@jbrowse/img 2.2.1 → 2.2.2

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Files changed (20) hide show
  1. package/dist/index.js +1 -0
  2. package/dist/index.js.map +1 -1
  3. package/esm/index.js +1 -0
  4. package/esm/index.js.map +1 -1
  5. package/package.json +4 -4
  6. package/src/{index.testmod.js → index.test.js} +30 -14
  7. package/src/index.ts +2 -1
  8. package/src/{parseArgv.testmod.js → parseArgv.test.js} +0 -0
  9. package/dist/index.testmod.d.ts +0 -1
  10. package/dist/index.testmod.js +0 -169
  11. package/dist/index.testmod.js.map +0 -1
  12. package/dist/parseArgv.testmod.d.ts +0 -1
  13. package/dist/parseArgv.testmod.js +0 -26
  14. package/dist/parseArgv.testmod.js.map +0 -1
  15. package/esm/index.testmod.d.ts +0 -1
  16. package/esm/index.testmod.js +0 -141
  17. package/esm/index.testmod.js.map +0 -1
  18. package/esm/parseArgv.testmod.d.ts +0 -1
  19. package/esm/parseArgv.testmod.js +0 -24
  20. package/esm/parseArgv.testmod.js.map +0 -1
package/dist/index.js CHANGED
@@ -83,6 +83,7 @@ console.warn = (...p) => {
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  };
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  // note: yargs is actually unused except for printing help
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  // we do custom command line parsing, see parseArgv.ts
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+ // eslint-disable-next-line @typescript-eslint/no-floating-promises
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  yargs_1.default
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  .command('jb2export', 'Creates a jbrowse 2 image snapshot')
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  .option('config', {
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,4CAAmB;AACnB,kDAAyB;AACzB,uEAAoE;AACpE,yDAA8D;AAC9D,iCAA6B;AAC7B,mCAA4C;AAE5C,SAAS;AACT,2CAAwD;AACxD,iDAAmD;AACnD,iCAAgC;AAEhC,aAAa;AACb,MAAM,CAAC,SAAS,GAAG,cAAK,CAAA;AACxB,aAAa;AACb,MAAM,CAAC,gBAAgB,GAAG,qBAAY,CAAA;AAEtC,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,aAAK,CAAC,KAAK,CAAC,CAAC,MAAM,CAAA;AAC5C,MAAM,CAAC,QAAQ,GAAG,QAAQ,CAAA;AAE1B,yEAAyE;AACzE,sEAAsE;AACtE,cAAc;AACd,EAAE;AACF,EAAE;AACF,mBAAmB;AACnB,WAAW;AACX,EAAE;AACF,+LAA+L;AAC/L,IAAI;AACJ,8HAA8H;AAC9H,gFAAgF;AAChF,IAAI;AACJ,IAAI;AACJ,wCAAwC;AACxC,wCAAwC;AACxC,2EAA2E;AAC3E,sFAAsF;AACtF,IAAI;AAEJ,aAAa;AACb,MAAM,CAAC,KAAK,GAAG,oBAAK,CAAA;AACpB,aAAa;AACb,MAAM,CAAC,OAAO,GAAG,oBAAO,CAAA;AACxB,aAAa;AACb,MAAM,CAAC,QAAQ,GAAG,qBAAQ,CAAA;AAC1B,aAAa;AACb,MAAM,CAAC,OAAO,GAAG,oBAAO,CAAA;AAExB,MAAM,GAAG,GAAG,OAAO,CAAC,KAAK,CAAA;AACzB,OAAO,CAAC,KAAK,GAAG,CAAC,GAAG,CAAY,EAAE,EAAE;IAClC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,iBAAiB,CAAC,EAAE;QACvC,GAAG,CAAC,CAAC,CAAC,CAAA;KACP;AACH,CAAC,CAAA;AAED,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,CAAA;AACzB,OAAO,CAAC,IAAI,GAAG,CAAC,GAAG,CAAY,EAAE,EAAE;IACjC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,4BAA4B,CAAC,EAAE;QAClD,IAAI,CAAC,CAAC,CAAC,CAAA;KACR;AACH,CAAC,CAAA;AAED,0DAA0D;AAC1D,sDAAsD;AACtD,mEAAmE;AACnE,eAAK;KACF,OAAO,CAAC,WAAW,EAAE,oCAAoC,CAAC;KAC1D,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EAAE,qBAAqB;IAClC,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,SAAS,EAAE;IACjB,WAAW,EAAE,sBAAsB;IACnC,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,UAAU,EAAE;IAClB,WAAW,EACT,+EAA+E;IACjF,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EAAE,qCAAqC;IAClD,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,mEAAmE;IACrE,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EAAE,iCAAiC;IAC9C,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,SAAS,EAAE;IACjB,WAAW,EACT,gIAAgI;IAClI,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,sEAAsE;IACxE,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,UAAU,EAAE;IAClB,WAAW,EACT,qEAAqE;IACvE,IAAI,EAAE,QAAQ;IACd,OAAO,EAAE,IAAI;CACd,CAAC;IACF,cAAc;KACb,MAAM,CAAC,cAAc,EAAE;IACtB,WAAW,EAAE,2CAA2C;IACxD,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,iFAAiF;IACnF,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EACT,8FAA8F;IAChG,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,MAAM,EAAE;IACd,WAAW,EACT,wFAAwF;IAC1F,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,4FAA4F;IAC9F,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,uFAAuF;IACzF,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,iFAAiF;IACnF,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EACT,0FAA0F;IAC5F,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,6FAA6F;IAC/F,IAAI,EAAE,OAAO;CACd,CAAC;IAEF,QAAQ;KACP,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,oKAAoK;IACtK,IAAI,EAAE,QAAQ;IACd,OAAO,EAAE,SAAS;CACnB,CAAC;KACD,MAAM,CAAC,aAAa,EAAE;IACrB,WAAW,EACT,4FAA4F;IAC9F,IAAI,EAAE,SAAS;CAChB,CAAC;KACD,MAAM,CAAC,gBAAgB,EAAE;IACxB,WAAW,EAAE,yCAAyC;IACtD,IAAI,EAAE,SAAS;CAChB,CAAC;KACD,IAAI,EAAE;KACN,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC;KAClB,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC,IAAI,CAAA;AAE3B,MAAM,IAAI,GAAG,IAAA,2BAAe,EAAC,IAAA,qBAAS,EAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE;IAC7D,KAAK;IACL,MAAM;IACN,OAAO;IACP,KAAK;IACL,QAAQ;IACR,QAAQ;IACR,OAAO;IACP,OAAO;IACP,cAAc;CACf,CAAC,CAGD;AAAA,CAAC,KAAK,IAAI,EAAE;IACX,IAAI;QACF,MAAM,MAAM,GAAG,MAAM,IAAA,2BAAY,EAAC,IAAY,CAAC,CAAA;QAC/C,MAAM,EAAE,GAAG,GAAG,SAAS,EAAE,QAAQ,GAAG,MAAM,EAAE,GAAG,IAAI,CAAA;QACnD,IAAI,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE;YACxB,IAAA,cAAO,EAAC,MAAM,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,CAAA;SACnC;aAAM,IAAI,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE;YAC/B,IAAA,cAAO,EAAC,MAAM,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC,CAAA;SAClD;aAAM;YACL,YAAE,CAAC,aAAa,CAAC,GAAG,EAAE,MAAM,CAAC,CAAA;SAC9B;QAED,qEAAqE;QACrE,kEAAkE;QAClE,6CAA6C;QAC7C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;KAChB;IAAC,OAAO,CAAC,EAAE;QACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAChB,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;KAChB;AACH,CAAC,CAAC,EAAE,CAAA"}
package/esm/index.js CHANGED
@@ -55,6 +55,7 @@ console.warn = (...p) => {
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  };
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  // note: yargs is actually unused except for printing help
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  // we do custom command line parsing, see parseArgv.ts
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+ // eslint-disable-next-line @typescript-eslint/no-floating-promises
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  yargs
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  .command('jb2export', 'Creates a jbrowse 2 image snapshot')
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  .option('config', {
package/esm/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,IAAI,CAAA;AACnB,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,6DAA6D,CAAA;AACpE,OAAO,KAAK,EAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,YAAY,CAAA;AAC9D,OAAO,EAAE,KAAK,EAAE,MAAM,OAAO,CAAA;AAC7B,OAAO,EAAE,KAAK,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAE5C,SAAS;AACT,OAAO,EAAE,eAAe,EAAE,SAAS,EAAE,MAAM,aAAa,CAAA;AACxD,OAAO,EAAE,YAAY,EAAQ,MAAM,gBAAgB,CAAA;AACnD,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAA;AAEhC,aAAa;AACb,MAAM,CAAC,SAAS,GAAG,KAAK,CAAA;AACxB,aAAa;AACb,MAAM,CAAC,gBAAgB,GAAG,YAAY,CAAA;AAEtC,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,MAAM,CAAA;AAC5C,MAAM,CAAC,QAAQ,GAAG,QAAQ,CAAA;AAE1B,yEAAyE;AACzE,sEAAsE;AACtE,cAAc;AACd,EAAE;AACF,EAAE;AACF,mBAAmB;AACnB,WAAW;AACX,EAAE;AACF,+LAA+L;AAC/L,IAAI;AACJ,8HAA8H;AAC9H,gFAAgF;AAChF,IAAI;AACJ,IAAI;AACJ,wCAAwC;AACxC,wCAAwC;AACxC,2EAA2E;AAC3E,sFAAsF;AACtF,IAAI;AAEJ,aAAa;AACb,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;AACpB,aAAa;AACb,MAAM,CAAC,OAAO,GAAG,OAAO,CAAA;AACxB,aAAa;AACb,MAAM,CAAC,QAAQ,GAAG,QAAQ,CAAA;AAC1B,aAAa;AACb,MAAM,CAAC,OAAO,GAAG,OAAO,CAAA;AAExB,MAAM,GAAG,GAAG,OAAO,CAAC,KAAK,CAAA;AACzB,OAAO,CAAC,KAAK,GAAG,CAAC,GAAG,CAAY,EAAE,EAAE;IAClC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,iBAAiB,CAAC,EAAE;QACvC,GAAG,CAAC,CAAC,CAAC,CAAA;KACP;AACH,CAAC,CAAA;AAED,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,CAAA;AACzB,OAAO,CAAC,IAAI,GAAG,CAAC,GAAG,CAAY,EAAE,EAAE;IACjC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,4BAA4B,CAAC,EAAE;QAClD,IAAI,CAAC,CAAC,CAAC,CAAA;KACR;AACH,CAAC,CAAA;AAED,0DAA0D;AAC1D,sDAAsD;AAEtD,KAAK;KACF,OAAO,CAAC,WAAW,EAAE,oCAAoC,CAAC;KAC1D,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EAAE,qBAAqB;IAClC,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,SAAS,EAAE;IACjB,WAAW,EAAE,sBAAsB;IACnC,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,UAAU,EAAE;IAClB,WAAW,EACT,+EAA+E;IACjF,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EAAE,qCAAqC;IAClD,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,mEAAmE;IACrE,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EAAE,iCAAiC;IAC9C,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,SAAS,EAAE;IACjB,WAAW,EACT,gIAAgI;IAClI,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,sEAAsE;IACxE,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,UAAU,EAAE;IAClB,WAAW,EACT,qEAAqE;IACvE,IAAI,EAAE,QAAQ;IACd,OAAO,EAAE,IAAI;CACd,CAAC;IACF,cAAc;KACb,MAAM,CAAC,cAAc,EAAE;IACtB,WAAW,EAAE,2CAA2C;IACxD,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,iFAAiF;IACnF,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EACT,8FAA8F;IAChG,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,MAAM,EAAE;IACd,WAAW,EACT,wFAAwF;IAC1F,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,4FAA4F;IAC9F,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,uFAAuF;IACzF,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,iFAAiF;IACnF,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EACT,0FAA0F;IAC5F,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,6FAA6F;IAC/F,IAAI,EAAE,OAAO;CACd,CAAC;IAEF,QAAQ;KACP,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,oKAAoK;IACtK,IAAI,EAAE,QAAQ;IACd,OAAO,EAAE,SAAS;CACnB,CAAC;KACD,MAAM,CAAC,aAAa,EAAE;IACrB,WAAW,EACT,4FAA4F;IAC9F,IAAI,EAAE,SAAS;CAChB,CAAC;KACD,MAAM,CAAC,gBAAgB,EAAE;IACxB,WAAW,EAAE,yCAAyC;IACtD,IAAI,EAAE,SAAS;CAChB,CAAC;KACD,IAAI,EAAE;KACN,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC;KAClB,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC,IAAI,CAAA;AAE3B,MAAM,IAAI,GAAG,eAAe,CAAC,SAAS,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE;IAC7D,KAAK;IACL,MAAM;IACN,OAAO;IACP,KAAK;IACL,QAAQ;IACR,QAAQ;IACR,OAAO;IACP,OAAO;IACP,cAAc;CACf,CAAC,CAED;AAAA,CAAC,KAAK,IAAI,EAAE;IACX,IAAI;QACF,MAAM,MAAM,GAAG,MAAM,YAAY,CAAC,IAAY,CAAC,CAAA;QAC/C,MAAM,EAAE,GAAG,GAAG,SAAS,EAAE,QAAQ,GAAG,MAAM,EAAE,GAAG,IAAI,CAAA;QACnD,IAAI,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE;YACxB,OAAO,CAAC,MAAM,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,CAAA;SACnC;aAAM,IAAI,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE;YAC/B,OAAO,CAAC,MAAM,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC,CAAA;SAClD;aAAM;YACL,EAAE,CAAC,aAAa,CAAC,GAAG,EAAE,MAAM,CAAC,CAAA;SAC9B;QAED,qEAAqE;QACrE,kEAAkE;QAClE,6CAA6C;QAC7C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;KAChB;IAAC,OAAO,CAAC,EAAE;QACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAChB,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;KAChB;AACH,CAAC,CAAC,EAAE,CAAA"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,IAAI,CAAA;AACnB,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,6DAA6D,CAAA;AACpE,OAAO,KAAK,EAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,YAAY,CAAA;AAC9D,OAAO,EAAE,KAAK,EAAE,MAAM,OAAO,CAAA;AAC7B,OAAO,EAAE,KAAK,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAE5C,SAAS;AACT,OAAO,EAAE,eAAe,EAAE,SAAS,EAAE,MAAM,aAAa,CAAA;AACxD,OAAO,EAAE,YAAY,EAAQ,MAAM,gBAAgB,CAAA;AACnD,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAA;AAEhC,aAAa;AACb,MAAM,CAAC,SAAS,GAAG,KAAK,CAAA;AACxB,aAAa;AACb,MAAM,CAAC,gBAAgB,GAAG,YAAY,CAAA;AAEtC,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,MAAM,CAAA;AAC5C,MAAM,CAAC,QAAQ,GAAG,QAAQ,CAAA;AAE1B,yEAAyE;AACzE,sEAAsE;AACtE,cAAc;AACd,EAAE;AACF,EAAE;AACF,mBAAmB;AACnB,WAAW;AACX,EAAE;AACF,+LAA+L;AAC/L,IAAI;AACJ,8HAA8H;AAC9H,gFAAgF;AAChF,IAAI;AACJ,IAAI;AACJ,wCAAwC;AACxC,wCAAwC;AACxC,2EAA2E;AAC3E,sFAAsF;AACtF,IAAI;AAEJ,aAAa;AACb,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;AACpB,aAAa;AACb,MAAM,CAAC,OAAO,GAAG,OAAO,CAAA;AACxB,aAAa;AACb,MAAM,CAAC,QAAQ,GAAG,QAAQ,CAAA;AAC1B,aAAa;AACb,MAAM,CAAC,OAAO,GAAG,OAAO,CAAA;AAExB,MAAM,GAAG,GAAG,OAAO,CAAC,KAAK,CAAA;AACzB,OAAO,CAAC,KAAK,GAAG,CAAC,GAAG,CAAY,EAAE,EAAE;IAClC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,iBAAiB,CAAC,EAAE;QACvC,GAAG,CAAC,CAAC,CAAC,CAAA;KACP;AACH,CAAC,CAAA;AAED,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,CAAA;AACzB,OAAO,CAAC,IAAI,GAAG,CAAC,GAAG,CAAY,EAAE,EAAE;IACjC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,4BAA4B,CAAC,EAAE;QAClD,IAAI,CAAC,CAAC,CAAC,CAAA;KACR;AACH,CAAC,CAAA;AAED,0DAA0D;AAC1D,sDAAsD;AACtD,mEAAmE;AACnE,KAAK;KACF,OAAO,CAAC,WAAW,EAAE,oCAAoC,CAAC;KAC1D,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EAAE,qBAAqB;IAClC,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,SAAS,EAAE;IACjB,WAAW,EAAE,sBAAsB;IACnC,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,UAAU,EAAE;IAClB,WAAW,EACT,+EAA+E;IACjF,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EAAE,qCAAqC;IAClD,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,mEAAmE;IACrE,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EAAE,iCAAiC;IAC9C,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,SAAS,EAAE;IACjB,WAAW,EACT,gIAAgI;IAClI,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,sEAAsE;IACxE,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,UAAU,EAAE;IAClB,WAAW,EACT,qEAAqE;IACvE,IAAI,EAAE,QAAQ;IACd,OAAO,EAAE,IAAI;CACd,CAAC;IACF,cAAc;KACb,MAAM,CAAC,cAAc,EAAE;IACtB,WAAW,EAAE,2CAA2C;IACxD,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,iFAAiF;IACnF,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EACT,8FAA8F;IAChG,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,MAAM,EAAE;IACd,WAAW,EACT,wFAAwF;IAC1F,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,4FAA4F;IAC9F,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,uFAAuF;IACzF,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,iFAAiF;IACnF,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EACT,0FAA0F;IAC5F,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,6FAA6F;IAC/F,IAAI,EAAE,OAAO;CACd,CAAC;IAEF,QAAQ;KACP,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,oKAAoK;IACtK,IAAI,EAAE,QAAQ;IACd,OAAO,EAAE,SAAS;CACnB,CAAC;KACD,MAAM,CAAC,aAAa,EAAE;IACrB,WAAW,EACT,4FAA4F;IAC9F,IAAI,EAAE,SAAS;CAChB,CAAC;KACD,MAAM,CAAC,gBAAgB,EAAE;IACxB,WAAW,EAAE,yCAAyC;IACtD,IAAI,EAAE,SAAS;CAChB,CAAC;KACD,IAAI,EAAE;KACN,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC;KAClB,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC,IAAI,CAAA;AAE3B,MAAM,IAAI,GAAG,eAAe,CAAC,SAAS,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE;IAC7D,KAAK;IACL,MAAM;IACN,OAAO;IACP,KAAK;IACL,QAAQ;IACR,QAAQ;IACR,OAAO;IACP,OAAO;IACP,cAAc;CACf,CAAC,CAGD;AAAA,CAAC,KAAK,IAAI,EAAE;IACX,IAAI;QACF,MAAM,MAAM,GAAG,MAAM,YAAY,CAAC,IAAY,CAAC,CAAA;QAC/C,MAAM,EAAE,GAAG,GAAG,SAAS,EAAE,QAAQ,GAAG,MAAM,EAAE,GAAG,IAAI,CAAA;QACnD,IAAI,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE;YACxB,OAAO,CAAC,MAAM,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,CAAA;SACnC;aAAM,IAAI,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE;YAC/B,OAAO,CAAC,MAAM,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC,CAAA;SAClD;aAAM;YACL,EAAE,CAAC,aAAa,CAAC,GAAG,EAAE,MAAM,CAAC,CAAA;SAC9B;QAED,qEAAqE;QACrE,kEAAkE;QAClE,6CAA6C;QAC7C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;KAChB;IAAC,OAAO,CAAC,EAAE;QACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAChB,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;KAChB;AACH,CAAC,CAAC,EAAE,CAAA"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/img",
3
- "version": "2.2.1",
3
+ "version": "2.2.2",
4
4
  "main": "dist/index.js",
5
5
  "module": "esm/index.js",
6
6
  "author": "JBrowse Team",
@@ -29,8 +29,8 @@
29
29
  "@babel/runtime": "^7.17.9",
30
30
  "@emotion/cache": "^11.7.1",
31
31
  "@emotion/react": "^11.9.0",
32
- "@jbrowse/plugin-linear-genome-view": "^2.2.1",
33
- "@jbrowse/react-linear-genome-view": "^2.2.1",
32
+ "@jbrowse/plugin-linear-genome-view": "^2.2.2",
33
+ "@jbrowse/react-linear-genome-view": "^2.2.2",
34
34
  "abortcontroller-polyfill": "^1.7.3",
35
35
  "canvas": "^2.9.1",
36
36
  "jsdom": "^19.0.0",
@@ -44,5 +44,5 @@
44
44
  "publishConfig": {
45
45
  "access": "public"
46
46
  },
47
- "gitHead": "896d175c5d9345049faea8e1155f243c912aac42"
47
+ "gitHead": "abbc00e8feedbc58de84a7a3e735ec0224909b29"
48
48
  }
package/src/{index.testmod.js → index.test.js} RENAMED
@@ -1,4 +1,11 @@
1
+ /**
2
+ * @jest-environment node
3
+ */
4
+
5
+ // the above jest-environment node is important to check true usage as a CLI tool
6
+
1
7
  import { renderRegion } from './renderRegion'
8
+ import path from 'path'
2
9
  import fs from 'fs'
3
10
  import { JSDOM } from 'jsdom'
4
11
  import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only'
@@ -17,8 +24,8 @@ global.nodeCreateCanvas = createCanvas
17
24
 
18
25
  xtest('renders a region with --session and --config args', async () => {
19
26
  const result = await renderRegion({
20
- session: require.resolve('../test/clingen_session.json'),
21
- config: require.resolve('../data/config.json'),
27
+ session: path.join(__dirname, '../test/clingen_session.json'),
28
+ config: path.join(__dirname, '../data/config.json'),
22
29
  })
23
30
  fs.writeFileSync('svg_from_config_and_session_param.svg', result)
24
31
  expect(result).toMatchSnapshot()
@@ -26,16 +33,16 @@ xtest('renders a region with --session and --config args', async () => {
26
33
 
27
34
  xtest('renders a region with --session, --tracks, and --assembly args', async () => {
28
35
  const result = await renderRegion({
29
- session: require.resolve('../test/clingen_session.json'),
30
- tracks: require.resolve('../data/tracks.json'),
31
- assembly: require.resolve('../data/assembly.json'),
36
+ session: path.join(__dirname, '../test/clingen_session.json'),
37
+ tracks: path.join(__dirname, '../data/tracks.json'),
38
+ assembly: path.join(__dirname, '../data/assembly.json'),
32
39
  })
33
40
  fs.writeFileSync('svg_from_separate_session_and_tracks.svg', result)
34
41
  expect(result).toMatchSnapshot()
35
42
  }, 40000)
36
43
 
37
44
  test('renders volvox with variety of args', async () => {
38
- const fp = f => require.resolve('../data/volvox/' + f)
45
+ const fp = f => path.join(__dirname, '../data/volvox/' + f)
39
46
  console.error = jest.fn()
40
47
  const result = await renderRegion({
41
48
  fasta: fp('volvox.fa'),
@@ -51,7 +58,7 @@ test('renders volvox with variety of args', async () => {
51
58
  loc: 'ctgA:1000-2000',
52
59
  })
53
60
  fs.writeFileSync(
54
- require.resolve('../test/svg_from_volvox_fasta_and_bam.svg'),
61
+ path.join(__dirname, '../test/svg_from_volvox_fasta_and_bam.svg'),
55
62
  result,
56
63
  )
57
64
  expect(result).toBeTruthy()
@@ -72,7 +79,7 @@ xtest('renders human large region with remote urls', async () => {
72
79
  loc: '1:10,000,000-10,030,000',
73
80
  })
74
81
  fs.writeFileSync(
75
- require.resolve('../test/human_remote_urls_large_region.svg'),
82
+ path.join(__dirname, '../test/human_remote_urls_large_region.svg'),
76
83
  result,
77
84
  )
78
85
  expect(result).toBeTruthy()
@@ -91,12 +98,15 @@ xtest('renders volvox with remote urls', async () => {
91
98
  ],
92
99
  loc: 'ctgA:1-1000',
93
100
  })
94
- fs.writeFileSync(require.resolve('../test/volvox_remote_region.svg'), result)
101
+ fs.writeFileSync(
102
+ path.join(__dirname, '../test/volvox_remote_region.svg'),
103
+ result,
104
+ )
95
105
  expect(result).toBeTruthy()
96
106
  }, 20000)
97
107
 
98
108
  test('renders volvox with variety of args (noRasterize)', async () => {
99
- const fp = f => require.resolve('../data/volvox/' + f)
109
+ const fp = f => path.join(__dirname, '../data/volvox/' + f)
100
110
  console.error = jest.fn()
101
111
  const result = await renderRegion({
102
112
  fasta: fp('volvox.fa'),
@@ -113,7 +123,10 @@ test('renders volvox with variety of args (noRasterize)', async () => {
113
123
  noRasterize: true,
114
124
  })
115
125
  fs.writeFileSync(
116
- require.resolve('../test/svg_from_volvox_fasta_and_bam_norasterize.svg'),
126
+ path.join(
127
+ __dirname,
128
+ '../test/svg_from_volvox_fasta_and_bam_norasterize.svg',
129
+ ),
117
130
  result,
118
131
  )
119
132
  expect(result).toBeTruthy()
@@ -133,13 +146,13 @@ xtest('configtracks arg with urls', async () => {
133
146
 
134
147
  test('configtracks arg with local files', async () => {
135
148
  const result = await renderRegion({
136
- config: require.resolve('../data/volvox/config.json'),
149
+ config: path.join(__dirname, '../data/volvox/config.json'),
137
150
  trackList: [['configtracks', ['volvox_sv']]],
138
151
  assembly: 'volvox',
139
152
  loc: 'ctgA:1-50,000',
140
153
  })
141
154
  fs.writeFileSync(
142
- require.resolve('../test/svg_configtracks_local.svg'),
155
+ path.join(__dirname, '../test/svg_configtracks_local.svg'),
143
156
  result,
144
157
  )
145
158
  expect(result).toBeTruthy()
@@ -158,6 +171,9 @@ xtest('renders --hic', async () => {
158
171
  ],
159
172
  loc: '1:2,000,000-10,000,000',
160
173
  })
161
- fs.writeFileSync(require.resolve('../test/svg_from_human_hic.svg'), result)
174
+ fs.writeFileSync(
175
+ path.join(__dirname, '../test/svg_from_human_hic.svg'),
176
+ result,
177
+ )
162
178
  expect(result).toBeTruthy()
163
179
  }, 20000)
package/src/index.ts CHANGED
@@ -63,7 +63,7 @@ console.warn = (...p: unknown[]) => {
63
63
 
64
64
  // note: yargs is actually unused except for printing help
65
65
  // we do custom command line parsing, see parseArgv.ts
66
-
66
+ // eslint-disable-next-line @typescript-eslint/no-floating-promises
67
67
  yargs
68
68
  .command('jb2export', 'Creates a jbrowse 2 image snapshot')
69
69
  .option('config', {
@@ -186,6 +186,7 @@ const args = standardizeArgv(parseArgv(process.argv.slice(2)), [
186
186
  'configtracks',
187
187
  ])
188
188
 
189
+ // eslint-disable-next-line @typescript-eslint/no-floating-promises
189
190
  ;(async () => {
190
191
  try {
191
192
  const result = await renderRegion(args as Opts)
package/src/{parseArgv.testmod.js → parseArgv.test.js} RENAMED
File without changes
package/dist/index.testmod.d.ts DELETED
@@ -1 +0,0 @@
1
- export {};
package/dist/index.testmod.js DELETED
@@ -1,169 +0,0 @@
1
- "use strict";
2
- var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
3
- if (k2 === undefined) k2 = k;
4
- var desc = Object.getOwnPropertyDescriptor(m, k);
5
- if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
6
- desc = { enumerable: true, get: function() { return m[k]; } };
7
- }
8
- Object.defineProperty(o, k2, desc);
9
- }) : (function(o, m, k, k2) {
10
- if (k2 === undefined) k2 = k;
11
- o[k2] = m[k];
12
- }));
13
- var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
14
- Object.defineProperty(o, "default", { enumerable: true, value: v });
15
- }) : function(o, v) {
16
- o["default"] = v;
17
- });
18
- var __importStar = (this && this.__importStar) || function (mod) {
19
- if (mod && mod.__esModule) return mod;
20
- var result = {};
21
- if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
22
- __setModuleDefault(result, mod);
23
- return result;
24
- };
25
- var __importDefault = (this && this.__importDefault) || function (mod) {
26
- return (mod && mod.__esModule) ? mod : { "default": mod };
27
- };
28
- Object.defineProperty(exports, "__esModule", { value: true });
29
- const renderRegion_1 = require("./renderRegion");
30
- const fs_1 = __importDefault(require("fs"));
31
- const jsdom_1 = require("jsdom");
32
- require("abortcontroller-polyfill/dist/abortcontroller-polyfill-only");
33
- const canvas_1 = require("canvas");
34
- const node_fetch_1 = __importStar(require("node-fetch"));
35
- global.fetch = node_fetch_1.default;
36
- global.Headers = node_fetch_1.Headers;
37
- global.Response = node_fetch_1.Response;
38
- global.Request = node_fetch_1.Request;
39
- const { document } = new jsdom_1.JSDOM(`...`).window;
40
- global.document = document;
41
- global.nodeImage = canvas_1.Image;
42
- global.nodeCreateCanvas = canvas_1.createCanvas;
43
- xtest('renders a region with --session and --config args', async () => {
44
- const result = await (0, renderRegion_1.renderRegion)({
45
- session: require.resolve('../test/clingen_session.json'),
46
- config: require.resolve('../data/config.json'),
47
- });
48
- fs_1.default.writeFileSync('svg_from_config_and_session_param.svg', result);
49
- expect(result).toMatchSnapshot();
50
- }, 40000);
51
- xtest('renders a region with --session, --tracks, and --assembly args', async () => {
52
- const result = await (0, renderRegion_1.renderRegion)({
53
- session: require.resolve('../test/clingen_session.json'),
54
- tracks: require.resolve('../data/tracks.json'),
55
- assembly: require.resolve('../data/assembly.json'),
56
- });
57
- fs_1.default.writeFileSync('svg_from_separate_session_and_tracks.svg', result);
58
- expect(result).toMatchSnapshot();
59
- }, 40000);
60
- test('renders volvox with variety of args', async () => {
61
- const fp = f => require.resolve('../data/volvox/' + f);
62
- console.error = jest.fn();
63
- const result = await (0, renderRegion_1.renderRegion)({
64
- fasta: fp('volvox.fa'),
65
- trackList: [
66
- ['bam', [fp('volvox-sorted.bam')]],
67
- ['cram', [fp('volvox-sorted.cram')]],
68
- ['bigwig', [fp('volvox-sorted.bam.coverage.bw')]],
69
- ['vcfgz', [fp('volvox.filtered.vcf.gz')]],
70
- ['gffgz', [fp('volvox.sort.gff3.gz')]],
71
- ['bigbed', [fp('volvox.bb')]],
72
- ['bedgz', [fp('volvox-bed12.bed.gz')]],
73
- ],
74
- loc: 'ctgA:1000-2000',
75
- });
76
- fs_1.default.writeFileSync(require.resolve('../test/svg_from_volvox_fasta_and_bam.svg'), result);
77
- expect(result).toBeTruthy();
78
- }, 40000);
79
- xtest('renders human large region with remote urls', async () => {
80
- const result = await (0, renderRegion_1.renderRegion)({
81
- fasta: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz',
82
- trackList: [
83
- [
84
- 'cram',
85
- [
86
- 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/skbr3/skbr3.ont.sort.mod.cram',
87
- 'force:true',
88
- ],
89
- ],
90
- ],
91
- loc: '1:10,000,000-10,030,000',
92
- });
93
- fs_1.default.writeFileSync(require.resolve('../test/human_remote_urls_large_region.svg'), result);
94
- expect(result).toBeTruthy();
95
- }, 120000);
96
- xtest('renders volvox with remote urls', async () => {
97
- const result = await (0, renderRegion_1.renderRegion)({
98
- fasta: 'https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.fa',
99
- trackList: [
100
- [
101
- 'bam',
102
- [
103
- 'https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam',
104
- ],
105
- ],
106
- ],
107
- loc: 'ctgA:1-1000',
108
- });
109
- fs_1.default.writeFileSync(require.resolve('../test/volvox_remote_region.svg'), result);
110
- expect(result).toBeTruthy();
111
- }, 20000);
112
- test('renders volvox with variety of args (noRasterize)', async () => {
113
- const fp = f => require.resolve('../data/volvox/' + f);
114
- console.error = jest.fn();
115
- const result = await (0, renderRegion_1.renderRegion)({
116
- fasta: fp('volvox.fa'),
117
- trackList: [
118
- ['bam', [fp('volvox-sorted.bam')]],
119
- ['cram', [fp('volvox-sorted.cram')]],
120
- ['bigwig', [fp('volvox-sorted.bam.coverage.bw')]],
121
- ['vcfgz', [fp('volvox.filtered.vcf.gz')]],
122
- ['gffgz', [fp('volvox.sort.gff3.gz')]],
123
- ['bigbed', [fp('volvox.bb')]],
124
- ['bedgz', [fp('volvox-bed12.bed.gz')]],
125
- ],
126
- loc: 'ctgA:1000-2000',
127
- noRasterize: true,
128
- });
129
- fs_1.default.writeFileSync(require.resolve('../test/svg_from_volvox_fasta_and_bam_norasterize.svg'), result);
130
- expect(result).toBeTruthy();
131
- }, 40000);
132
- // commented out for using remote files currently
133
- xtest('configtracks arg with urls', async () => {
134
- const result = await (0, renderRegion_1.renderRegion)({
135
- config: 'data/config.json',
136
- trackList: [['configtracks', ['ncbi_refseq_109_hg38']]],
137
- assembly: 'GRCh38',
138
- loc: 'chr1:50,000-60,000',
139
- });
140
- fs_1.default.writeFileSync('svg_configtracks_simple.svg', result);
141
- expect(result).toBeTruthy();
142
- }, 40000);
143
- test('configtracks arg with local files', async () => {
144
- const result = await (0, renderRegion_1.renderRegion)({
145
- config: require.resolve('../data/volvox/config.json'),
146
- trackList: [['configtracks', ['volvox_sv']]],
147
- assembly: 'volvox',
148
- loc: 'ctgA:1-50,000',
149
- });
150
- fs_1.default.writeFileSync(require.resolve('../test/svg_configtracks_local.svg'), result);
151
- expect(result).toBeTruthy();
152
- }, 40000);
153
- xtest('renders --hic', async () => {
154
- const result = await (0, renderRegion_1.renderRegion)({
155
- fasta: 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz',
156
- trackList: [
157
- [
158
- 'hic',
159
- [
160
- 'https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic',
161
- ],
162
- ],
163
- ],
164
- loc: '1:2,000,000-10,000,000',
165
- });
166
- fs_1.default.writeFileSync(require.resolve('../test/svg_from_human_hic.svg'), result);
167
- expect(result).toBeTruthy();
168
- }, 20000);
169
- //# sourceMappingURL=index.testmod.js.map
package/dist/index.testmod.js.map DELETED
@@ -1 +0,0 @@
1
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package/dist/parseArgv.testmod.d.ts DELETED
@@ -1 +0,0 @@
1
- export {};
package/dist/parseArgv.testmod.js DELETED
@@ -1,26 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- const parseArgv_1 = require("./parseArgv");
4
- test('parse', () => {
5
- const args = '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam --defaultSession --out out.svg --noRasterize';
6
- expect((0, parseArgv_1.parseArgv)(args.split(' '))).toEqual([
7
- ['bam', ['dad.bam', 'color:red']],
8
- ['vcf', ['variants.vcf']],
9
- ['bam', ['mom.bam']],
10
- ['defaultSession', []],
11
- ['out', ['out.svg']],
12
- ['noRasterize', []],
13
- ]);
14
- });
15
- test('parse', () => {
16
- const args = '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam force:true --defaultSession --out out.svg --noRasterize';
17
- expect((0, parseArgv_1.parseArgv)(args.split(' '))).toEqual([
18
- ['bam', ['dad.bam', 'color:red']],
19
- ['vcf', ['variants.vcf']],
20
- ['bam', ['mom.bam', 'force:true']],
21
- ['defaultSession', []],
22
- ['out', ['out.svg']],
23
- ['noRasterize', []],
24
- ]);
25
- });
26
- //# sourceMappingURL=parseArgv.testmod.js.map
package/dist/parseArgv.testmod.js.map DELETED
@@ -1 +0,0 @@
1
- {"version":3,"file":"parseArgv.testmod.js","sourceRoot":"","sources":["../src/parseArgv.testmod.js"],"names":[],"mappings":";;AAAA,2CAAuC;AAEvC,IAAI,CAAC,OAAO,EAAE,GAAG,EAAE;IACjB,MAAM,IAAI,GACR,uGAAuG,CAAA;IAEzG,MAAM,CAAC,IAAA,qBAAS,EAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;QACzC,CAAC,KAAK,EAAE,CAAC,SAAS,EAAE,WAAW,CAAC,CAAC;QACjC,CAAC,KAAK,EAAE,CAAC,cAAc,CAAC,CAAC;QACzB,CAAC,KAAK,EAAE,CAAC,SAAS,CAAC,CAAC;QACpB,CAAC,gBAAgB,EAAE,EAAE,CAAC;QACtB,CAAC,KAAK,EAAE,CAAC,SAAS,CAAC,CAAC;QACpB,CAAC,aAAa,EAAE,EAAE,CAAC;KACpB,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,OAAO,EAAE,GAAG,EAAE;IACjB,MAAM,IAAI,GACR,kHAAkH,CAAA;IAEpH,MAAM,CAAC,IAAA,qBAAS,EAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;QACzC,CAAC,KAAK,EAAE,CAAC,SAAS,EAAE,WAAW,CAAC,CAAC;QACjC,CAAC,KAAK,EAAE,CAAC,cAAc,CAAC,CAAC;QACzB,CAAC,KAAK,EAAE,CAAC,SAAS,EAAE,YAAY,CAAC,CAAC;QAClC,CAAC,gBAAgB,EAAE,EAAE,CAAC;QACtB,CAAC,KAAK,EAAE,CAAC,SAAS,CAAC,CAAC;QACpB,CAAC,aAAa,EAAE,EAAE,CAAC;KACpB,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
package/esm/index.testmod.d.ts DELETED
@@ -1 +0,0 @@
1
- export {};
package/esm/index.testmod.js DELETED
@@ -1,141 +0,0 @@
1
- import { renderRegion } from './renderRegion';
2
- import fs from 'fs';
3
- import { JSDOM } from 'jsdom';
4
- import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only';
5
- import { Image, createCanvas } from 'canvas';
6
- import fetch, { Headers, Response, Request } from 'node-fetch';
7
- global.fetch = fetch;
8
- global.Headers = Headers;
9
- global.Response = Response;
10
- global.Request = Request;
11
- const { document } = new JSDOM(`...`).window;
12
- global.document = document;
13
- global.nodeImage = Image;
14
- global.nodeCreateCanvas = createCanvas;
15
- xtest('renders a region with --session and --config args', async () => {
16
- const result = await renderRegion({
17
- session: require.resolve('../test/clingen_session.json'),
18
- config: require.resolve('../data/config.json'),
19
- });
20
- fs.writeFileSync('svg_from_config_and_session_param.svg', result);
21
- expect(result).toMatchSnapshot();
22
- }, 40000);
23
- xtest('renders a region with --session, --tracks, and --assembly args', async () => {
24
- const result = await renderRegion({
25
- session: require.resolve('../test/clingen_session.json'),
26
- tracks: require.resolve('../data/tracks.json'),
27
- assembly: require.resolve('../data/assembly.json'),
28
- });
29
- fs.writeFileSync('svg_from_separate_session_and_tracks.svg', result);
30
- expect(result).toMatchSnapshot();
31
- }, 40000);
32
- test('renders volvox with variety of args', async () => {
33
- const fp = f => require.resolve('../data/volvox/' + f);
34
- console.error = jest.fn();
35
- const result = await renderRegion({
36
- fasta: fp('volvox.fa'),
37
- trackList: [
38
- ['bam', [fp('volvox-sorted.bam')]],
39
- ['cram', [fp('volvox-sorted.cram')]],
40
- ['bigwig', [fp('volvox-sorted.bam.coverage.bw')]],
41
- ['vcfgz', [fp('volvox.filtered.vcf.gz')]],
42
- ['gffgz', [fp('volvox.sort.gff3.gz')]],
43
- ['bigbed', [fp('volvox.bb')]],
44
- ['bedgz', [fp('volvox-bed12.bed.gz')]],
45
- ],
46
- loc: 'ctgA:1000-2000',
47
- });
48
- fs.writeFileSync(require.resolve('../test/svg_from_volvox_fasta_and_bam.svg'), result);
49
- expect(result).toBeTruthy();
50
- }, 40000);
51
- xtest('renders human large region with remote urls', async () => {
52
- const result = await renderRegion({
53
- fasta: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz',
54
- trackList: [
55
- [
56
- 'cram',
57
- [
58
- 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/skbr3/skbr3.ont.sort.mod.cram',
59
- 'force:true',
60
- ],
61
- ],
62
- ],
63
- loc: '1:10,000,000-10,030,000',
64
- });
65
- fs.writeFileSync(require.resolve('../test/human_remote_urls_large_region.svg'), result);
66
- expect(result).toBeTruthy();
67
- }, 120000);
68
- xtest('renders volvox with remote urls', async () => {
69
- const result = await renderRegion({
70
- fasta: 'https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.fa',
71
- trackList: [
72
- [
73
- 'bam',
74
- [
75
- 'https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam',
76
- ],
77
- ],
78
- ],
79
- loc: 'ctgA:1-1000',
80
- });
81
- fs.writeFileSync(require.resolve('../test/volvox_remote_region.svg'), result);
82
- expect(result).toBeTruthy();
83
- }, 20000);
84
- test('renders volvox with variety of args (noRasterize)', async () => {
85
- const fp = f => require.resolve('../data/volvox/' + f);
86
- console.error = jest.fn();
87
- const result = await renderRegion({
88
- fasta: fp('volvox.fa'),
89
- trackList: [
90
- ['bam', [fp('volvox-sorted.bam')]],
91
- ['cram', [fp('volvox-sorted.cram')]],
92
- ['bigwig', [fp('volvox-sorted.bam.coverage.bw')]],
93
- ['vcfgz', [fp('volvox.filtered.vcf.gz')]],
94
- ['gffgz', [fp('volvox.sort.gff3.gz')]],
95
- ['bigbed', [fp('volvox.bb')]],
96
- ['bedgz', [fp('volvox-bed12.bed.gz')]],
97
- ],
98
- loc: 'ctgA:1000-2000',
99
- noRasterize: true,
100
- });
101
- fs.writeFileSync(require.resolve('../test/svg_from_volvox_fasta_and_bam_norasterize.svg'), result);
102
- expect(result).toBeTruthy();
103
- }, 40000);
104
- // commented out for using remote files currently
105
- xtest('configtracks arg with urls', async () => {
106
- const result = await renderRegion({
107
- config: 'data/config.json',
108
- trackList: [['configtracks', ['ncbi_refseq_109_hg38']]],
109
- assembly: 'GRCh38',
110
- loc: 'chr1:50,000-60,000',
111
- });
112
- fs.writeFileSync('svg_configtracks_simple.svg', result);
113
- expect(result).toBeTruthy();
114
- }, 40000);
115
- test('configtracks arg with local files', async () => {
116
- const result = await renderRegion({
117
- config: require.resolve('../data/volvox/config.json'),
118
- trackList: [['configtracks', ['volvox_sv']]],
119
- assembly: 'volvox',
120
- loc: 'ctgA:1-50,000',
121
- });
122
- fs.writeFileSync(require.resolve('../test/svg_configtracks_local.svg'), result);
123
- expect(result).toBeTruthy();
124
- }, 40000);
125
- xtest('renders --hic', async () => {
126
- const result = await renderRegion({
127
- fasta: 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz',
128
- trackList: [
129
- [
130
- 'hic',
131
- [
132
- 'https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic',
133
- ],
134
- ],
135
- ],
136
- loc: '1:2,000,000-10,000,000',
137
- });
138
- fs.writeFileSync(require.resolve('../test/svg_from_human_hic.svg'), result);
139
- expect(result).toBeTruthy();
140
- }, 20000);
141
- //# sourceMappingURL=index.testmod.js.map
package/esm/index.testmod.js.map DELETED
@@ -1 +0,0 @@
1
- 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package/esm/parseArgv.testmod.d.ts DELETED
@@ -1 +0,0 @@
1
- export {};
package/esm/parseArgv.testmod.js DELETED
@@ -1,24 +0,0 @@
1
- import { parseArgv } from './parseArgv';
2
- test('parse', () => {
3
- const args = '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam --defaultSession --out out.svg --noRasterize';
4
- expect(parseArgv(args.split(' '))).toEqual([
5
- ['bam', ['dad.bam', 'color:red']],
6
- ['vcf', ['variants.vcf']],
7
- ['bam', ['mom.bam']],
8
- ['defaultSession', []],
9
- ['out', ['out.svg']],
10
- ['noRasterize', []],
11
- ]);
12
- });
13
- test('parse', () => {
14
- const args = '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam force:true --defaultSession --out out.svg --noRasterize';
15
- expect(parseArgv(args.split(' '))).toEqual([
16
- ['bam', ['dad.bam', 'color:red']],
17
- ['vcf', ['variants.vcf']],
18
- ['bam', ['mom.bam', 'force:true']],
19
- ['defaultSession', []],
20
- ['out', ['out.svg']],
21
- ['noRasterize', []],
22
- ]);
23
- });
24
- //# sourceMappingURL=parseArgv.testmod.js.map
package/esm/parseArgv.testmod.js.map DELETED
@@ -1 +0,0 @@
1
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