@gmod/tabix 1.5.10 → 1.5.12
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 +15 -5
- package/dist/chunk.d.ts +0 -6
- package/dist/chunk.js +1 -6
- package/dist/chunk.js.map +1 -1
- package/dist/csi.d.ts +7 -16
- package/dist/csi.js +4 -7
- package/dist/csi.js.map +1 -1
- package/dist/index.d.ts +3 -4
- package/dist/index.js +7 -7
- package/dist/index.js.map +1 -1
- package/dist/indexFile.d.ts +2 -6
- package/dist/indexFile.js +4 -3
- package/dist/indexFile.js.map +1 -1
- package/dist/tabixIndexedFile.d.ts +3 -4
- package/dist/tabixIndexedFile.js +27 -48
- package/dist/tabixIndexedFile.js.map +1 -1
- package/dist/tbi.d.ts +4 -9
- package/dist/tbi.js +2 -3
- package/dist/tbi.js.map +1 -1
- package/dist/util.js +1 -6
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.d.ts +1 -0
- package/dist/virtualOffset.js.map +1 -1
- package/esm/chunk.d.ts +0 -6
- package/esm/chunk.js +1 -6
- package/esm/chunk.js.map +1 -1
- package/esm/csi.d.ts +7 -16
- package/esm/csi.js +4 -5
- package/esm/csi.js.map +1 -1
- package/esm/index.d.ts +3 -4
- package/esm/index.js +3 -4
- package/esm/index.js.map +1 -1
- package/esm/indexFile.d.ts +2 -6
- package/esm/indexFile.js +4 -3
- package/esm/indexFile.js.map +1 -1
- package/esm/tabixIndexedFile.d.ts +3 -4
- package/esm/tabixIndexedFile.js +26 -47
- package/esm/tabixIndexedFile.js.map +1 -1
- package/esm/tbi.d.ts +4 -9
- package/esm/tbi.js +2 -3
- package/esm/tbi.js.map +1 -1
- package/esm/util.js +1 -6
- package/esm/util.js.map +1 -1
- package/esm/virtualOffset.d.ts +1 -0
- package/esm/virtualOffset.js.map +1 -1
- package/package.json +16 -16
- package/src/chunk.ts +1 -6
- package/src/csi.ts +7 -7
- package/src/index.ts +3 -5
- package/src/indexFile.ts +4 -4
- package/src/tabixIndexedFile.ts +33 -52
- package/src/tbi.ts +6 -6
- package/src/util.ts +1 -5
- package/src/virtualOffset.ts +1 -0
package/dist/tbi.js.map
CHANGED
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@@ -1 +1 @@
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1
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1
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{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,gDAAuB;AAEvB,iEAA0D;AAC1D,oDAA2B;AAC3B,2DAA6C;AAC7C,iCAAuE;AACvE,4DAAgD;AAEhD,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACnC,MAAM,cAAc,GAAG,EAAE,CAAA;AAEzB;;GAEG;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;KACzC,CAAA;AACH,CAAC;AAED,MAAqB,UAAW,SAAQ,mBAAS;IACzC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;;YACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,IAAI,CAAC,SAAS,EAAE,CAAC;gBACf,OAAO,CAAC,CAAC,CAAA;YACX,CAAC;YACD,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACpC,IAAI,CAAC,GAAG,EAAE,CAAC;gBACT,OAAO,CAAC,CAAC,CAAA;YACX,CAAC;YACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YAC1C,IAAI,KAAK,EAAE,CAAC;gBACV,OAAO,KAAK,CAAC,SAAS,CAAA;YACxB,CAAC;YACD,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;KAAA;IAED,4BAA4B;IACtB,MAAM,CAAC,OAAgB,EAAE;;YAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;YAChD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAA;YAC9B,IAAA,uBAAgB,EAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YAE7B,0BAA0B;YAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,aAAa,EAAE,CAAC;gBACtD,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;gBACjC,oDAAoD;YACtD,CAAC;YAED,6CAA6C;YAC7C,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACrC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACxC,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;YACnE,MAAM,UAAU,GAA2B;gBACzC,CAAC,EAAE,SAAS;gBACZ,CAAC,EAAE,KAAK;gBACR,CAAC,EAAE,KAAK;aACT,CAAA;YACD,MAAM,MAAM,GAAG,UAAU,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;YAC5C,IAAI,CAAC,MAAM,EAAE,CAAC;gBACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;YACrE,CAAC;YACD,MAAM,aAAa,GAAG;gBACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;gBAC1B,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;gBAC5B,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;aAC3B,CAAA;YACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACvC,MAAM,KAAK,GAAG,CAAC,CAAA;YACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YACvD,MAAM,YAAY,GAAG,SAAA,CAAC,EAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA,CAAA;YAC1C,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;YAClE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YAEvC,2BAA2B;YAC3B,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YAC/C,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,GAAG,iBAAiB,CAAC,CACxC,CAAA;YAED,+CAA+C;YAC/C,IAAI,UAAU,GAAG,EAAE,GAAG,iBAAiB,CAAA;YACvC,IAAI,aAAwC,CAAA;YAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;gBACnD,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gBAC9C,UAAU,IAAI,CAAC,CAAA;gBACf,MAAM,QAAQ,GAA4B,EAAE,CAAA;gBAC5C,IAAI,KAAK,CAAA;gBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;oBACrC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;oBAC1C,UAAU,IAAI,CAAC,CAAA;oBACf,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;wBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;oBACH,CAAC;yBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;wBACpC,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAChD,UAAU,IAAI,CAAC,CAAA;wBACf,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;4BACrB,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBAChD,CAAC;wBACD,UAAU,IAAI,EAAE,GAAG,UAAU,CAAA;oBAC/B,CAAC;yBAAM,CAAC;wBACN,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAChD,UAAU,IAAI,CAAC,CAAA;wBACf,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;wBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;4BACvC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;4BACtC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;4BAC1C,UAAU,IAAI,EAAE,CAAA;4BAChB,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;4BACrD,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;wBAClC,CAAC;wBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;oBACxB,CAAC;gBACH,CAAC;gBAED,mBAAmB;gBACnB,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gBACjD,UAAU,IAAI,CAAC,CAAA;gBACf,MAAM,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;gBAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;oBACxC,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oBAC7C,UAAU,IAAI,CAAC,CAAA;oBACf,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;gBACpE,CAAC;gBACD,OA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+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;AAGA,SAAgB,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;AARD,oCAQC;AAED,MAAM,UAAW,SAAQ,KAAK;CAE7B;AACD;;;;;;;;;;GAUG;AACH,SAAgB,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,qCAAqC;YACrC,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;AAfD,4CAeC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;QACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;QACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAC1B,CAAC;CAAA;AAHD,0CAGC;AAED,SAAgB,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;AALD,wCAKC;AAED,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAqB;IACnE,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;AAhCD,wCAgCC"}
|
package/dist/virtualOffset.d.ts
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;
|
|
1
|
+
{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AACA,MAAqB,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;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACpB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AA/BD,gCA+BC;AACD,SAAgB,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,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC;AAdD,8BAcC"}
|
package/esm/chunk.d.ts
CHANGED
|
@@ -4,12 +4,6 @@ export default class Chunk {
|
|
|
4
4
|
maxv: VirtualOffset;
|
|
5
5
|
bin: number;
|
|
6
6
|
_fetchedSize?: number;
|
|
7
|
-
/**
|
|
8
|
-
* @param {VirtualOffset} minv
|
|
9
|
-
* @param {VirtualOffset} maxv
|
|
10
|
-
* @param {number} bin
|
|
11
|
-
* @param {number} [fetchedSize]
|
|
12
|
-
*/
|
|
13
7
|
constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?: undefined);
|
|
14
8
|
toUniqueString(): string;
|
|
15
9
|
toString(): string;
|
package/esm/chunk.js
CHANGED
|
@@ -1,11 +1,5 @@
|
|
|
1
1
|
// little class representing a chunk in the index
|
|
2
2
|
export default class Chunk {
|
|
3
|
-
/**
|
|
4
|
-
* @param {VirtualOffset} minv
|
|
5
|
-
* @param {VirtualOffset} maxv
|
|
6
|
-
* @param {number} bin
|
|
7
|
-
* @param {number} [fetchedSize]
|
|
8
|
-
*/
|
|
9
3
|
constructor(minv, maxv, bin, fetchedSize = undefined) {
|
|
10
4
|
this.minv = minv;
|
|
11
5
|
this.maxv = maxv;
|
|
@@ -13,6 +7,7 @@ export default class Chunk {
|
|
|
13
7
|
this._fetchedSize = fetchedSize;
|
|
14
8
|
}
|
|
15
9
|
toUniqueString() {
|
|
10
|
+
// eslint-disable-next-line @typescript-eslint/restrict-template-expressions
|
|
16
11
|
return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
|
|
17
12
|
}
|
|
18
13
|
toString() {
|
package/esm/chunk.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAMxB
|
|
1
|
+
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,SAAS;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,4EAA4E;QAC5E,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}
|
package/esm/csi.d.ts
CHANGED
|
@@ -1,4 +1,5 @@
|
|
|
1
1
|
/// <reference types="node" />
|
|
2
|
+
import { Buffer } from 'buffer';
|
|
2
3
|
import VirtualOffset from './virtualOffset';
|
|
3
4
|
import Chunk from './chunk';
|
|
4
5
|
import IndexFile, { Options } from './indexFile';
|
|
@@ -8,12 +9,10 @@ export default class CSI extends IndexFile {
|
|
|
8
9
|
private minShift;
|
|
9
10
|
constructor(args: any);
|
|
10
11
|
lineCount(refName: string, opts?: Options): Promise<number>;
|
|
11
|
-
indexCov():
|
|
12
|
+
indexCov(): void;
|
|
12
13
|
parseAuxData(bytes: Buffer, offset: number): {
|
|
13
14
|
refIdToName: string[];
|
|
14
|
-
refNameToId:
|
|
15
|
-
[key: string]: number;
|
|
16
|
-
};
|
|
15
|
+
refNameToId: Record<string, number>;
|
|
17
16
|
skipLines: number;
|
|
18
17
|
metaChar: string | null;
|
|
19
18
|
columnNumbers: {
|
|
@@ -25,9 +24,7 @@ export default class CSI extends IndexFile {
|
|
|
25
24
|
coordinateType: string;
|
|
26
25
|
};
|
|
27
26
|
_parseNameBytes(namesBytes: Buffer): {
|
|
28
|
-
refNameToId:
|
|
29
|
-
[key: string]: number;
|
|
30
|
-
};
|
|
27
|
+
refNameToId: Record<string, number>;
|
|
31
28
|
refIdToName: string[];
|
|
32
29
|
};
|
|
33
30
|
_parse(opts?: Options): Promise<{
|
|
@@ -37,9 +34,7 @@ export default class CSI extends IndexFile {
|
|
|
37
34
|
firstDataLine: VirtualOffset | undefined;
|
|
38
35
|
csiVersion: number;
|
|
39
36
|
indices: {
|
|
40
|
-
binIndex:
|
|
41
|
-
[key: string]: Chunk[];
|
|
42
|
-
};
|
|
37
|
+
binIndex: Record<string, Chunk[]>;
|
|
43
38
|
stats: {
|
|
44
39
|
lineCount: number;
|
|
45
40
|
} | undefined;
|
|
@@ -48,9 +43,7 @@ export default class CSI extends IndexFile {
|
|
|
48
43
|
maxBinNumber: number;
|
|
49
44
|
maxRefLength: number;
|
|
50
45
|
refIdToName: string[];
|
|
51
|
-
refNameToId:
|
|
52
|
-
[key: string]: number;
|
|
53
|
-
};
|
|
46
|
+
refNameToId: Record<string, number>;
|
|
54
47
|
skipLines: number;
|
|
55
48
|
metaChar: string | null;
|
|
56
49
|
columnNumbers: {
|
|
@@ -67,9 +60,7 @@ export default class CSI extends IndexFile {
|
|
|
67
60
|
firstDataLine: VirtualOffset | undefined;
|
|
68
61
|
csiVersion: number;
|
|
69
62
|
indices: {
|
|
70
|
-
binIndex:
|
|
71
|
-
[key: string]: Chunk[];
|
|
72
|
-
};
|
|
63
|
+
binIndex: Record<string, Chunk[]>;
|
|
73
64
|
stats: {
|
|
74
65
|
lineCount: number;
|
|
75
66
|
} | undefined;
|
package/esm/csi.js
CHANGED
|
@@ -35,7 +35,7 @@ export default class CSI extends IndexFile {
|
|
|
35
35
|
}
|
|
36
36
|
return -1;
|
|
37
37
|
}
|
|
38
|
-
|
|
38
|
+
indexCov() {
|
|
39
39
|
throw new Error('CSI indexes do not support indexcov');
|
|
40
40
|
}
|
|
41
41
|
parseAuxData(bytes, offset) {
|
|
@@ -86,7 +86,7 @@ export default class CSI extends IndexFile {
|
|
|
86
86
|
}
|
|
87
87
|
// fetch and parse the index
|
|
88
88
|
async _parse(opts = {}) {
|
|
89
|
-
const bytes = await unzip(
|
|
89
|
+
const bytes = await unzip(await this.filehandle.readFile(opts));
|
|
90
90
|
// check TBI magic numbers
|
|
91
91
|
let csiVersion;
|
|
92
92
|
if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
|
|
@@ -187,9 +187,8 @@ export default class CSI extends IndexFile {
|
|
|
187
187
|
for (const [start, end] of overlappingBins) {
|
|
188
188
|
for (let bin = start; bin <= end; bin++) {
|
|
189
189
|
if (ba.binIndex[bin]) {
|
|
190
|
-
const
|
|
191
|
-
|
|
192
|
-
chunks.push(new Chunk(binChunks[c].minv, binChunks[c].maxv, bin));
|
|
190
|
+
for (const c of ba.binIndex[bin]) {
|
|
191
|
+
chunks.push(new Chunk(c.minv, c.maxv, bin));
|
|
193
192
|
}
|
|
194
193
|
}
|
|
195
194
|
}
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,MAAM,CAAA;
|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,MAAM,CAAA;AAEvB,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,KAAK,MAAM,SAAS,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,QAAQ,CAAA;AAErD,OAAO,SAAsB,MAAM,aAAa,CAAA;AAEhD,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAIxC,YAAY,IAAS;QACnB,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACD,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,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;IACD,QAAQ;QACN,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;IACxD,CAAC;IAED,YAAY,CAAC,KAAa,EAAE,MAAc;QACxC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACtE,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,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,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,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC1D,CAAA;QAED,OAAO;YACL,WAAW;YACX,WAAW;YACX,SAAS;YACT,QAAQ;YACR,aAAa;YACb,MAAM;YACN,cAAc;SACf,CAAA;IACH,CAAC;IAED,eAAe,CAAC,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,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,4BAA4B;IAE5B,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAA;QAE/D,0BAA0B;QAC1B,IAAI,UAAU,CAAA;QACd,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE,CAAC;YACzC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE,CAAC;YAChD,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACjC,oDAAoD;QACtD,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACjC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1D,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QACvC,MAAM,GAAG,GACP,SAAS,IAAI,SAAS,IAAI,EAAE;YAC1B,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC;YAC9B,CAAC,CAAC;gBACE,WAAW,EAAE,EAAE;gBACf,WAAW,EAAE,EAAE;gBACf,QAAQ,EAAE,IAAI;gBACd,aAAa,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE;gBAC3C,cAAc,EAAE,sBAAsB;gBACtC,MAAM,EAAE,SAAS;aAClB,CAAA;QACP,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;QAElD,+CAA+C;QAC/C,IAAI,aAAwC,CAAA;QAC5C,IAAI,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QACnC,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,CAAC,iDAAiD;YAC3D,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,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,yDAAyD;oBACzD,qCAAqC;oBACrC,KAAK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|
package/esm/index.d.ts
CHANGED
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
|
|
2
|
-
|
|
3
|
-
|
|
4
|
-
export { TabixIndexedFile, TBI, CSI };
|
|
1
|
+
export { default as TabixIndexedFile } from './tabixIndexedFile';
|
|
2
|
+
export { default as CSI } from './csi';
|
|
3
|
+
export { default as TBI } from './tbi';
|
package/esm/index.js
CHANGED
|
@@ -1,5 +1,4 @@
|
|
|
1
|
-
|
|
2
|
-
|
|
3
|
-
|
|
4
|
-
export { TabixIndexedFile, TBI, CSI };
|
|
1
|
+
export { default as TabixIndexedFile } from './tabixIndexedFile';
|
|
2
|
+
export { default as CSI } from './csi';
|
|
3
|
+
export { default as TBI } from './tbi';
|
|
5
4
|
//# sourceMappingURL=index.js.map
|
package/esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AAChE,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,OAAO,CAAA;AACtC,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,OAAO,CAAA"}
|
package/esm/indexFile.d.ts
CHANGED
|
@@ -6,9 +6,7 @@ export interface Options {
|
|
|
6
6
|
signal?: AbortSignal;
|
|
7
7
|
}
|
|
8
8
|
export interface IndexData {
|
|
9
|
-
refNameToId:
|
|
10
|
-
[key: string]: number;
|
|
11
|
-
};
|
|
9
|
+
refNameToId: Record<string, number>;
|
|
12
10
|
refIdToName: string[];
|
|
13
11
|
metaChar: string | null;
|
|
14
12
|
columnNumbers: {
|
|
@@ -32,9 +30,7 @@ export default abstract class IndexFile {
|
|
|
32
30
|
protected abstract _parse(opts: Options): Promise<IndexData>;
|
|
33
31
|
getMetadata(opts?: Options): Promise<{
|
|
34
32
|
[key: string]: any;
|
|
35
|
-
refNameToId:
|
|
36
|
-
[key: string]: number;
|
|
37
|
-
};
|
|
33
|
+
refNameToId: Record<string, number>;
|
|
38
34
|
refIdToName: string[];
|
|
39
35
|
metaChar: string | null;
|
|
40
36
|
columnNumbers: {
|
package/esm/indexFile.js
CHANGED
|
@@ -4,8 +4,7 @@ export default class IndexFile {
|
|
|
4
4
|
this.renameRefSeq = renameRefSeqs;
|
|
5
5
|
}
|
|
6
6
|
async getMetadata(opts = {}) {
|
|
7
|
-
|
|
8
|
-
const { indices, ...rest } = await this.parse(opts);
|
|
7
|
+
const { indices: _indices, ...rest } = await this.parse(opts);
|
|
9
8
|
return rest;
|
|
10
9
|
}
|
|
11
10
|
_findFirstData(currentFdl, virtualOffset) {
|
|
@@ -28,7 +27,9 @@ export default class IndexFile {
|
|
|
28
27
|
return this.parseP;
|
|
29
28
|
}
|
|
30
29
|
async hasRefSeq(seqId, opts = {}) {
|
|
31
|
-
|
|
30
|
+
var _a;
|
|
31
|
+
const idx = await this.parse(opts);
|
|
32
|
+
return !!((_a = idx.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
|
|
32
33
|
}
|
|
33
34
|
}
|
|
34
35
|
//# sourceMappingURL=indexFile.js.map
|
package/esm/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAoBA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMM,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,
|
|
1
|
+
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAoBA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMM,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7D,OAAO,IAAI,CAAA;IACb,CAAC;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;;QAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAClC,OAAO,CAAC,CAAC,CAAA,MAAA,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,QAAQ,CAAA,CAAA;IACvC,CAAC;CACF"}
|
|
@@ -1,4 +1,5 @@
|
|
|
1
1
|
/// <reference types="node" />
|
|
2
|
+
import { Buffer } from 'buffer';
|
|
2
3
|
import { GenericFilehandle } from 'generic-filehandle';
|
|
3
4
|
import { Options, IndexData } from './indexFile';
|
|
4
5
|
import Chunk from './chunk';
|
|
@@ -47,12 +48,10 @@ export default class TabixIndexedFile {
|
|
|
47
48
|
* @param opts callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
|
|
48
49
|
* @returns promise that is resolved when the whole read is finished, rejected on error
|
|
49
50
|
*/
|
|
50
|
-
getLines(refName: string,
|
|
51
|
+
getLines(refName: string, s: number | undefined, e: number | undefined, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
|
|
51
52
|
getMetadata(opts?: Options): Promise<{
|
|
52
53
|
[key: string]: any;
|
|
53
|
-
refNameToId:
|
|
54
|
-
[key: string]: number;
|
|
55
|
-
};
|
|
54
|
+
refNameToId: Record<string, number>;
|
|
56
55
|
refIdToName: string[];
|
|
57
56
|
metaChar: string | null;
|
|
58
57
|
columnNumbers: {
|
package/esm/tabixIndexedFile.js
CHANGED
|
@@ -1,11 +1,12 @@
|
|
|
1
1
|
import AbortablePromiseCache from 'abortable-promise-cache';
|
|
2
2
|
import LRU from 'quick-lru';
|
|
3
|
+
import { Buffer } from 'buffer';
|
|
3
4
|
import { LocalFile } from 'generic-filehandle';
|
|
4
5
|
import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
|
|
5
6
|
import { checkAbortSignal } from './util';
|
|
6
7
|
import TBI from './tbi';
|
|
7
8
|
import CSI from './csi';
|
|
8
|
-
const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('
|
|
9
|
+
const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
|
|
9
10
|
function timeout(time) {
|
|
10
11
|
return new Promise(resolve => setTimeout(resolve, time));
|
|
11
12
|
}
|
|
@@ -81,11 +82,12 @@ export default class TabixIndexedFile {
|
|
|
81
82
|
* @param opts callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
|
|
82
83
|
* @returns promise that is resolved when the whole read is finished, rejected on error
|
|
83
84
|
*/
|
|
84
|
-
async getLines(refName,
|
|
85
|
+
async getLines(refName, s, e, opts) {
|
|
86
|
+
var _a;
|
|
85
87
|
let signal;
|
|
86
88
|
let options = {};
|
|
87
89
|
let callback;
|
|
88
|
-
if (
|
|
90
|
+
if (opts === undefined) {
|
|
89
91
|
throw new TypeError('line callback must be provided');
|
|
90
92
|
}
|
|
91
93
|
if (typeof opts === 'function') {
|
|
@@ -103,12 +105,8 @@ export default class TabixIndexedFile {
|
|
|
103
105
|
}
|
|
104
106
|
const metadata = await this.index.getMetadata(options);
|
|
105
107
|
checkAbortSignal(signal);
|
|
106
|
-
|
|
107
|
-
|
|
108
|
-
}
|
|
109
|
-
if (!end) {
|
|
110
|
-
end = metadata.maxRefLength;
|
|
111
|
-
}
|
|
108
|
+
const start = s !== null && s !== void 0 ? s : 0;
|
|
109
|
+
const end = e !== null && e !== void 0 ? e : metadata.maxRefLength;
|
|
112
110
|
if (!(start <= end)) {
|
|
113
111
|
throw new TypeError('invalid start and end coordinates. start must be less than or equal to end');
|
|
114
112
|
}
|
|
@@ -119,18 +117,17 @@ export default class TabixIndexedFile {
|
|
|
119
117
|
checkAbortSignal(signal);
|
|
120
118
|
// check the chunks for any that are over the size limit. if
|
|
121
119
|
// any are, don't fetch any of them
|
|
122
|
-
for (
|
|
123
|
-
const size =
|
|
120
|
+
for (const chunk of chunks) {
|
|
121
|
+
const size = chunk.fetchedSize();
|
|
124
122
|
if (size > this.chunkSizeLimit) {
|
|
125
123
|
throw new Error(`Too much data. Chunk size ${size.toLocaleString()} bytes exceeds chunkSizeLimit of ${this.chunkSizeLimit.toLocaleString()}.`);
|
|
126
124
|
}
|
|
127
125
|
}
|
|
128
126
|
// now go through each chunk and parse and filter the lines out of it
|
|
129
127
|
let last = Date.now();
|
|
130
|
-
for (
|
|
128
|
+
for (const c of chunks) {
|
|
131
129
|
let previousStartCoordinate;
|
|
132
|
-
const
|
|
133
|
-
const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c);
|
|
130
|
+
const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c, signal);
|
|
134
131
|
checkAbortSignal(signal);
|
|
135
132
|
let blockStart = 0;
|
|
136
133
|
let pos = 0;
|
|
@@ -140,7 +137,7 @@ export default class TabixIndexedFile {
|
|
|
140
137
|
break;
|
|
141
138
|
}
|
|
142
139
|
const b = buffer.slice(blockStart, n);
|
|
143
|
-
const line = (decoder === null || decoder === void 0 ? void 0 : decoder.decode(b))
|
|
140
|
+
const line = (_a = decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) !== null && _a !== void 0 ? _a : b.toString();
|
|
144
141
|
if (dpositions) {
|
|
145
142
|
while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
|
|
146
143
|
pos--;
|
|
@@ -200,17 +197,8 @@ export default class TabixIndexedFile {
|
|
|
200
197
|
const maxFetch = ((firstDataLine === null || firstDataLine === void 0 ? void 0 : firstDataLine.blockPosition) || 0) + maxBlockSize;
|
|
201
198
|
// TODO: what if we don't have a firstDataLine, and the header
|
|
202
199
|
// actually takes up more than one block? this case is not covered here
|
|
203
|
-
|
|
204
|
-
|
|
205
|
-
try {
|
|
206
|
-
bytes = await unzip(bytes);
|
|
207
|
-
}
|
|
208
|
-
catch (e) {
|
|
209
|
-
console.error(e);
|
|
210
|
-
throw new Error(
|
|
211
|
-
//@ts-ignore
|
|
212
|
-
`error decompressing block ${e.code} at 0 (length ${maxFetch}) ${e}`);
|
|
213
|
-
}
|
|
200
|
+
const buf = await this._readRegion(0, maxFetch, opts);
|
|
201
|
+
const bytes = await unzip(buf);
|
|
214
202
|
// trim off lines after the last non-meta line
|
|
215
203
|
if (metaChar) {
|
|
216
204
|
// trim backward from the end
|
|
@@ -225,7 +213,7 @@ export default class TabixIndexedFile {
|
|
|
225
213
|
lastNewline = i;
|
|
226
214
|
}
|
|
227
215
|
}
|
|
228
|
-
|
|
216
|
+
return bytes.slice(0, lastNewline + 1);
|
|
229
217
|
}
|
|
230
218
|
return bytes;
|
|
231
219
|
}
|
|
@@ -261,7 +249,7 @@ export default class TabixIndexedFile {
|
|
|
261
249
|
checkLine(metadata, regionRefName, regionStart, regionEnd, line) {
|
|
262
250
|
const { columnNumbers, metaChar, coordinateType, format } = metadata;
|
|
263
251
|
// skip meta lines
|
|
264
|
-
if (line.
|
|
252
|
+
if (metaChar && line.startsWith(metaChar)) {
|
|
265
253
|
return { overlaps: false };
|
|
266
254
|
}
|
|
267
255
|
// check ref/start/end using column metadata from index
|
|
@@ -314,14 +302,10 @@ export default class TabixIndexedFile {
|
|
|
314
302
|
refSeq = line.slice(currentColumnStart, i);
|
|
315
303
|
}
|
|
316
304
|
else if (currentColumnNumber === end) {
|
|
317
|
-
let endCoordinate;
|
|
318
305
|
// this will never match if there is no end column
|
|
319
|
-
|
|
320
|
-
|
|
321
|
-
|
|
322
|
-
else {
|
|
323
|
-
endCoordinate = parseInt(line.slice(currentColumnStart, i), 10);
|
|
324
|
-
}
|
|
306
|
+
const endCoordinate = format === 'VCF'
|
|
307
|
+
? this._getVcfEnd(startCoordinate, refSeq, line.slice(currentColumnStart, i))
|
|
308
|
+
: parseInt(line.slice(currentColumnStart, i), 10);
|
|
325
309
|
if (endCoordinate <= regionStart) {
|
|
326
310
|
return { overlaps: false };
|
|
327
311
|
}
|
|
@@ -337,12 +321,12 @@ export default class TabixIndexedFile {
|
|
|
337
321
|
}
|
|
338
322
|
_getVcfEnd(startCoordinate, refSeq, info) {
|
|
339
323
|
let endCoordinate = startCoordinate + refSeq.length;
|
|
340
|
-
// ignore TRA features as they specify CHR2 and END
|
|
341
|
-
//
|
|
342
|
-
//
|
|
343
|
-
//
|
|
344
|
-
// at the end of this one
|
|
345
|
-
const isTRA = info.
|
|
324
|
+
// ignore TRA features as they specify CHR2 and END as being on a different
|
|
325
|
+
// chromosome
|
|
326
|
+
//
|
|
327
|
+
// if CHR2 is on the same chromosome, still ignore it because there should
|
|
328
|
+
// be another pairwise feature at the end of this one
|
|
329
|
+
const isTRA = info.includes('SVTYPE=TRA');
|
|
346
330
|
if (info[0] !== '.' && !isTRA) {
|
|
347
331
|
let prevChar = ';';
|
|
348
332
|
for (let j = 0; j < info.length; j += 1) {
|
|
@@ -383,12 +367,7 @@ export default class TabixIndexedFile {
|
|
|
383
367
|
// fetch the uncompressed data, uncompress carefully a block at a time,
|
|
384
368
|
// and stop when done
|
|
385
369
|
const data = await this._readRegion(c.minv.blockPosition, c.fetchedSize(), opts);
|
|
386
|
-
|
|
387
|
-
return unzipChunkSlice(data, c);
|
|
388
|
-
}
|
|
389
|
-
catch (e) {
|
|
390
|
-
throw new Error(`error decompressing c ${c.toString()} ${e}`);
|
|
391
|
-
}
|
|
370
|
+
return unzipChunkSlice(data, c);
|
|
392
371
|
}
|
|
393
372
|
}
|
|
394
373
|
//# sourceMappingURL=tabixIndexedFile.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
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package/esm/tbi.d.ts
CHANGED
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@@ -1,4 +1,5 @@
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|
|
1
1
|
/// <reference types="node" />
|
|
2
|
+
import { Buffer } from 'buffer';
|
|
2
3
|
import VirtualOffset from './virtualOffset';
|
|
3
4
|
import Chunk from './chunk';
|
|
4
5
|
import IndexFile, { Options } from './indexFile';
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@@ -6,9 +7,7 @@ export default class TabixIndex extends IndexFile {
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lineCount(refName: string, opts?: Options): Promise<any>;
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_parse(opts?: Options): Promise<{
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indices: {
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9
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binIndex:
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10
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[key: number]: Chunk[];
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};
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10
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binIndex: Record<number, Chunk[]>;
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linearIndex: any[];
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stats: {
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lineCount: number;
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@@ -27,18 +26,14 @@ export default class TabixIndex extends IndexFile {
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coordinateType: string;
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format: string;
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refIdToName: string[];
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refNameToId:
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[key: string]: number;
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};
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refNameToId: Record<string, number>;
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maxBlockSize: number;
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}>;
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parsePseudoBin(bytes: Buffer, offset: number): {
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lineCount: number;
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};
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_parseNameBytes(namesBytes: Buffer): {
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39
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refNameToId:
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[key: string]: number;
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};
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+
refNameToId: Record<string, number>;
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refIdToName: string[];
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};
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blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
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