@gmod/tabix 1.5.14 → 1.6.0
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 +9 -5
- package/README.md +182 -35
- package/dist/chunk.js +0 -1
- package/dist/chunk.js.map +1 -1
- package/dist/csi.d.ts +1 -1
- package/dist/csi.js +132 -128
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.js +15 -41
- package/dist/indexFile.js.map +1 -1
- package/dist/tabix-bundle.js +2 -0
- package/dist/tabix-bundle.js.LICENSE.txt +8 -0
- package/dist/tabixIndexedFile.d.ts +49 -25
- package/dist/tabixIndexedFile.js +214 -195
- package/dist/tabixIndexedFile.js.map +1 -1
- package/dist/tbi.js +169 -173
- package/dist/tbi.js.map +1 -1
- package/dist/util.d.ts +7 -6
- package/dist/util.js +9 -19
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.d.ts +0 -1
- package/dist/virtualOffset.js +0 -13
- package/dist/virtualOffset.js.map +1 -1
- package/esm/chunk.js +0 -1
- package/esm/chunk.js.map +1 -1
- package/esm/csi.d.ts +1 -1
- package/esm/csi.js +4 -4
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.js +1 -1
- package/esm/indexFile.js.map +1 -1
- package/esm/tabixIndexedFile.d.ts +49 -25
- package/esm/tabixIndexedFile.js +134 -90
- package/esm/tabixIndexedFile.js.map +1 -1
- package/esm/tbi.js +6 -5
- package/esm/tbi.js.map +1 -1
- package/esm/util.d.ts +7 -6
- package/esm/util.js +6 -5
- package/esm/util.js.map +1 -1
- package/esm/virtualOffset.d.ts +0 -1
- package/esm/virtualOffset.js +0 -13
- package/esm/virtualOffset.js.map +1 -1
- package/package.json +24 -19
- package/src/chunk.ts +0 -1
- package/src/csi.ts +6 -5
- package/src/indexFile.ts +1 -1
- package/src/tabixIndexedFile.ts +141 -106
- package/src/tbi.ts +7 -6
- package/src/util.ts +7 -6
- package/src/virtualOffset.ts +7 -21
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+
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|
package/esm/tbi.js
CHANGED
|
@@ -7,7 +7,8 @@ import IndexFile from './indexFile';
|
|
|
7
7
|
const TBI_MAGIC = 21578324; // TBI\1
|
|
8
8
|
const TAD_LIDX_SHIFT = 14;
|
|
9
9
|
/**
|
|
10
|
-
* calculate the list of bins that may overlap with region [beg,end)
|
|
10
|
+
* calculate the list of bins that may overlap with region [beg,end)
|
|
11
|
+
* (zero-based half-open)
|
|
11
12
|
*/
|
|
12
13
|
function reg2bins(beg, end) {
|
|
13
14
|
beg += 1; // < convert to 1-based closed
|
|
@@ -24,10 +25,10 @@ function reg2bins(beg, end) {
|
|
|
24
25
|
export default class TabixIndex extends IndexFile {
|
|
25
26
|
async lineCount(refName, opts = {}) {
|
|
26
27
|
const indexData = await this.parse(opts);
|
|
27
|
-
|
|
28
|
+
const refId = indexData.refNameToId[refName];
|
|
29
|
+
if (refId === undefined) {
|
|
28
30
|
return -1;
|
|
29
31
|
}
|
|
30
|
-
const refId = indexData.refNameToId[refName];
|
|
31
32
|
const idx = indexData.indices[refId];
|
|
32
33
|
if (!idx) {
|
|
33
34
|
return -1;
|
|
@@ -166,10 +167,10 @@ export default class TabixIndex extends IndexFile {
|
|
|
166
167
|
min = 0;
|
|
167
168
|
}
|
|
168
169
|
const indexData = await this.parse(opts);
|
|
169
|
-
|
|
170
|
+
const refId = indexData.refNameToId[refName];
|
|
171
|
+
if (refId === undefined) {
|
|
170
172
|
return [];
|
|
171
173
|
}
|
|
172
|
-
const refId = indexData.refNameToId[refName];
|
|
173
174
|
const ba = indexData.indices[refId];
|
|
174
175
|
if (!ba) {
|
|
175
176
|
return [];
|
package/esm/tbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,MAAM,CAAA;AAEvB,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,KAAK,MAAM,SAAS,CAAA;AAC3B,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EAAE,YAAY,EAAE,cAAc,EAAE,gBAAgB,EAAE,MAAM,QAAQ,CAAA;AACvE,OAAO,SAAsB,MAAM,aAAa,CAAA;AAEhD,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACnC,MAAM,cAAc,GAAG,EAAE,CAAA;AAEzB
|
|
1
|
+
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,MAAM,CAAA;AAEvB,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,KAAK,MAAM,SAAS,CAAA;AAC3B,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EAAE,YAAY,EAAE,cAAc,EAAE,gBAAgB,EAAE,MAAM,QAAQ,CAAA;AACvE,OAAO,SAAsB,MAAM,aAAa,CAAA;AAEhD,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACnC,MAAM,cAAc,GAAG,EAAE,CAAA;AAEzB;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;IACvC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAAS;IAC/C,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC1C,IAAI,KAAK,EAAE,CAAC;YACV,OAAO,KAAK,CAAC,SAAS,CAAA;QACxB,CAAC;QACD,OAAO,CAAC,CAAC,CAAA;IACX,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAChD,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAA;QAC9B,gBAAgB,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAE7B,0BAA0B;QAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,aAAa,EAAE,CAAC;YACtD,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACjC,oDAAoD;QACtD,CAAC;QAED,6CAA6C;QAC7C,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACrC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACxC,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,UAAU,GAA2B;YACzC,CAAC,EAAE,SAAS;YACZ,CAAC,EAAE,KAAK;YACR,CAAC,EAAE,KAAK;SACT,CAAA;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QAC5C,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;YAC1B,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;YAC5B,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;SAC3B,CAAA;QACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QACvC,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QACvD,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1C,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;QAClE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QAEvC,2BAA2B;QAC3B,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QAC/C,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,GAAG,iBAAiB,CAAC,CACxC,CAAA;QAED,+CAA+C;QAC/C,IAAI,UAAU,GAAG,EAAE,GAAG,iBAAiB,CAAA;QACvC,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;YACnD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YAC9C,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;gBAC1C,UAAU,IAAI,CAAC,CAAA;gBACf,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;gBACH,CAAC;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;oBACpC,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;oBAChD,UAAU,IAAI,CAAC,CAAA;oBACf,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;wBACrB,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oBAChD,CAAC;oBACD,UAAU,IAAI,EAAE,GAAG,UAAU,CAAA;gBAC/B,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;oBAChD,UAAU,IAAI,CAAC,CAAA;oBACf,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;oBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAC1C,UAAU,IAAI,EAAE,CAAA;wBAChB,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBACrD,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,mBAAmB;YACnB,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YACjD,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;YAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACxC,WAAW,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;gBAC7C,UAAU,IAAI,CAAC,CAAA;gBACf,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;YACpE,CAAC;YACD,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;QACzC,CAAC,CAAC,CAAA;QAEF,OAAO;YACL,OAAO;YACP,QAAQ;YACR,YAAY;YACZ,YAAY;YACZ,SAAS;YACT,aAAa;YACb,aAAa;YACb,cAAc;YACd,MAAM;YACN,WAAW;YACX,WAAW;YACX,YAAY,EAAE,CAAC,IAAI,EAAE;SACtB,CAAA;IACH,CAAC;IAED,cAAc,CAAC,KAAa,EAAE,MAAc;QAC1C,MAAM,SAAS,GAAG,YAAY,CAC5B,IAAI,CAAC,WAAW,CACd,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,CAAwB,EAC5D,IAAI,CACL,CACF,CAAA;QACD,OAAO,EAAE,SAAS,EAAE,CAAA;IACtB,CAAC;IAED,eAAe,CAAC,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAa,EAAE,CAAA;QAChC,MAAM,WAAW,GAA2B,EAAE,CAAA;QAC9C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;gBACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;oBACtB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;gBAClC,CAAC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;YAChB,CAAC;QACH,CAAC;QACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;IACrC,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,OAAe,EACf,GAAW,EACX,GAAW,EACX,OAAgB,EAAE;QAElB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,SAAS,GAAG,EAAE,CAAC,WAAW,CAAC,MAAM;YACrC,CAAC,CAAC,EAAE,CAAC,WAAW,CACZ,GAAG,IAAI,cAAc,IAAI,EAAE,CAAC,WAAW,CAAC,MAAM;gBAC5C,CAAC,CAAC,EAAE,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC;gBAC3B,CAAC,CAAC,GAAG,IAAI,cAAc,CAC1B;YACH,CAAC,CAAC,IAAI,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QAC3B,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,OAAO,CAAC,IAAI,CAAC,0CAA0C,CAAC,CAAA;QAC1D,CAAC;QAED,4CAA4C;QAE5C,MAAM,eAAe,GAAG,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA,CAAC,uCAAuC;QAClF,MAAM,MAAM,GAAY,EAAE,CAAA;QAE1B,sEAAsE;QACtE,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;YAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;gBACxC,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBACrB,KAAK,MAAM,CAAC,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;wBACjC,MAAM,CAAC,IAAI,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;oBAC7C,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,0EAA0E;QAC1E,mCAAmC;QACnC,MAAM,KAAK,GAAG,EAAE,CAAC,WAAW,CAAC,MAAM,CAAA;QACnC,IAAI,MAAM,GAAG,IAAI,CAAA;QACjB,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;QAC7C,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;QAC7C,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,IAAI,MAAM,EAAE,EAAE,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YAC5B,IAAI,EAAE,EAAE,CAAC;gBACP,IAAI,CAAC,MAAM,IAAI,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;oBACxC,MAAM,GAAG,EAAE,CAAA;gBACb,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,cAAc,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;IACvC,CAAC;CACF"}
|
package/esm/util.d.ts
CHANGED
|
@@ -2,14 +2,15 @@ import Chunk from './chunk';
|
|
|
2
2
|
import VirtualOffset from './virtualOffset';
|
|
3
3
|
export declare function longToNumber(long: Long): number;
|
|
4
4
|
/**
|
|
5
|
-
* Properly check if the given AbortSignal is aborted.
|
|
6
|
-
*
|
|
7
|
-
*
|
|
8
|
-
* with a `code` attribute set to `ERR_ABORTED`.
|
|
5
|
+
* Properly check if the given AbortSignal is aborted. Per the standard, if the
|
|
6
|
+
* signal reads as aborted, this function throws either a DOMException
|
|
7
|
+
* AbortError, or a regular error with a `code` attribute set to `ERR_ABORTED`.
|
|
9
8
|
*
|
|
10
9
|
* For convenience, passing `undefined` is a no-op
|
|
11
10
|
*
|
|
12
|
-
* @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted`
|
|
11
|
+
* @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted`
|
|
12
|
+
* attribute
|
|
13
|
+
*
|
|
13
14
|
* @returns nothing
|
|
14
15
|
*/
|
|
15
16
|
export declare function checkAbortSignal(signal?: AbortSignal): void;
|
|
@@ -21,4 +22,4 @@ export declare function checkAbortSignal(signal?: AbortSignal): void;
|
|
|
21
22
|
*/
|
|
22
23
|
export declare function abortBreakPoint(signal?: AbortSignal): Promise<void>;
|
|
23
24
|
export declare function canMergeBlocks(chunk1: Chunk, chunk2: Chunk): boolean;
|
|
24
|
-
export declare function optimizeChunks(chunks: Chunk[], lowest
|
|
25
|
+
export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
|
package/esm/util.js
CHANGED
|
@@ -8,14 +8,15 @@ export function longToNumber(long) {
|
|
|
8
8
|
class AbortError extends Error {
|
|
9
9
|
}
|
|
10
10
|
/**
|
|
11
|
-
* Properly check if the given AbortSignal is aborted.
|
|
12
|
-
*
|
|
13
|
-
*
|
|
14
|
-
* with a `code` attribute set to `ERR_ABORTED`.
|
|
11
|
+
* Properly check if the given AbortSignal is aborted. Per the standard, if the
|
|
12
|
+
* signal reads as aborted, this function throws either a DOMException
|
|
13
|
+
* AbortError, or a regular error with a `code` attribute set to `ERR_ABORTED`.
|
|
15
14
|
*
|
|
16
15
|
* For convenience, passing `undefined` is a no-op
|
|
17
16
|
*
|
|
18
|
-
* @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted`
|
|
17
|
+
* @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted`
|
|
18
|
+
* attribute
|
|
19
|
+
*
|
|
19
20
|
* @returns nothing
|
|
20
21
|
*/
|
|
21
22
|
export function checkAbortSignal(signal) {
|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AAED,MAAM,UAAW,SAAQ,KAAK;CAE7B;AACD
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AAED,MAAM,UAAW,SAAQ,KAAK;CAE7B;AACD;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,eAAe,CAAC,MAAoB;IACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;IACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAAS,GAAiB,IAAI,CAAA;IAElC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;IAED,MAAM,CAAC,IAAI,CAAC,UAAU,EAAE,EAAE,EAAE;QAC1B,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;QACrB,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;YAChD,IAAI,SAAS,KAAK,IAAI,EAAE,CAAC;gBACvB,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE,CAAC;oBACrC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC7C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;oBAC7B,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC,CAAC,CAAA;IAEF,OAAO,YAAY,CAAA;AACrB,CAAC"}
|
package/esm/virtualOffset.d.ts
CHANGED
|
@@ -5,6 +5,5 @@ export default class VirtualOffset {
|
|
|
5
5
|
constructor(blockPosition: number, dataPosition: number);
|
|
6
6
|
toString(): string;
|
|
7
7
|
compareTo(b: VirtualOffset): number;
|
|
8
|
-
static min(...args: VirtualOffset[]): VirtualOffset;
|
|
9
8
|
}
|
|
10
9
|
export declare function fromBytes(bytes: Buffer, offset?: number, bigendian?: boolean): VirtualOffset;
|
package/esm/virtualOffset.js
CHANGED
|
@@ -9,19 +9,6 @@ export default class VirtualOffset {
|
|
|
9
9
|
compareTo(b) {
|
|
10
10
|
return (this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition);
|
|
11
11
|
}
|
|
12
|
-
static min(...args) {
|
|
13
|
-
let min;
|
|
14
|
-
let i = 0;
|
|
15
|
-
for (; !min; i += 1) {
|
|
16
|
-
min = args[i];
|
|
17
|
-
}
|
|
18
|
-
for (; i < args.length; i += 1) {
|
|
19
|
-
if (min.compareTo(args[i]) > 0) {
|
|
20
|
-
min = args[i];
|
|
21
|
-
}
|
|
22
|
-
}
|
|
23
|
-
return min;
|
|
24
|
-
}
|
|
25
12
|
}
|
|
26
13
|
export function fromBytes(bytes, offset = 0, bigendian = false) {
|
|
27
14
|
if (bigendian) {
|
package/esm/virtualOffset.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AACA,MAAM,CAAC,OAAO,OAAO,aAAa;IAGhC,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;
|
|
1
|
+
{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AACA,MAAM,CAAC,OAAO,OAAO,aAAa;IAGhC,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/tabix",
|
|
3
|
-
"version": "1.
|
|
3
|
+
"version": "1.6.0",
|
|
4
4
|
"description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/tabix-js",
|
|
@@ -20,16 +20,18 @@
|
|
|
20
20
|
"src"
|
|
21
21
|
],
|
|
22
22
|
"scripts": {
|
|
23
|
-
"test": "
|
|
24
|
-
"
|
|
25
|
-
"
|
|
23
|
+
"test": "vitest",
|
|
24
|
+
"lint": "eslint --report-unused-disable-directives --max-warnings 0",
|
|
25
|
+
"format": "prettier --write .",
|
|
26
|
+
"docs": "documentation readme --shallow src/tabixIndexedFile.ts --section TabixIndexedFile",
|
|
26
27
|
"clean": "rimraf dist esm",
|
|
27
28
|
"prebuild": "npm run clean && npm run lint",
|
|
28
|
-
"build:esm": "tsc --
|
|
29
|
-
"build:es5": "tsc --
|
|
29
|
+
"build:esm": "tsc --outDir esm",
|
|
30
|
+
"build:es5": "tsc --module commonjs --outDir dist",
|
|
30
31
|
"build": "npm run build:esm && npm run build:es5",
|
|
31
|
-
"
|
|
32
|
-
"
|
|
32
|
+
"postbuild": "webpack",
|
|
33
|
+
"preversion": "npm run lint && npm test run && npm run build",
|
|
34
|
+
"prepublishOnly": "npm run lint && npm test run && npm run build",
|
|
33
35
|
"version": "standard-changelog && git add CHANGELOG.md",
|
|
34
36
|
"postversion": "git push --follow-tags"
|
|
35
37
|
},
|
|
@@ -47,23 +49,26 @@
|
|
|
47
49
|
},
|
|
48
50
|
"devDependencies": {
|
|
49
51
|
"@eslint/eslintrc": "^3.1.0",
|
|
50
|
-
"@eslint/js": "^9.
|
|
51
|
-
"@types/jest": "^29.5.12",
|
|
52
|
+
"@eslint/js": "^9.9.0",
|
|
52
53
|
"@types/long": "^4.0.0",
|
|
53
54
|
"@types/node": "^20.11.16",
|
|
54
|
-
"@typescript-eslint/eslint-plugin": "^
|
|
55
|
-
"@typescript-eslint/parser": "^
|
|
56
|
-
"
|
|
55
|
+
"@typescript-eslint/eslint-plugin": "^8.0.1",
|
|
56
|
+
"@typescript-eslint/parser": "^8.0.1",
|
|
57
|
+
"@vitest/coverage-v8": "^2.0.5",
|
|
58
|
+
"buffer": "^6.0.3",
|
|
59
|
+
"documentation": "^14.0.3",
|
|
60
|
+
"eslint": "^9.9.0",
|
|
57
61
|
"eslint-config-prettier": "^9.1.0",
|
|
58
62
|
"eslint-plugin-prettier": "^5.0.1",
|
|
59
|
-
"eslint-plugin-unicorn": "^
|
|
60
|
-
"
|
|
61
|
-
"jest-environment-jsdom": "^29.5.0",
|
|
62
|
-
"prettier": "^3.2.5",
|
|
63
|
+
"eslint-plugin-unicorn": "^56.0.0",
|
|
64
|
+
"prettier": "^3.3.3",
|
|
63
65
|
"rimraf": "^6.0.1",
|
|
64
66
|
"standard-changelog": "^6.0.0",
|
|
65
|
-
"
|
|
66
|
-
"typescript": "^
|
|
67
|
+
"typescript": "^5.3.3",
|
|
68
|
+
"typescript-eslint": "^8.0.1",
|
|
69
|
+
"vitest": "^2.0.5",
|
|
70
|
+
"webpack": "^5.93.0",
|
|
71
|
+
"webpack-cli": "^5.1.4"
|
|
67
72
|
},
|
|
68
73
|
"publishConfig": {
|
|
69
74
|
"access": "public"
|
package/src/chunk.ts
CHANGED
package/src/csi.ts
CHANGED
|
@@ -30,10 +30,10 @@ export default class CSI extends IndexFile {
|
|
|
30
30
|
}
|
|
31
31
|
async lineCount(refName: string, opts: Options = {}): Promise<number> {
|
|
32
32
|
const indexData = await this.parse(opts)
|
|
33
|
-
|
|
33
|
+
const refId = indexData.refNameToId[refName]
|
|
34
|
+
if (refId === undefined) {
|
|
34
35
|
return -1
|
|
35
36
|
}
|
|
36
|
-
const refId = indexData.refNameToId[refName]
|
|
37
37
|
const idx = indexData.indices[refId]
|
|
38
38
|
if (!idx) {
|
|
39
39
|
return -1
|
|
@@ -44,6 +44,7 @@ export default class CSI extends IndexFile {
|
|
|
44
44
|
}
|
|
45
45
|
return -1
|
|
46
46
|
}
|
|
47
|
+
|
|
47
48
|
indexCov() {
|
|
48
49
|
throw new Error('CSI indexes do not support indexcov')
|
|
49
50
|
}
|
|
@@ -206,10 +207,10 @@ export default class CSI extends IndexFile {
|
|
|
206
207
|
}
|
|
207
208
|
|
|
208
209
|
const indexData = await this.parse(opts)
|
|
209
|
-
|
|
210
|
+
const refId = indexData.refNameToId[refName]
|
|
211
|
+
if (refId === undefined) {
|
|
210
212
|
return []
|
|
211
213
|
}
|
|
212
|
-
const refId = indexData.refNameToId[refName]
|
|
213
214
|
const ba = indexData.indices[refId]
|
|
214
215
|
if (!ba) {
|
|
215
216
|
return []
|
|
@@ -258,7 +259,7 @@ export default class CSI extends IndexFile {
|
|
|
258
259
|
`query ${beg}-${end} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`,
|
|
259
260
|
)
|
|
260
261
|
}
|
|
261
|
-
bins.push([b, e])
|
|
262
|
+
bins.push([b, e] as const)
|
|
262
263
|
}
|
|
263
264
|
return bins
|
|
264
265
|
}
|
package/src/indexFile.ts
CHANGED