@gmod/bbi 4.0.1 → 4.0.2
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/CHANGELOG.md +5 -1
- package/README.md +1 -1
- package/dist/bbi.js +8 -2
- package/dist/bbi.js.map +1 -1
- package/esm/bbi.js +8 -2
- package/esm/bbi.js.map +1 -1
- package/package.json +1 -1
- package/src/bbi.ts +10 -2
package/CHANGELOG.md
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@@ -1,6 +1,10 @@
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1
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-
## [4.0.
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## [4.0.2](https://github.com/GMOD/bbi-js/compare/v4.0.1...v4.0.2) (2023-07-30)
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+
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5
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- Fix issue with fetching headers that are large in certain cases
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## [4.0.1](https://github.com/GMOD/bbi-js/compare/v4.0.0...v4.0.1) (2023-07-13)
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- Fix eslint plugin being in dependencies Accidentally
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10
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package/README.md
CHANGED
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@@ -148,7 +148,7 @@ https://genome.ucsc.edu/goldenpath/help/bigBed.html
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This function accepts two arguments
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- name: a string to search for in the BigBed extra indices
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-
- opts: an
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- opts: an object that can optionally contain opts.signal, an abort signal
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Returns a Promise to an array of Features, with an extra field indicating the
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field that was matched
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package/dist/bbi.js
CHANGED
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@@ -94,9 +94,13 @@ class BBI {
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}
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/*
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* @param filehandle - a filehandle from generic-filehandle or implementing something similar to the node10 fs.promises API
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*
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* @param path - a Local file path as a string
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*
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* @param url - a URL string
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*
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*
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* @param renameRefSeqs - an optional method to rename the internal reference
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* sequences using a mapping function
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*/
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constructor(args) {
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const { filehandle, renameRefSeqs = s => s, path, url } = args;
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@@ -136,7 +140,9 @@ class BBI {
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const off = Number(header.asOffset);
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header.autoSql = toString(buffer.subarray(off, buffer.indexOf(0, off)));
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}
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-
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// refetch header if it is too large on first pass,
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// 8*5 is the sizeof the totalSummary struct
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if (header.totalSummaryOffset > requestSize - 8 * 5) {
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return this._getMainHeader(opts, requestSize * 2);
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}
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if (header.totalSummaryOffset) {
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package/dist/bbi.js.map
CHANGED
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@@ -1 +1 @@
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1
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+
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|
package/esm/bbi.js
CHANGED
|
@@ -82,9 +82,13 @@ export class BBI {
|
|
|
82
82
|
}
|
|
83
83
|
/*
|
|
84
84
|
* @param filehandle - a filehandle from generic-filehandle or implementing something similar to the node10 fs.promises API
|
|
85
|
+
*
|
|
85
86
|
* @param path - a Local file path as a string
|
|
87
|
+
*
|
|
86
88
|
* @param url - a URL string
|
|
87
|
-
*
|
|
89
|
+
*
|
|
90
|
+
* @param renameRefSeqs - an optional method to rename the internal reference
|
|
91
|
+
* sequences using a mapping function
|
|
88
92
|
*/
|
|
89
93
|
constructor(args) {
|
|
90
94
|
const { filehandle, renameRefSeqs = s => s, path, url } = args;
|
|
@@ -121,7 +125,9 @@ export class BBI {
|
|
|
121
125
|
const off = Number(header.asOffset);
|
|
122
126
|
header.autoSql = toString(buffer.subarray(off, buffer.indexOf(0, off)));
|
|
123
127
|
}
|
|
124
|
-
|
|
128
|
+
// refetch header if it is too large on first pass,
|
|
129
|
+
// 8*5 is the sizeof the totalSummary struct
|
|
130
|
+
if (header.totalSummaryOffset > requestSize - 8 * 5) {
|
|
125
131
|
return this._getMainHeader(opts, requestSize * 2);
|
|
126
132
|
}
|
|
127
133
|
if (header.totalSummaryOffset) {
|
package/esm/bbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAC/B,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,SAAS,EAAE,UAAU,EAAqB,MAAM,oBAAoB,CAAA;AAC7E,OAAO,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AACjD,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AAExC,MAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AACjC,MAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AAEjC,SAAS,QAAQ,CAAC,GAAe;IAC/B,OAAO,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;AACtC,CAAC;AAyCD;;;;GAIG;AACH,SAAS,UAAU,CAAC,IAAa;IAC/B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;IAClC,MAAM,YAAY,GAAG,IAAI,MAAM,EAAE;SAC9B,SAAS,CAAC,EAAE,CAAC;SACb,KAAK,CAAC,OAAO,CAAC;SACd,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,eAAe,CAAC;SACvB,MAAM,CAAC,iBAAiB,CAAC;SACzB,MAAM,CAAC,oBAAoB,CAAC;SAC5B,MAAM,CAAC,qBAAqB,CAAC;SAC7B,MAAM,CAAC,YAAY,CAAC;SACpB,MAAM,CAAC,mBAAmB,CAAC;SAC3B,MAAM,CAAC,UAAU,CAAC,CAAC,iCAAiC;SACpD,MAAM,CAAC,oBAAoB,CAAC;SAC5B,MAAM,CAAC,mBAAmB,CAAC;SAC3B,MAAM,CAAC,iBAAiB,CAAC,CAAC,oCAAoC;SAC9D,KAAK,CAAC,YAAY,EAAE;QACnB,MAAM,EAAE,eAAe;QACvB,IAAI,EAAE,IAAI,MAAM,EAAE;aACf,SAAS,CAAC,EAAE,CAAC;aACb,MAAM,CAAC,gBAAgB,CAAC;aACxB,MAAM,CAAC,UAAU,CAAC;aAClB,MAAM,CAAC,YAAY,CAAC;aACpB,MAAM,CAAC,aAAa,CAAC;KACzB,CAAC,CAAA;IAEJ,MAAM,kBAAkB,GAAG,IAAI,MAAM,EAAE;SACpC,SAAS,CAAC,EAAE,CAAC;SACb,MAAM,CAAC,cAAc,CAAC;SACtB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,iBAAiB,CAAC,CAAA;IAE9B,MAAM,eAAe,GAAG,IAAI,MAAM,EAAE;SACjC,SAAS,CAAC,EAAE,CAAC;SACb,MAAM,CAAC,OAAO,CAAC;SACf,MAAM,CAAC,WAAW,CAAC;SACnB,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,WAAW,CAAC,CAAA;IAEtB,MAAM,UAAU,GAAG,IAAI,MAAM,EAAE;SAC5B,SAAS,CAAC,EAAE,CAAC;SACb,KAAK,CAAC,YAAY,CAAC;SACnB,IAAI,CAAC,CAAC,CAAC;SACP,MAAM,CAAC,KAAK,CAAC;SACb,UAAU,CAAC,QAAQ,CAAC,CAAA;IAEvB,OAAO;QACL,eAAe;QACf,kBAAkB;QAClB,YAAY;QACZ,UAAU;KACX,CAAA;AACH,CAAC;AAQD,MAAM,OAAgB,GAAG;IAOvB;;;OAGG;IACI,SAAS,CAAC,IAAqB;QACpC,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE;YACjB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC7C,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;gBACxB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,OAAO,CAAA;IACrB,CAAC;IAED
|
|
1
|
+
{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAC/B,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,SAAS,EAAE,UAAU,EAAqB,MAAM,oBAAoB,CAAA;AAC7E,OAAO,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AACjD,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AAExC,MAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AACjC,MAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AAEjC,SAAS,QAAQ,CAAC,GAAe;IAC/B,OAAO,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;AACtC,CAAC;AAyCD;;;;GAIG;AACH,SAAS,UAAU,CAAC,IAAa;IAC/B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;IAClC,MAAM,YAAY,GAAG,IAAI,MAAM,EAAE;SAC9B,SAAS,CAAC,EAAE,CAAC;SACb,KAAK,CAAC,OAAO,CAAC;SACd,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,eAAe,CAAC;SACvB,MAAM,CAAC,iBAAiB,CAAC;SACzB,MAAM,CAAC,oBAAoB,CAAC;SAC5B,MAAM,CAAC,qBAAqB,CAAC;SAC7B,MAAM,CAAC,YAAY,CAAC;SACpB,MAAM,CAAC,mBAAmB,CAAC;SAC3B,MAAM,CAAC,UAAU,CAAC,CAAC,iCAAiC;SACpD,MAAM,CAAC,oBAAoB,CAAC;SAC5B,MAAM,CAAC,mBAAmB,CAAC;SAC3B,MAAM,CAAC,iBAAiB,CAAC,CAAC,oCAAoC;SAC9D,KAAK,CAAC,YAAY,EAAE;QACnB,MAAM,EAAE,eAAe;QACvB,IAAI,EAAE,IAAI,MAAM,EAAE;aACf,SAAS,CAAC,EAAE,CAAC;aACb,MAAM,CAAC,gBAAgB,CAAC;aACxB,MAAM,CAAC,UAAU,CAAC;aAClB,MAAM,CAAC,YAAY,CAAC;aACpB,MAAM,CAAC,aAAa,CAAC;KACzB,CAAC,CAAA;IAEJ,MAAM,kBAAkB,GAAG,IAAI,MAAM,EAAE;SACpC,SAAS,CAAC,EAAE,CAAC;SACb,MAAM,CAAC,cAAc,CAAC;SACtB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,iBAAiB,CAAC,CAAA;IAE9B,MAAM,eAAe,GAAG,IAAI,MAAM,EAAE;SACjC,SAAS,CAAC,EAAE,CAAC;SACb,MAAM,CAAC,OAAO,CAAC;SACf,MAAM,CAAC,WAAW,CAAC;SACnB,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,WAAW,CAAC,CAAA;IAEtB,MAAM,UAAU,GAAG,IAAI,MAAM,EAAE;SAC5B,SAAS,CAAC,EAAE,CAAC;SACb,KAAK,CAAC,YAAY,CAAC;SACnB,IAAI,CAAC,CAAC,CAAC;SACP,MAAM,CAAC,KAAK,CAAC;SACb,UAAU,CAAC,QAAQ,CAAC,CAAA;IAEvB,OAAO;QACL,eAAe;QACf,kBAAkB;QAClB,YAAY;QACZ,UAAU;KACX,CAAA;AACH,CAAC;AAQD,MAAM,OAAgB,GAAG;IAOvB;;;OAGG;IACI,SAAS,CAAC,IAAqB;QACpC,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE;YACjB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC7C,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;gBACxB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,OAAO,CAAA;IACrB,CAAC;IAED;;;;;;;;;OASG;IACH,YAAmB,IAKlB;QACC,MAAM,EAAE,UAAU,EAAE,aAAa,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,IAAI,CAAA;QAC9D,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;QAClC,IAAI,UAAU,EAAE;YACd,IAAI,CAAC,GAAG,GAAG,UAAU,CAAA;SACtB;aAAM,IAAI,GAAG,EAAE;YACd,IAAI,CAAC,GAAG,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,CAAA;SAC/B;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,GAAG,GAAG,IAAI,SAAS,CAAC,IAAI,CAAC,CAAA;SAC/B;aAAM;YACL,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;SACjC;IACH,CAAC;IAEO,KAAK,CAAC,UAAU,CAAC,IAAqB;QAC5C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;QAC9C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACtD,OAAO,EAAE,GAAG,MAAM,EAAE,GAAG,MAAM,EAAE,CAAA;IACjC,CAAC;IAEO,KAAK,CAAC,cAAc,CAC1B,IAAqB,EACrB,WAAW,GAAG,IAAI;QAElB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,EACzB,CAAC,EACD,WAAW,EACX,CAAC,EACD,IAAI,CACL,CAAA;QACD,MAAM,WAAW,GAAG,IAAI,CAAC,YAAY,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,UAAU,CAAC,WAAW,CAAC,CAAA;QACnC,MAAM,MAAM,GAAG,GAAG,CAAC,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,kBAAkB,EAAE,GAAG,MAAM,CAAA;QACtD,MAAM,CAAC,QAAQ,GAAG,KAAK,KAAK,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAA;QAC/D,IAAI,QAAQ,GAAG,WAAW,IAAI,kBAAkB,GAAG,WAAW,EAAE;YAC9D,OAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;SAClD;QACD,IAAI,QAAQ,EAAE;YACZ,MAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;YACnC,MAAM,CAAC,OAAO,GAAG,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAA;SACxE;QAED,mDAAmD;QACnD,4CAA4C;QAC5C,IAAI,MAAM,CAAC,kBAAkB,GAAG,WAAW,GAAG,CAAC,GAAG,CAAC,EAAE;YACnD,OAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;SAClD;QAED,IAAI,MAAM,CAAC,kBAAkB,EAAE;YAC7B,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,kBAAkB,CAAC,CAAC,CAAA;YAC/D,MAAM,GAAG,GAAG,GAAG,CAAC,kBAAkB,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC9C,MAAM,CAAC,YAAY,GAAG,EAAE,GAAG,GAAG,EAAE,YAAY,EAAE,MAAM,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,CAAA;SACzE;QACD,OAAO,EAAE,GAAG,MAAM,EAAE,WAAW,EAAE,CAAA;IACnC,CAAC;IAEO,YAAY,CAAC,MAAc;QACjC,IAAI,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC/B,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE;YAClD,OAAO,KAAK,CAAA;SACb;QACD,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC3B,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE;YAClD,OAAO,IAAI,CAAA;SACZ;QACD,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;IAC7C,CAAC;IAED,qCAAqC;IAC7B,KAAK,CAAC,cAAc,CAC1B,MAAc,EACd,IAA+B;QAE/B,MAAM,IAAI,GAAG,MAAM,CAAC,WAAW,CAAA;QAC/B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;QAClC,MAAM,YAAY,GAEd,EAAE,CAAA;QACN,MAAM,UAAU,GAA8B,EAAE,CAAA;QAEhD,IAAI,kBAAkB,GAAG,MAAM,CAAC,MAAM,CAAC,kBAAkB,CAAC,CAAA;QAC1D,MAAM,eAAe,GAAG,MAAM,CAAC,MAAM,CAAC,eAAe,CAAC,CAAA;QACtD,OAAO,kBAAkB,GAAG,CAAC,KAAK,CAAC,EAAE;YACnC,kBAAkB,IAAI,CAAC,CAAA;SACxB;QACD,M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|
package/package.json
CHANGED
package/src/bbi.ts
CHANGED
|
@@ -142,9 +142,13 @@ export abstract class BBI {
|
|
|
142
142
|
|
|
143
143
|
/*
|
|
144
144
|
* @param filehandle - a filehandle from generic-filehandle or implementing something similar to the node10 fs.promises API
|
|
145
|
+
*
|
|
145
146
|
* @param path - a Local file path as a string
|
|
147
|
+
*
|
|
146
148
|
* @param url - a URL string
|
|
147
|
-
*
|
|
149
|
+
*
|
|
150
|
+
* @param renameRefSeqs - an optional method to rename the internal reference
|
|
151
|
+
* sequences using a mapping function
|
|
148
152
|
*/
|
|
149
153
|
public constructor(args: {
|
|
150
154
|
filehandle?: GenericFilehandle
|
|
@@ -194,9 +198,13 @@ export abstract class BBI {
|
|
|
194
198
|
const off = Number(header.asOffset)
|
|
195
199
|
header.autoSql = toString(buffer.subarray(off, buffer.indexOf(0, off)))
|
|
196
200
|
}
|
|
197
|
-
|
|
201
|
+
|
|
202
|
+
// refetch header if it is too large on first pass,
|
|
203
|
+
// 8*5 is the sizeof the totalSummary struct
|
|
204
|
+
if (header.totalSummaryOffset > requestSize - 8 * 5) {
|
|
198
205
|
return this._getMainHeader(opts, requestSize * 2)
|
|
199
206
|
}
|
|
207
|
+
|
|
200
208
|
if (header.totalSummaryOffset) {
|
|
201
209
|
const tail = buffer.subarray(Number(header.totalSummaryOffset))
|
|
202
210
|
const sum = ret.totalSummaryParser.parse(tail)
|