gff-nostream 3.0.1 → 3.0.4
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/README.md +16 -75
- package/dist/api.js +14 -21
- package/dist/api.js.map +1 -1
- package/dist/util.d.ts +1 -1
- package/dist/util.js +135 -216
- package/dist/util.js.map +1 -1
- package/esm/api.js +14 -21
- package/esm/api.js.map +1 -1
- package/esm/util.d.ts +1 -1
- package/esm/util.js +135 -216
- package/esm/util.js.map +1 -1
- package/package.json +15 -22
- package/src/api.ts +15 -22
- package/src/util.ts +185 -254
package/esm/api.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,YAAY,EACZ,mBAAmB,EACnB,6BAA6B,EAC7B,sBAAsB,GACvB,MAAM,WAAW,CAAA;AAgBlB;;;;;;GAMG;AACH,MAAM,UAAU,eAAe,CAAC,GAAW;IACzC,OAAO,YAAY,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAA;AAC3C,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,sBAAsB,CAAC,GAAW;IAChD,OAAO,mBAAmB,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAA;AAClD,CAAC;AAED,SAAS,eAAe,CAAC,GAAW;IAClC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IAChC,MAAM,OAAO,GAAiB,EAAE,CAAA;IAChC,KAAK,
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1
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+
{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,YAAY,EACZ,mBAAmB,EACnB,6BAA6B,EAC7B,sBAAsB,GACvB,MAAM,WAAW,CAAA;AAgBlB;;;;;;GAMG;AACH,MAAM,UAAU,eAAe,CAAC,GAAW;IACzC,OAAO,YAAY,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAA;AAC3C,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,sBAAsB,CAAC,GAAW;IAChD,OAAO,mBAAmB,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAA;AAClD,CAAC;AAED,SAAS,eAAe,CAAC,GAAW;IAClC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IAChC,MAAM,OAAO,GAAiB,EAAE,CAAA;IAChC,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAC9C,IAAI,IAAI,CAAC,UAAU,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC/B,MAAK;YACP,CAAC;YACD,SAAQ;QACV,CAAC;QACD,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YACzB,MAAK;QACP,CAAC;QACD,OAAO,CAAC,IAAI,CAAC;YACX,IAAI;YACJ,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,CAAC;YACN,UAAU,EAAE,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC;SAC/B,CAAC,CAAA;IACJ,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,YAAY,CAAC,OAAqB;IAChD,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,IAAI,GAAG,IAAI,GAAG,EAAuB,CAAA;IAC3C,MAAM,OAAO,GAAG,IAAI,GAAG,EAAyB,CAAA;IAEhD,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,MAAM,WAAW,GAAG,CAClB,MAAM,CAAC,UAAU;YACf,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,IAAI,CAAC;YAC3B,CAAC,CAAC,sBAAsB,CAAC,MAAM,CAAC,IAAI,CAAC,CACb,CAAA;QAC5B,WAAW,CAAC,cAAc,GAAG,EAAE,CAAA;QAC/B,WAAW,CAAC,gBAAgB,GAAG,EAAE,CAAA;QAEjC,IAAI,MAAM,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YAClC,WAAW,CAAC,UAAU,KAAK,EAAE,CAAA;YAC7B,WAAW,CAAC,UAAU,CAAC,SAAS,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC9D,CAAC;QAED,MAAM,KAAK,GAAG,WAAW,CAAC,UAAU,CAAA;QACpC,MAAM,GAAG,GAAG,KAAK,EAAE,EAAE,CAAA;QACrB,MAAM,OAAO,GAAG,KAAK,EAAE,MAAM,CAAA;QAE7B,IAAI,CAAC,GAAG,IAAI,CAAC,OAAO,EAAE,CAAC;YACrB,KAAK,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;YACzB,SAAQ;QACV,CAAC;QAED,IAAI,OAAoB,CAAA;QACxB,IAAI,GAAG,EAAE,CAAC;YACR,MAAM,EAAE,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;YACjB,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;YAC7B,IAAI,QAAQ,EAAE,CAAC;gBACb,QAAQ,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;gBAC1B,OAAO,GAAG,QAAQ,CAAA;YACpB,CAAC;iBAAM,CAAC;gBACN,OAAO,GAAG,CAAC,WAAW,CAAC,CAAA;gBACvB,IAAI,CAAC,OAAO,EAAE,CAAC;oBACb,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACrB,CAAC;gBACD,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;gBACrB,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,OAAO,EAAE,CAAC;oBACZ,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;wBACxB,WAAW,CAAC,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;oBACpC,CAAC;oBACD,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;gBACpB,CAAC;YACH,CAAC;QACH,CAAC;aAAM,CAAC;YACN,OAAO,GAAG,CAAC,WAAW,CAAC,CAAA;QACzB,CAAC;QAED,IAAI,OAAO,EAAE,CAAC;YACZ,KAAK,MAAM,QAAQ,IAAI,OAAO,EAAE,CAAC;gBAC/B,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;gBACjC,IAAI,MAAM,EAAE,CAAC;oBACX,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;wBACvB,CAAC,CAAC,cAAc,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;oBAChC,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,IAAI,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;oBAC/B,IAAI,CAAC,GAAG,EAAE,CAAC;wBACT,GAAG,GAAG,EAAE,CAAA;wBACR,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAA;oBAC5B,CAAC;oBACD,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,KAAK,CAAA;AACd,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,mBAAmB,CAAC,OAAqB;IACvD,MAAM,KAAK,GAAqB,EAAE,CAAA;IAClC,MAAM,IAAI,GAAG,IAAI,GAAG,EAA0B,CAAA;IAC9C,MAAM,OAAO,GAAG,IAAI,GAAG,EAA4B,CAAA;IAEnD,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,MAAM,OAAO,GAAG,MAAM,CAAC,UAAU;YAC/B,CAAC,CAAC,mBAAmB,CAAC,MAAM,CAAC,IAAI,CAAC;YAClC,CAAC,CAAC,6BAA6B,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;QAE9C,IAAI,MAAM,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YAClC,OAAO,CAAC,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;QAC7C,CAAC;QAED,MAAM,EAAE,GAAG,OAAO,CAAC,EAAwB,CAAA;QAC3C,MAAM,MAAM,GAAG,OAAO,CAAC,MAAuC,CAAA;QAE9D,IAAI,CAAC,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC;YACnB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACnB,SAAQ;QACV,CAAC;QAED,IAAI,EAAE,EAAE,CAAC;YACP,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;YAC7B,IAAI,CAAC,QAAQ,EAAE,CAAC;gBACd,IAAI,CAAC,MAAM,EAAE,CAAC;oBACZ,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACrB,CAAC;gBACD,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;gBACrB,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,OAAO,EAAE,CAAC;oBACZ,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;wBACxB,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;oBAC7B,CAAC;oBACD,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;gBACpB,CAAC;YACH,CAAC;QACH,CAAC;QAED,IAAI,MAAM,EAAE,CAAC;YACX,MAAM,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAA;YACzD,KAAK,MAAM,QAAQ,IAAI,OAAO,EAAE,CAAC;gBAC/B,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;gBACxC,IAAI,aAAa,EAAE,CAAC;oBAClB,aAAa,CAAC,WAAW,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACzC,CAAC;qBAAM,CAAC;oBACN,IAAI,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;oBAC/B,IAAI,CAAC,GAAG,EAAE,CAAC;wBACT,GAAG,GAAG,EAAE,CAAA;wBACR,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAA;oBAC5B,CAAC;oBACD,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,KAAK,CAAA;AACd,CAAC"}
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package/esm/util.d.ts
CHANGED
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* @param stringVal - Escaped GFF3 string value
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* @returns An unescaped string value
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*/
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export declare function unescape(
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export declare function unescape(stringVal: string): string;
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/**
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* Parse the 9th column (attributes) of a GFF3 feature line.
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*
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package/esm/util.js
CHANGED
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// Fast, low-level functions for parsing and formatting GFF3.
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// JavaScript port of Robert Buels's Bio::GFF3::LowLevel Perl module.
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const escapeRegex = /%([0-9A-Fa-f]{2})/g;
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const directiveRegex = /^\s*##\s*(\S+)\s*(.*)/;
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const lineEndRegex = /\r?\n$/;
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const whitespaceRegex = /\s+/;
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const nonDigitRegex = /\D/g;
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// eslint-disable-next-line no-control-regex
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const attrEscapeRegex = /[\n;\r\t=%&,\u0000-\u001f\u007f-\u00ff]/g;
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// eslint-disable-next-line no-control-regex
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const columnEscapeRegex = /[\n\r\t%\u0000-\u001f\u007f-\u00ff]/g;
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const HEX_LOOKUP = {};
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for (let i = 0; i < 256; i++) {
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const hex = i.toString(16).toUpperCase().padStart(2, '0');
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* @param stringVal - Escaped GFF3 string value
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export function unescape(
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export function unescape(stringVal) {
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return stringVal;
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}
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let result = '';
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result += stringVal.slice(lastIdx, i);
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const hex = stringVal.slice(i + 1, i + 3);
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const char = HEX_LOOKUP[hex];
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if (char !== undefined) {
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result += char;
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}
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else {
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result += stringVal.slice(i, i + 3);
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}
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i += 3;
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lastIdx = i;
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}
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else {
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i++;
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}
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}
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return result + stringVal.slice(lastIdx);
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}
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*
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* @param attrString - String of GFF3 9th column
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export function parseAttributes(attrString) {
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function parseAttributesImpl(attrString, shouldUnescape) {
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if (attrString.length === 0 || attrString === '.') {
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return {};
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if (commaIdx > valStart) {
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const val = attrString.slice(valStart, commaIdx);
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arec.push(unescape(val));
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arec.push(shouldUnescape ? unescape(val) : val);
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}
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valStart = commaIdx + 1;
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}
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return attrs;
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}
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*
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* @param attrString - String of GFF3 9th column
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* @returns Parsed attributes
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*/
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export function parseAttributes(attrString) {
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return parseAttributesImpl(attrString, true);
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}
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* Parse the 9th column (attributes) of a GFF3 feature line without unescaping.
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* Fast path for data known to contain no escaped characters.
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export function parseAttributesNoUnescape(attrString) {
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return {};
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}
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const attrs = {};
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let len = attrString.length;
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if (attrString[len - 1] === '\n') {
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len = attrString[len - 2] === '\r' ? len - 2 : len - 1;
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attrString = attrString.slice(0, len);
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}
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let start = 0;
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while (start < len) {
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let semiIdx = attrString.indexOf(';', start);
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if (semiIdx === -1) {
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semiIdx = len;
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}
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if (semiIdx > start) {
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const eqIdx = attrString.indexOf('=', start);
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if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
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const tag = attrString.slice(start, eqIdx);
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let arec = attrs[tag];
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if (!arec) {
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attrs[tag] = arec;
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}
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let valStart = eqIdx + 1;
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while (valStart < semiIdx) {
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let commaIdx = attrString.indexOf(',', valStart);
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if (commaIdx === -1 || commaIdx > semiIdx) {
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commaIdx = semiIdx;
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}
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if (commaIdx > valStart) {
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arec.push(attrString.slice(valStart, commaIdx));
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}
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valStart = commaIdx + 1;
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}
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}
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}
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start = semiIdx + 1;
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}
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return attrs;
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return parseAttributesImpl(attrString, false);
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}
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function
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return
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function normImpl(s, shouldUnescape) {
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if (s.length === 0 || s === '.') {
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return null;
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}
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return shouldUnescape ? unescape(s) : s;
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}
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* Parse a GFF3 feature line
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*
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* @param line - GFF3 feature line
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* @returns The parsed feature
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*/
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export function parseFeature(line) {
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function parseFeatureImpl(line, shouldUnescape) {
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const f = line.split('\t');
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const seq_id = f[0];
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const source = f[1];
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const type = f[2];
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const startStr = f[3];
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const endStr = f[4];
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const scoreStr = f[5];
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type:
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source: normImpl(f[1], shouldUnescape),
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type: normImpl(f[2], shouldUnescape),
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start: startStr.length === 0 || startStr === '.' ? null : +startStr,
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end: endStr.length === 0 || endStr === '.' ? null : +endStr,
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score: scoreStr.length === 0 || scoreStr === '.' ? null : +scoreStr,
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strand:
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attributes: attrString.length === 0 || attrString === '.'
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strand: normImpl(strand, false),
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phase: normImpl(phase, false),
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attributes: attrString.length === 0 || attrString === '.'
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? null
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: parseAttributesImpl(attrString, shouldUnescape),
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};
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}
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/**
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* Parse a GFF3 feature line
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*
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* @param line - GFF3 feature line
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* @returns The parsed feature
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*/
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export function parseFeature(line) {
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return parseFeatureImpl(line, true);
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}
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function parseFieldsArrayImpl(f, shouldUnescape) {
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source:
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type:
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end: endStr
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score: scoreStr
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strand:
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attributes: attrString
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seq_id: seq_id ? normImpl(seq_id, shouldUnescape) : null,
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source: source ? normImpl(source, shouldUnescape) : null,
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type: type ? normImpl(type, shouldUnescape) : null,
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start: !startStr || startStr === '.' ? null : +startStr,
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strand: strand && strand !== '.' ? strand : null,
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phase: phase && phase !== '.' ? phase : null,
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attributes: !attrString || attrString === '.'
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? null
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: parseAttributesImpl(attrString, shouldUnescape),
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|
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*/
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export function parseFieldsArray(f) {
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const type = f[2];
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const startStr = f[3];
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const endStr = f[4];
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const scoreStr = f[5];
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const strand = f[6];
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return {
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strand: strand && strand !== '.' ? strand : null,
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attributes: !attrString || attrString === '.' ? null : parseAttributes(attrString),
|
|
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};
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return parseFieldsArrayImpl(f, true);
|
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|
}
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/**
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|
* Parse a GFF3 feature from a pre-split fields array without unescaping.
|
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*/
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const source = f[1];
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const type = f[2];
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const startStr = f[3];
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const endStr = f[4];
|
|
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|
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const scoreStr = f[5];
|
|
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|
-
const strand = f[6];
|
|
233
|
-
const phase = f[7];
|
|
234
|
-
const attrString = f[8];
|
|
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|
-
return {
|
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seq_id: seq_id && seq_id !== '.' ? seq_id : null,
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source: source && source !== '.' ? source : null,
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|
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type: type && type !== '.' ? type : null,
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start: !startStr || startStr === '.' ? null : +startStr,
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end: !endStr || endStr === '.' ? null : +endStr,
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|
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|
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score: !scoreStr || scoreStr === '.' ? null : +scoreStr,
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|
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strand: strand && strand !== '.' ? strand : null,
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|
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|
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phase: phase && phase !== '.' ? phase : null,
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|
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|
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attributes: !attrString || attrString === '.' ? null : parseAttributesNoUnescape(attrString),
|
|
245
|
-
};
|
|
197
|
+
return parseFieldsArrayImpl(f, false);
|
|
246
198
|
}
|
|
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|
/**
|
|
248
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|
* Parse a GFF3 directive line.
|
|
@@ -262,7 +214,6 @@ export function parseDirective(line) {
|
|
|
262
214
|
contents = contents.replace(lineEndRegex, '');
|
|
263
215
|
parsed.value = contents;
|
|
264
216
|
}
|
|
265
|
-
// do a little additional parsing for sequence-region and genome-build directives
|
|
266
217
|
if (name === 'sequence-region') {
|
|
267
218
|
const c = contents.split(whitespaceRegex, 3);
|
|
268
219
|
return {
|
|
@@ -293,19 +244,30 @@ const JBROWSE_DEFAULT_FIELDS = new Set([
|
|
|
293
244
|
'phase',
|
|
294
245
|
'strand',
|
|
295
246
|
]);
|
|
296
|
-
|
|
297
|
-
|
|
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|
-
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|
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-
|
|
300
|
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|
|
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|
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|
|
302
|
-
|
|
303
|
-
|
|
304
|
-
|
|
305
|
-
|
|
306
|
-
|
|
307
|
-
|
|
308
|
-
|
|
247
|
+
// Pre-computed lowercase for common GFF3 spec attribute names to avoid
|
|
248
|
+
// toLowerCase() calls in the hot path
|
|
249
|
+
const COMMON_ATTRS = {
|
|
250
|
+
ID: 'id',
|
|
251
|
+
Name: 'name',
|
|
252
|
+
Parent: 'parent',
|
|
253
|
+
Note: 'note',
|
|
254
|
+
Dbxref: 'dbxref',
|
|
255
|
+
Ontology_term: 'ontology_term',
|
|
256
|
+
Is_circular: 'is_circular',
|
|
257
|
+
Alias: 'alias',
|
|
258
|
+
Target: 'target',
|
|
259
|
+
Gap: 'gap',
|
|
260
|
+
Derives_from: 'derives_from',
|
|
261
|
+
id: 'id',
|
|
262
|
+
name: 'name',
|
|
263
|
+
parent: 'parent',
|
|
264
|
+
note: 'note',
|
|
265
|
+
dbxref: 'dbxref',
|
|
266
|
+
alias: 'alias',
|
|
267
|
+
target: 'target',
|
|
268
|
+
gap: 'gap',
|
|
269
|
+
};
|
|
270
|
+
function parseAttributesJBrowseImpl(attrString, result, shouldUnescape) {
|
|
309
271
|
if (attrString.length === 0 || attrString === '.') {
|
|
310
272
|
return;
|
|
311
273
|
}
|
|
@@ -328,9 +290,12 @@ export function parseAttributesJBrowse(attrString, result) {
|
|
|
328
290
|
start = semiIdx + 1;
|
|
329
291
|
continue;
|
|
330
292
|
}
|
|
331
|
-
let key = tag
|
|
332
|
-
if (
|
|
333
|
-
key
|
|
293
|
+
let key = COMMON_ATTRS[tag];
|
|
294
|
+
if (key === undefined) {
|
|
295
|
+
key = tag.toLowerCase();
|
|
296
|
+
if (JBROWSE_DEFAULT_FIELDS.has(key)) {
|
|
297
|
+
key += '2';
|
|
298
|
+
}
|
|
334
299
|
}
|
|
335
300
|
const values = [];
|
|
336
301
|
let valStart = eqIdx + 1;
|
|
@@ -341,7 +306,7 @@ export function parseAttributesJBrowse(attrString, result) {
|
|
|
341
306
|
}
|
|
342
307
|
if (commaIdx > valStart) {
|
|
343
308
|
const val = attrString.slice(valStart, commaIdx);
|
|
344
|
-
values.push(unescape(val));
|
|
309
|
+
values.push(shouldUnescape ? unescape(val) : val);
|
|
345
310
|
}
|
|
346
311
|
valStart = commaIdx + 1;
|
|
347
312
|
}
|
|
@@ -351,52 +316,13 @@ export function parseAttributesJBrowse(attrString, result) {
|
|
|
351
316
|
start = semiIdx + 1;
|
|
352
317
|
}
|
|
353
318
|
}
|
|
319
|
+
export function parseAttributesJBrowse(attrString, result) {
|
|
320
|
+
parseAttributesJBrowseImpl(attrString, result, true);
|
|
321
|
+
}
|
|
354
322
|
export function parseAttributesJBrowseNoUnescape(attrString, result) {
|
|
355
|
-
|
|
356
|
-
return;
|
|
357
|
-
}
|
|
358
|
-
let len = attrString.length;
|
|
359
|
-
if (attrString[len - 1] === '\n') {
|
|
360
|
-
len = attrString[len - 2] === '\r' ? len - 2 : len - 1;
|
|
361
|
-
attrString = attrString.slice(0, len);
|
|
362
|
-
}
|
|
363
|
-
let start = 0;
|
|
364
|
-
while (start < len) {
|
|
365
|
-
let semiIdx = attrString.indexOf(';', start);
|
|
366
|
-
if (semiIdx === -1) {
|
|
367
|
-
semiIdx = len;
|
|
368
|
-
}
|
|
369
|
-
if (semiIdx > start) {
|
|
370
|
-
const eqIdx = attrString.indexOf('=', start);
|
|
371
|
-
if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
|
|
372
|
-
const tag = attrString.slice(start, eqIdx);
|
|
373
|
-
if (tag === '_lineHash') {
|
|
374
|
-
start = semiIdx + 1;
|
|
375
|
-
continue;
|
|
376
|
-
}
|
|
377
|
-
let key = tag.toLowerCase();
|
|
378
|
-
if (JBROWSE_DEFAULT_FIELDS.has(key)) {
|
|
379
|
-
key += '2';
|
|
380
|
-
}
|
|
381
|
-
const values = [];
|
|
382
|
-
let valStart = eqIdx + 1;
|
|
383
|
-
while (valStart < semiIdx) {
|
|
384
|
-
let commaIdx = attrString.indexOf(',', valStart);
|
|
385
|
-
if (commaIdx === -1 || commaIdx > semiIdx) {
|
|
386
|
-
commaIdx = semiIdx;
|
|
387
|
-
}
|
|
388
|
-
if (commaIdx > valStart) {
|
|
389
|
-
values.push(attrString.slice(valStart, commaIdx));
|
|
390
|
-
}
|
|
391
|
-
valStart = commaIdx + 1;
|
|
392
|
-
}
|
|
393
|
-
result[key] = values.length === 1 ? values[0] : values;
|
|
394
|
-
}
|
|
395
|
-
}
|
|
396
|
-
start = semiIdx + 1;
|
|
397
|
-
}
|
|
323
|
+
parseAttributesJBrowseImpl(attrString, result, false);
|
|
398
324
|
}
|
|
399
|
-
|
|
325
|
+
function parseFeatureJBrowseImpl(line, shouldUnescape) {
|
|
400
326
|
const f = line.split('\t');
|
|
401
327
|
const seq_id = f[0];
|
|
402
328
|
const source = f[1];
|
|
@@ -408,42 +334,35 @@ export function parseFeatureJBrowse(line) {
|
|
|
408
334
|
const phase = f[7];
|
|
409
335
|
const attrString = f[8];
|
|
410
336
|
const result = {
|
|
411
|
-
refName: seq_id.length === 0 || seq_id === '.'
|
|
412
|
-
|
|
413
|
-
|
|
337
|
+
refName: seq_id.length === 0 || seq_id === '.'
|
|
338
|
+
? ''
|
|
339
|
+
: shouldUnescape
|
|
340
|
+
? unescape(seq_id)
|
|
341
|
+
: seq_id,
|
|
342
|
+
source: source.length === 0 || source === '.'
|
|
343
|
+
? null
|
|
344
|
+
: shouldUnescape
|
|
345
|
+
? unescape(source)
|
|
346
|
+
: source,
|
|
347
|
+
type: type.length === 0 || type === '.'
|
|
348
|
+
? null
|
|
349
|
+
: shouldUnescape
|
|
350
|
+
? unescape(type)
|
|
351
|
+
: type,
|
|
414
352
|
start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
|
|
415
353
|
end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
|
|
416
354
|
score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
|
|
417
|
-
strand:
|
|
355
|
+
strand: strand === '+' ? 1 : strand === '-' ? -1 : strand === '.' ? 0 : undefined,
|
|
418
356
|
phase: phase.length === 0 || phase === '.' ? undefined : +phase,
|
|
419
357
|
subfeatures: [],
|
|
420
358
|
};
|
|
421
|
-
|
|
359
|
+
parseAttributesJBrowseImpl(attrString, result, shouldUnescape);
|
|
422
360
|
return result;
|
|
423
361
|
}
|
|
362
|
+
export function parseFeatureJBrowse(line) {
|
|
363
|
+
return parseFeatureJBrowseImpl(line, true);
|
|
364
|
+
}
|
|
424
365
|
export function parseFeatureJBrowseNoUnescape(line) {
|
|
425
|
-
|
|
426
|
-
const seq_id = f[0];
|
|
427
|
-
const source = f[1];
|
|
428
|
-
const type = f[2];
|
|
429
|
-
const startStr = f[3];
|
|
430
|
-
const endStr = f[4];
|
|
431
|
-
const scoreStr = f[5];
|
|
432
|
-
const strand = f[6];
|
|
433
|
-
const phase = f[7];
|
|
434
|
-
const attrString = f[8];
|
|
435
|
-
const result = {
|
|
436
|
-
refName: seq_id.length === 0 || seq_id === '.' ? '' : seq_id,
|
|
437
|
-
source: source.length === 0 || source === '.' ? null : source,
|
|
438
|
-
type: type.length === 0 || type === '.' ? null : type,
|
|
439
|
-
start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
|
|
440
|
-
end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
|
|
441
|
-
score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
|
|
442
|
-
strand: parseStrand(strand),
|
|
443
|
-
phase: phase.length === 0 || phase === '.' ? undefined : +phase,
|
|
444
|
-
subfeatures: [],
|
|
445
|
-
};
|
|
446
|
-
parseAttributesJBrowseNoUnescape(attrString, result);
|
|
447
|
-
return result;
|
|
366
|
+
return parseFeatureJBrowseImpl(line, false);
|
|
448
367
|
}
|
|
449
368
|
//# sourceMappingURL=util.js.map
|
package/esm/util.js.map
CHANGED
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|
|
1
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+
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|
package/package.json
CHANGED
|
@@ -1,18 +1,17 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "gff-nostream",
|
|
3
|
-
"version": "3.0.
|
|
3
|
+
"version": "3.0.4",
|
|
4
4
|
"description": "utilities to read GFF3 data",
|
|
5
5
|
"license": "MIT",
|
|
6
|
-
"repository":
|
|
6
|
+
"repository": {
|
|
7
|
+
"type": "git",
|
|
8
|
+
"url": "https://github.com/GMOD/gff-nostream.git"
|
|
9
|
+
},
|
|
7
10
|
"type": "module",
|
|
8
11
|
"types": "./dist/index.d.ts",
|
|
9
12
|
"exports": {
|
|
10
|
-
"import":
|
|
11
|
-
|
|
12
|
-
},
|
|
13
|
-
"require": {
|
|
14
|
-
"require": "./dist/index.js"
|
|
15
|
-
}
|
|
13
|
+
"import": "./esm/index.js",
|
|
14
|
+
"require": "./dist/index.js"
|
|
16
15
|
},
|
|
17
16
|
"author": {
|
|
18
17
|
"name": "Colin Diesh",
|
|
@@ -28,13 +27,12 @@
|
|
|
28
27
|
"test": "vitest",
|
|
29
28
|
"benchonly": "vitest bench",
|
|
30
29
|
"bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
|
|
31
|
-
"clean": "
|
|
30
|
+
"clean": "rm -rf dist esm",
|
|
32
31
|
"lint": "eslint --report-unused-disable-directives --max-warnings 0",
|
|
33
|
-
"docs": "documentation readme src/api.ts --section=API --shallow && yarn format",
|
|
34
32
|
"format": "prettier --write .",
|
|
35
33
|
"prebuild": "yarn clean",
|
|
36
34
|
"build:esm": "tsc --target esnext --outDir esm",
|
|
37
|
-
"build:es5": "tsc --target es2020 --module commonjs --outDir dist",
|
|
35
|
+
"build:es5": "tsc --target es2020 --module commonjs --moduleResolution bundler --outDir dist",
|
|
38
36
|
"postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
|
|
39
37
|
"build": "yarn build:es5 && yarn build:esm",
|
|
40
38
|
"prepublishOnly": "yarn test --run && yarn build",
|
|
@@ -48,17 +46,12 @@
|
|
|
48
46
|
"genomics"
|
|
49
47
|
],
|
|
50
48
|
"devDependencies": {
|
|
51
|
-
"@types/node": "^
|
|
52
|
-
"
|
|
53
|
-
"@typescript-eslint/parser": "^8.48.0",
|
|
54
|
-
"@vitest/coverage-v8": "^4.0.14",
|
|
55
|
-
"documentation": "^14.0.1",
|
|
56
|
-
"eslint": "^9.39.1",
|
|
49
|
+
"@types/node": "^25.6.0",
|
|
50
|
+
"eslint": "^10.2.1",
|
|
57
51
|
"eslint-plugin-import": "^2.32.0",
|
|
58
|
-
"prettier": "^3.
|
|
59
|
-
"
|
|
60
|
-
"typescript": "^
|
|
61
|
-
"
|
|
62
|
-
"vitest": "^4.0.14"
|
|
52
|
+
"prettier": "^3.8.3",
|
|
53
|
+
"typescript": "^6.0.3",
|
|
54
|
+
"typescript-eslint": "^8.59.0",
|
|
55
|
+
"vitest": "^4.1.5"
|
|
63
56
|
}
|
|
64
57
|
}
|