@ -30,7 +30,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
30
30
|
throw new Error('Data exceeds maximum string length (512MB)')
|
|
31
31
|
}
|
|
32
32
|
const data = new TextDecoder('utf8', { fatal: true }).decode(buffer)
|
|
33
|
-
const lines = data.split(
|
|
33
|
+
const lines = data.split(/\n|\r\n|\r/)
|
|
34
34
|
const headerLines = []
|
|
35
35
|
for (let i = 0; i < lines.length && lines[i].startsWith('#'); i++) {
|
|
36
36
|
headerLines.push(lines[i])
|
|
@@ -42,6 +42,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
42
42
|
parseComments: false,
|
|
43
43
|
parseDirectives: false,
|
|
44
44
|
parseSequences: false,
|
|
45
|
+
disableDerivesFromReferences: true,
|
|
45
46
|
})
|
|
46
47
|
|
|
47
48
|
const intervalTree = feats
|
|
@@ -158,7 +159,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
158
159
|
|
|
159
160
|
delete f.child_features
|
|
160
161
|
delete f.data
|
|
161
|
-
delete f.derived_features
|
|
162
|
+
// delete f.derived_features
|
|
162
163
|
delete f.attributes
|
|
163
164
|
delete f.seq_id
|
|
164
165
|
return f
|
|
@@ -3,6 +3,7 @@
|
|
|
3
3
|
exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff plain text adapter 1`] = `
|
|
4
4
|
Array [
|
|
5
5
|
Object {
|
|
6
|
+
"derived_features": Array [],
|
|
6
7
|
"end": 6079,
|
|
7
8
|
"name": "ctgB",
|
|
8
9
|
"phase": 0,
|
|
@@ -14,6 +15,7 @@ Array [
|
|
|
14
15
|
"uniqueId": "test-offset-187",
|
|
15
16
|
},
|
|
16
17
|
Object {
|
|
18
|
+
"derived_features": Array [],
|
|
17
19
|
"end": 1984,
|
|
18
20
|
"name": "f07",
|
|
19
21
|
"note": "This is an example",
|
|
@@ -26,6 +28,7 @@ Array [
|
|
|
26
28
|
"uniqueId": "test-offset-188",
|
|
27
29
|
},
|
|
28
30
|
Object {
|
|
31
|
+
"derived_features": Array [],
|
|
29
32
|
"end": 6130,
|
|
30
33
|
"name": "f06",
|
|
31
34
|
"note": "This is another example",
|
|
@@ -38,6 +41,7 @@ Array [
|
|
|
38
41
|
"uniqueId": "test-offset-189",
|
|
39
42
|
},
|
|
40
43
|
Object {
|
|
44
|
+
"derived_features": Array [],
|
|
41
45
|
"end": 5968,
|
|
42
46
|
"name": "f05",
|
|
43
47
|
"note": "ああ、この機能は、世界中を旅しています！",
|
|
@@ -141,6 +141,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
141
141
|
parseComments: false,
|
|
142
142
|
parseDirectives: false,
|
|
143
143
|
parseSequences: false,
|
|
144
|
+
disableDerivesFromReferences: true,
|
|
144
145
|
})
|
|
145
146
|
|
|
146
147
|
features.forEach(featureLocs =>
|
|
@@ -247,10 +248,11 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
247
248
|
|
|
248
249
|
delete f.child_features
|
|
249
250
|
delete f.data
|
|
250
|
-
delete f.derived_features
|
|
251
|
+
// delete f.derived_features
|
|
251
252
|
delete f._linehash
|
|
252
253
|
delete f.attributes
|
|
253
254
|
delete f.seq_id
|
|
255
|
+
|
|
254
256
|
return f
|
|
255
257
|
}
|
|
256
258
|
|
|
@@ -3,6 +3,7 @@
|
|
|
3
3
|
exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff plain text adapter 1`] = `
|
|
4
4
|
Array [
|
|
5
5
|
Object {
|
|
6
|
+
"derived_features": Array [],
|
|
6
7
|
"end": 6079,
|
|
7
8
|
"name": "ctgB",
|
|
8
9
|
"phase": 0,
|
|
@@ -14,6 +15,7 @@ Array [
|
|
|
14
15
|
"uniqueId": "test-offset-794327",
|
|
15
16
|
},
|
|
16
17
|
Object {
|
|
18
|
+
"derived_features": Array [],
|
|
17
19
|
"end": 1984,
|
|
18
20
|
"name": "f07",
|
|
19
21
|
"note": "This is an example",
|
|
@@ -26,6 +28,7 @@ Array [
|
|
|
26
28
|
"uniqueId": "test-offset-794370",
|
|
27
29
|
},
|
|
28
30
|
Object {
|
|
31
|
+
"derived_features": Array [],
|
|
29
32
|
"end": 6130,
|
|
30
33
|
"name": "f06",
|
|
31
34
|
"note": "This is another example",
|
|
@@ -38,6 +41,7 @@ Array [
|
|
|
38
41
|
"uniqueId": "test-offset-794439",
|
|
39
42
|
},
|
|
40
43
|
Object {
|
|
44
|
+
"derived_features": Array [],
|
|
41
45
|
"end": 5968,
|
|
42
46
|
"name": "f05",
|
|
43
47
|
"note": "ああ、この機能は、世界中を旅しています！",
|