clustal-js 2.0.13 → 2.0.14
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +8 -0
- package/dist/index.js +1 -1
- package/dist/index.js.map +1 -1
- package/dist/pairwise.js.map +1 -1
- package/dist/util.js.map +1 -1
- package/esm/index.js +1 -1
- package/esm/index.js.map +1 -1
- package/esm/pairwise.js.map +1 -1
- package/esm/util.js.map +1 -1
- package/package.json +35 -25
- package/src/index.ts +1 -1
- package/src/pairwise.ts +1 -1
- package/src/util.ts +2 -2
- package/CHANGELOG.md +0 -27
package/README.md
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@@ -159,3 +159,11 @@ b 209 ENSSRSMVSSVSL* 222
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### Notes
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See tests for example files
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+
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## Publishing
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[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub Actions.
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```bash
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npm version patch # or minor/major
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```
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package/dist/index.js
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@@ -17,7 +17,7 @@ function parseClustalIter(arr) {
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}
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const alns = res.seqs.map((n, index) => ({ id: res.ids[index], seq: n }));
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const { consensus } = res;
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-
if (consensus.length
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20
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+
if (consensus.length !== alns[0].seq.length) {
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throw new Error(`Consensus length != sequence length. Con ${consensus.length} seq ${alns[0].seq.length}`);
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}
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return { consensus, alns, header };
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package/dist/index.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
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1
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;AAGA,4CAqBC;AAOD,sBAGC;AAED,sCA+BC;AAnED,+CAAmD;AACnD,uCAA0E;AAE1E,SAAgB,gBAAgB,CAAC,GAAqB;IACpD,MAAM,IAAI,GAAG,IAAA,8BAAoB,EAAC,GAAG,CAAC,CAAA;IACtC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,MAAM,MAAM,GAAG,IAAA,qBAAW,EAAC,IAAI,CAAC,CAAA;IAEhC,MAAM,GAAG,GAAG,IAAA,qBAAW,EAAC,GAAG,CAAC,CAAA;IAC5B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IAED,MAAM,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAE,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;IAC1E,MAAM,EAAE,SAAS,EAAE,GAAG,GAAG,CAAA;IACzB,IAAI,SAAS,CAAC,MAAM,KAAK,IAAI,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;QAC7C,MAAM,IAAI,KAAK,CACb,4CAA4C,SAAS,CAAC,MAAM,QAAQ,IAAI,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,EAAE,CAC1F,CAAA;IACH,CAAC;IAED,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,MAAM,EAAE,CAAA;AACpC,CAAC;AAOD,SAAgB,KAAK,CAAC,QAAgB;IACpC,MAAM,IAAI,GAAG,QAAQ,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAA;IACpD,OAAO,gBAAgB,CAAC,IAAI,CAAC,CAAA;AAC/B,CAAC;AAED,SAAgB,aAAa,CAAC,QAAgB;IAC5C,MAAM,QAAQ,GAAG,QAAQ;SACtB,KAAK,CAAC,IAAI,CAAC;SACX,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SAC/B,IAAI,CAAC,IAAI,CAAC,CAAA;IAEb,MAAM,GAAG,GAAG,IAAA,iCAAmB,EAAC,QAAQ,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;IACxE,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IAED,MAAM,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAE,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;IAC1E,MAAM,EAAE,SAAS,EAAE,GAAG,GAAG,CAAA;IACzB,MAAM,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;IACxB,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,IAAI,SAAS,CAAC,MAAM,KAAK,QAAQ,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;QAC7C,MAAM,IAAI,KAAK,CACb,6CAA6C,SAAS,CAAC,MAAM,QAAQ,QAAQ,CAAC,GAAG,CAAC,MAAM,EAAE,CAC3F,CAAA;IACH,CAAC;IACD,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CACb,2DAA2D,IAAI,CAAC,MAAM,EAAE,CACzE,CAAA;IACH,CAAC;IACD,OAAO;QACL,SAAS;QACT,IAAI,EAAE,IAAkB;KACzB,CAAA;AACH,CAAC"}
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package/dist/pairwise.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"pairwise.js","sourceRoot":"","sources":["../src/pairwise.ts"],"names":[],"mappings":";;AAgCA,gDA+CC;AAED,kDAYC;AA7FD,uCAAgD;AAEhD,SAAS,WAAW,CAAC,IAAY;IAC/B,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,OAAO,KAAK,CAAA;IACd,CAAC;IACD,MAAM,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IACnC,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;AAC3C,CAAC;AAED,SAAS,cAAc,CAAC,IAAY;IAClC,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,OAAO,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;AACtD,CAAC;AAED,SAAS,kBAAkB,CAAC,MAAgB;IAC1C,OAAO,MAAM,CAAC,MAAM,IAAI,CAAC,IAAI,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAE,CAAC,CAAA;AACvD,CAAC;AAED,SAAS,YAAY,CAAC,IAAY,EAAE,QAAgB;IAClD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IACnC,MAAM,GAAG,GAAG,MAAM,CAAC,QAAQ,CAAE,CAAA;IAC7B,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAC3B,GAAG,EACH,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAE,CAAC,GAAG,MAAM,CAAC,CAAC,CAAE,CAAC,MAAM,CAC7C,CAAA;IACD,OAAO,CAAC,QAAQ,EAAE,QAAQ,GAAG,GAAG,CAAC,MAAM,CAAU,CAAA;AACnD,CAAC;AAED,sDAAsD;AACtD,SAAgB,kBAAkB,CAAC,GAAqB;IACtD,IAAI,IAAI,GAAG,IAAA,8BAAoB,EAAC,GAAG,CAAC,CAAA;IACpC,MAAM,KAAK,GAAa,EAAE,CAAA;IAC1B,IAAI,aAAa,GAAG,EAAE,CAAA;IACtB,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,OAAO,IAAI,EAAE,CAAC;QACZ,IAAI,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC;YACtB,4BAA4B;QAC9B,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;aAAM,CAAC;YACN,aAAa,GAAG,IAAI,CAAA;QACtB,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;IACzB,CAAC;IAED,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvB,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAA;IACpD,MAAM,UAAU,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;IAC5B,IAAI,CAAC,UAAU,EAAE,CAAC;QAChB,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,QAAQ,GAAG,kBAAkB,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACvD,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,YAAY,CAAC,KAAK,CAAC,CAAC,CAAE,EAAE,QAAQ,CAAC,CAAA;IACtD,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAA;IAClC,MAAM,IAAI,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAE,CAAC,CAAA;IAC1C,IAAI,SAAS,GAAG,aAAa,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAE/C,0DAA0D;IAC1D,MAAM,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;IACxB,IAAI,QAAQ,EAAE,CAAC;QACb,MAAM,SAAS,GAAG,QAAQ,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;QACpD,IAAI,SAAS,GAAG,CAAC,EAAE,CAAC;YAClB,SAAS,IAAI,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,CAAA;QACpC,CAAC;IACH,CAAC;IACD,OAAO;QACL,GAAG;QACH,IAAI;QACJ,SAAS;KACV,CAAA;AACH,CAAC;AAED,SAAgB,mBAAmB,CAAC,GAAqB;IACvD,IAAI,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAA;IACnC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,CAAC,KAAK,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;YACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3C,GAAG,CAAC,IAAI,CAAC,CAAC,
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{"version":3,"file":"pairwise.js","sourceRoot":"","sources":["../src/pairwise.ts"],"names":[],"mappings":";;AAgCA,gDA+CC;AAED,kDAYC;AA7FD,uCAAgD;AAEhD,SAAS,WAAW,CAAC,IAAY;IAC/B,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,OAAO,KAAK,CAAA;IACd,CAAC;IACD,MAAM,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IACnC,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;AAC3C,CAAC;AAED,SAAS,cAAc,CAAC,IAAY;IAClC,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,OAAO,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;AACtD,CAAC;AAED,SAAS,kBAAkB,CAAC,MAAgB;IAC1C,OAAO,MAAM,CAAC,MAAM,IAAI,CAAC,IAAI,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAE,CAAC,CAAA;AACvD,CAAC;AAED,SAAS,YAAY,CAAC,IAAY,EAAE,QAAgB;IAClD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IACnC,MAAM,GAAG,GAAG,MAAM,CAAC,QAAQ,CAAE,CAAA;IAC7B,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAC3B,GAAG,EACH,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAE,CAAC,GAAG,MAAM,CAAC,CAAC,CAAE,CAAC,MAAM,CAC7C,CAAA;IACD,OAAO,CAAC,QAAQ,EAAE,QAAQ,GAAG,GAAG,CAAC,MAAM,CAAU,CAAA;AACnD,CAAC;AAED,sDAAsD;AACtD,SAAgB,kBAAkB,CAAC,GAAqB;IACtD,IAAI,IAAI,GAAG,IAAA,8BAAoB,EAAC,GAAG,CAAC,CAAA;IACpC,MAAM,KAAK,GAAa,EAAE,CAAA;IAC1B,IAAI,aAAa,GAAG,EAAE,CAAA;IACtB,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,OAAO,IAAI,EAAE,CAAC;QACZ,IAAI,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC;YACtB,4BAA4B;QAC9B,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;aAAM,CAAC;YACN,aAAa,GAAG,IAAI,CAAA;QACtB,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;IACzB,CAAC;IAED,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvB,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAA;IACpD,MAAM,UAAU,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;IAC5B,IAAI,CAAC,UAAU,EAAE,CAAC;QAChB,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,QAAQ,GAAG,kBAAkB,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACvD,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,YAAY,CAAC,KAAK,CAAC,CAAC,CAAE,EAAE,QAAQ,CAAC,CAAA;IACtD,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAA;IAClC,MAAM,IAAI,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAE,CAAC,CAAA;IAC1C,IAAI,SAAS,GAAG,aAAa,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAE/C,0DAA0D;IAC1D,MAAM,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;IACxB,IAAI,QAAQ,EAAE,CAAC;QACb,MAAM,SAAS,GAAG,QAAQ,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;QACpD,IAAI,SAAS,GAAG,CAAC,EAAE,CAAC;YAClB,SAAS,IAAI,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,CAAA;QACpC,CAAC;IACH,CAAC;IACD,OAAO;QACL,GAAG;QACH,IAAI;QACJ,SAAS;KACV,CAAA;AACH,CAAC;AAED,SAAgB,mBAAmB,CAAC,GAAqB;IACvD,IAAI,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAA;IACnC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,CAAC,KAAK,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;YACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3C,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAE,CAAA;YAC/B,CAAC;YACD,GAAG,CAAC,SAAS,IAAI,KAAK,CAAC,SAAS,CAAA;QAClC,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
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package/dist/util.js.map
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+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAAA,oCAGC;AACD,kCAYC;AAED,oDAOC;AAED,oCAMC;AAGD,gCAgCC;AAED,kCAYC;AAlFD,SAAgB,YAAY,CAAC,IAAY;IACvC,MAAM,GAAG,GAAG,qBAAqB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAC5C,OAAO,GAAG,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;AAC5C,CAAC;AACD,SAAgB,WAAW,CAAC,IAAY;IACtC,MAAM,YAAY,GAAG,CAAC,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,CAAC,CAAA;IAE5E,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;QAChD,OAAO,CAAC,IAAI,CACV,GAAG,IAAI,mCAAmC,YAAY,CAAC,IAAI,CACzD,GAAG,CACJ,0CAA0C,CAC5C,CAAA;IACH,CAAC;IACD,MAAM,OAAO,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;IAClC,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,CAAA;AAC1B,CAAC;AAED,SAAgB,oBAAoB,CAAC,GAAqB;IACxD,wDAAwD;IACxD,IAAI,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;IACrB,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;QAC9C,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;IACnB,CAAC;IACD,OAAO,IAAI,CAAC,KAAM,CAAA;AACpB,CAAC;AAED,SAAgB,YAAY,CAAC,IAAY;IACvC,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IAChC,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAE,CAAC,MAAM,CAAC,CAAA;IAC1C,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,CAAE,CAAC,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAE,CAAC,CAAA;IACtD,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,CAAE,CAAC,MAAM,CAAA;IAC/B,OAAO,CAAC,CAAC,EAAE,CAAC,CAAU,CAAA;AACxB,CAAC;AAED,sDAAsD;AACtD,SAAgB,UAAU,CAAC,GAAqB;IAC9C,IAAI,IAAI,GAAG,oBAAoB,CAAC,GAAG,CAAC,CAAA;IACpC,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,IAAI,aAAa,GAAG,EAAE,CAAA;IACtB,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,OAAO,IAAI,EAAE,CAAC;QACZ,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YACzB,aAAa,GAAG,IAAI,CAAA;QACtB,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;IACzB,CAAC;IACD,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,YAAY,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;IAC5C,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAA;IAC7C,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAA;IAClC,MAAM,IAAI,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAA;IAChD,IAAI,SAAS,GAAG,aAAa,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAE/C,0DAA0D;IAC1D,MAAM,SAAS,GAAG,IAAI,CAAC,CAAC,CAAE,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;IACpD,IAAI,SAAS,EAAE,CAAC;QACd,SAAS,IAAI,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,CAAA;IACpC,CAAC;IACD,OAAO;QACL,GAAG;QACH,IAAI;QACJ,SAAS;KACV,CAAA;AACH,CAAC;AAED,SAAgB,WAAW,CAAC,GAAqB;IAC/C,IAAI,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,UAAU,CAAC,GAAG,CAAC,CAAA;IAC3B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,CAAC,KAAK,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;YACjC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3C,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAE,CAAA;YAC/B,CAAC;YACD,GAAG,CAAC,SAAS,IAAI,KAAK,CAAC,SAAS,CAAA;QAClC,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
|
package/esm/index.js
CHANGED
|
@@ -12,7 +12,7 @@ export function parseClustalIter(arr) {
|
|
|
12
12
|
}
|
|
13
13
|
const alns = res.seqs.map((n, index) => ({ id: res.ids[index], seq: n }));
|
|
14
14
|
const { consensus } = res;
|
|
15
|
-
if (consensus.length
|
|
15
|
+
if (consensus.length !== alns[0].seq.length) {
|
|
16
16
|
throw new Error(`Consensus length != sequence length. Con ${consensus.length} seq ${alns[0].seq.length}`);
|
|
17
17
|
}
|
|
18
18
|
return { consensus, alns, header };
|
package/esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,oBAAoB,EAAE,MAAM,WAAW,CAAA;AAE1E,MAAM,UAAU,gBAAgB,CAAC,GAAqB;IACpD,MAAM,IAAI,GAAG,oBAAoB,CAAC,GAAG,CAAC,CAAA;IACtC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAEhC,MAAM,GAAG,GAAG,WAAW,CAAC,GAAG,CAAC,CAAA;IAC5B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IAED,MAAM,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAE,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;IAC1E,MAAM,EAAE,SAAS,EAAE,GAAG,GAAG,CAAA;IACzB,IAAI,SAAS,CAAC,MAAM,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,oBAAoB,EAAE,MAAM,WAAW,CAAA;AAE1E,MAAM,UAAU,gBAAgB,CAAC,GAAqB;IACpD,MAAM,IAAI,GAAG,oBAAoB,CAAC,GAAG,CAAC,CAAA;IACtC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAEhC,MAAM,GAAG,GAAG,WAAW,CAAC,GAAG,CAAC,CAAA;IAC5B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IAED,MAAM,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAE,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;IAC1E,MAAM,EAAE,SAAS,EAAE,GAAG,GAAG,CAAA;IACzB,IAAI,SAAS,CAAC,MAAM,KAAK,IAAI,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;QAC7C,MAAM,IAAI,KAAK,CACb,4CAA4C,SAAS,CAAC,MAAM,QAAQ,IAAI,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,EAAE,CAC1F,CAAA;IACH,CAAC;IAED,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,MAAM,EAAE,CAAA;AACpC,CAAC;AAOD,MAAM,UAAU,KAAK,CAAC,QAAgB;IACpC,MAAM,IAAI,GAAG,QAAQ,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAA;IACpD,OAAO,gBAAgB,CAAC,IAAI,CAAC,CAAA;AAC/B,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,QAAgB;IAC5C,MAAM,QAAQ,GAAG,QAAQ;SACtB,KAAK,CAAC,IAAI,CAAC;SACX,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SAC/B,IAAI,CAAC,IAAI,CAAC,CAAA;IAEb,MAAM,GAAG,GAAG,mBAAmB,CAAC,QAAQ,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;IACxE,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IAED,MAAM,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAE,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;IAC1E,MAAM,EAAE,SAAS,EAAE,GAAG,GAAG,CAAA;IACzB,MAAM,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;IACxB,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,IAAI,SAAS,CAAC,MAAM,KAAK,QAAQ,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;QAC7C,MAAM,IAAI,KAAK,CACb,6CAA6C,SAAS,CAAC,MAAM,QAAQ,QAAQ,CAAC,GAAG,CAAC,MAAM,EAAE,CAC3F,CAAA;IACH,CAAC;IACD,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CACb,2DAA2D,IAAI,CAAC,MAAM,EAAE,CACzE,CAAA;IACH,CAAC;IACD,OAAO;QACL,SAAS;QACT,IAAI,EAAE,IAAkB;KACzB,CAAA;AACH,CAAC"}
|
package/esm/pairwise.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"pairwise.js","sourceRoot":"","sources":["../src/pairwise.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,oBAAoB,EAAE,MAAM,WAAW,CAAA;AAEhD,SAAS,WAAW,CAAC,IAAY;IAC/B,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,OAAO,KAAK,CAAA;IACd,CAAC;IACD,MAAM,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IACnC,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;AAC3C,CAAC;AAED,SAAS,cAAc,CAAC,IAAY;IAClC,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,OAAO,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;AACtD,CAAC;AAED,SAAS,kBAAkB,CAAC,MAAgB;IAC1C,OAAO,MAAM,CAAC,MAAM,IAAI,CAAC,IAAI,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAE,CAAC,CAAA;AACvD,CAAC;AAED,SAAS,YAAY,CAAC,IAAY,EAAE,QAAgB;IAClD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IACnC,MAAM,GAAG,GAAG,MAAM,CAAC,QAAQ,CAAE,CAAA;IAC7B,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAC3B,GAAG,EACH,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAE,CAAC,GAAG,MAAM,CAAC,CAAC,CAAE,CAAC,MAAM,CAC7C,CAAA;IACD,OAAO,CAAC,QAAQ,EAAE,QAAQ,GAAG,GAAG,CAAC,MAAM,CAAU,CAAA;AACnD,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,kBAAkB,CAAC,GAAqB;IACtD,IAAI,IAAI,GAAG,oBAAoB,CAAC,GAAG,CAAC,CAAA;IACpC,MAAM,KAAK,GAAa,EAAE,CAAA;IAC1B,IAAI,aAAa,GAAG,EAAE,CAAA;IACtB,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,OAAO,IAAI,EAAE,CAAC;QACZ,IAAI,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC;YACtB,4BAA4B;QAC9B,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;aAAM,CAAC;YACN,aAAa,GAAG,IAAI,CAAA;QACtB,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;IACzB,CAAC;IAED,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvB,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAA;IACpD,MAAM,UAAU,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;IAC5B,IAAI,CAAC,UAAU,EAAE,CAAC;QAChB,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,QAAQ,GAAG,kBAAkB,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACvD,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,YAAY,CAAC,KAAK,CAAC,CAAC,CAAE,EAAE,QAAQ,CAAC,CAAA;IACtD,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAA;IAClC,MAAM,IAAI,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAE,CAAC,CAAA;IAC1C,IAAI,SAAS,GAAG,aAAa,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAE/C,0DAA0D;IAC1D,MAAM,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;IACxB,IAAI,QAAQ,EAAE,CAAC;QACb,MAAM,SAAS,GAAG,QAAQ,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;QACpD,IAAI,SAAS,GAAG,CAAC,EAAE,CAAC;YAClB,SAAS,IAAI,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,CAAA;QACpC,CAAC;IACH,CAAC;IACD,OAAO;QACL,GAAG;QACH,IAAI;QACJ,SAAS;KACV,CAAA;AACH,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,GAAqB;IACvD,IAAI,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAA;IACnC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,CAAC,KAAK,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;YACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3C,GAAG,CAAC,IAAI,CAAC,CAAC,
|
|
1
|
+
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|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,YAAY,CAAC,IAAY;IACvC,MAAM,GAAG,GAAG,qBAAqB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAC5C,OAAO,GAAG,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;AAC5C,CAAC;AACD,MAAM,UAAU,WAAW,CAAC,IAAY;IACtC,MAAM,YAAY,GAAG,CAAC,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,CAAC,CAAA;IAE5E,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;QAChD,OAAO,CAAC,IAAI,CACV,GAAG,IAAI,mCAAmC,YAAY,CAAC,IAAI,CACzD,GAAG,CACJ,0CAA0C,CAC5C,CAAA;IACH,CAAC;IACD,MAAM,OAAO,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;IAClC,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,GAAqB;IACxD,wDAAwD;IACxD,IAAI,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;IACrB,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;QAC9C,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;IACnB,CAAC;IACD,OAAO,IAAI,CAAC,
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,YAAY,CAAC,IAAY;IACvC,MAAM,GAAG,GAAG,qBAAqB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAC5C,OAAO,GAAG,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;AAC5C,CAAC;AACD,MAAM,UAAU,WAAW,CAAC,IAAY;IACtC,MAAM,YAAY,GAAG,CAAC,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,CAAC,CAAA;IAE5E,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;QAChD,OAAO,CAAC,IAAI,CACV,GAAG,IAAI,mCAAmC,YAAY,CAAC,IAAI,CACzD,GAAG,CACJ,0CAA0C,CAC5C,CAAA;IACH,CAAC;IACD,MAAM,OAAO,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;IAClC,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,GAAqB;IACxD,wDAAwD;IACxD,IAAI,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;IACrB,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;QAC9C,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;IACnB,CAAC;IACD,OAAO,IAAI,CAAC,KAAM,CAAA;AACpB,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,IAAY;IACvC,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IAChC,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAE,CAAC,MAAM,CAAC,CAAA;IAC1C,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,CAAE,CAAC,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAE,CAAC,CAAA;IACtD,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,CAAE,CAAC,MAAM,CAAA;IAC/B,OAAO,CAAC,CAAC,EAAE,CAAC,CAAU,CAAA;AACxB,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,UAAU,CAAC,GAAqB;IAC9C,IAAI,IAAI,GAAG,oBAAoB,CAAC,GAAG,CAAC,CAAA;IACpC,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,IAAI,aAAa,GAAG,EAAE,CAAA;IACtB,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,OAAO,IAAI,EAAE,CAAC;QACZ,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YACzB,aAAa,GAAG,IAAI,CAAA;QACtB,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;IACzB,CAAC;IACD,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,YAAY,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;IAC5C,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAA;IAC7C,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAA;IAClC,MAAM,IAAI,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAA;IAChD,IAAI,SAAS,GAAG,aAAa,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAE/C,0DAA0D;IAC1D,MAAM,SAAS,GAAG,IAAI,CAAC,CAAC,CAAE,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;IACpD,IAAI,SAAS,EAAE,CAAC;QACd,SAAS,IAAI,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,CAAA;IACpC,CAAC;IACD,OAAO;QACL,GAAG;QACH,IAAI;QACJ,SAAS;KACV,CAAA;AACH,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,GAAqB;IAC/C,IAAI,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,UAAU,CAAC,GAAG,CAAC,CAAA;IAC3B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,CAAC,KAAK,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;YACjC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3C,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAE,CAAA;YAC/B,CAAC;YACD,GAAG,CAAC,SAAS,IAAI,KAAK,CAAC,SAAS,CAAA;QAClC,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,17 +1,16 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "clustal-js",
|
|
3
|
-
"version": "2.0.
|
|
3
|
+
"version": "2.0.14",
|
|
4
4
|
"type": "module",
|
|
5
|
-
"
|
|
5
|
+
"main": "dist/index.js",
|
|
6
6
|
"exports": {
|
|
7
|
-
"import":
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
7
|
+
"import": "./esm/index.js",
|
|
8
|
+
"require": "./dist/index.js"
|
|
9
|
+
},
|
|
10
|
+
"repository": {
|
|
11
|
+
"type": "git",
|
|
12
|
+
"url": "https://github.com/cmdcolin/clustal-js.git"
|
|
13
13
|
},
|
|
14
|
-
"repository": "cmdcolin/clustal-js",
|
|
15
14
|
"files": [
|
|
16
15
|
"dist",
|
|
17
16
|
"esm",
|
|
@@ -19,27 +18,38 @@
|
|
|
19
18
|
],
|
|
20
19
|
"license": "MIT",
|
|
21
20
|
"devDependencies": {
|
|
22
|
-
"@
|
|
23
|
-
"
|
|
24
|
-
"eslint
|
|
25
|
-
"eslint-plugin-
|
|
26
|
-
"
|
|
27
|
-
"
|
|
28
|
-
"
|
|
29
|
-
"typescript
|
|
30
|
-
"
|
|
21
|
+
"@eslint/js": "^10.0.1",
|
|
22
|
+
"@types/node": "^25.5.0",
|
|
23
|
+
"eslint": "^10.2.1",
|
|
24
|
+
"eslint-plugin-import-x": "^4.16.2",
|
|
25
|
+
"eslint-plugin-unicorn": "^64.0.0",
|
|
26
|
+
"prettier": "^3.8.1",
|
|
27
|
+
"rimraf": "^6.1.3",
|
|
28
|
+
"typescript": "^6.0.2",
|
|
29
|
+
"typescript-eslint": "^8.57.2",
|
|
30
|
+
"vitest": "^4.1.2"
|
|
31
31
|
},
|
|
32
32
|
"scripts": {
|
|
33
|
-
"clean": "rimraf dist esm",
|
|
34
33
|
"test": "vitest",
|
|
35
|
-
"
|
|
34
|
+
"clean": "rimraf dist esm",
|
|
36
35
|
"format": "prettier --write .",
|
|
36
|
+
"lint": "eslint --report-unused-disable-directives --max-warnings 0",
|
|
37
|
+
"prebuild": "pnpm clean",
|
|
37
38
|
"build:esm": "tsc --outDir esm",
|
|
38
|
-
"build:es5": "tsc --module commonjs --outDir dist",
|
|
39
|
-
"build": "yarn build:esm && yarn build:es5",
|
|
40
|
-
"prebuild": "yarn clean",
|
|
39
|
+
"build:es5": "tsc --module commonjs --moduleResolution bundler --outDir dist",
|
|
41
40
|
"postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
|
|
42
|
-
"preversion": "
|
|
43
|
-
"postversion": "git push --follow-tags"
|
|
41
|
+
"preversion": "pnpm lint && pnpm test --run && pnpm build",
|
|
42
|
+
"postversion": "git push --follow-tags",
|
|
43
|
+
"build": "pnpm build:esm && pnpm build:es5"
|
|
44
|
+
},
|
|
45
|
+
"dependencies": {
|
|
46
|
+
"@jbrowse/quick-lru": "^7.3.5"
|
|
47
|
+
},
|
|
48
|
+
"keywords": [
|
|
49
|
+
"bioinformatics"
|
|
50
|
+
],
|
|
51
|
+
"author": {
|
|
52
|
+
"name": "Colin Diesh",
|
|
53
|
+
"email": "colin.diesh@gmail.com"
|
|
44
54
|
}
|
|
45
55
|
}
|
package/src/index.ts
CHANGED
|
@@ -15,7 +15,7 @@ export function parseClustalIter(arr: Iterator<string>) {
|
|
|
15
15
|
|
|
16
16
|
const alns = res.seqs.map((n, index) => ({ id: res.ids[index]!, seq: n }))
|
|
17
17
|
const { consensus } = res
|
|
18
|
-
if (consensus.length
|
|
18
|
+
if (consensus.length !== alns[0]!.seq.length) {
|
|
19
19
|
throw new Error(
|
|
20
20
|
`Consensus length != sequence length. Con ${consensus.length} seq ${alns[0]!.seq.length}`,
|
|
21
21
|
)
|
package/src/pairwise.ts
CHANGED
|
@@ -85,7 +85,7 @@ export function parsePairwiseBlocks(arr: Iterator<string>) {
|
|
|
85
85
|
if (res !== undefined) {
|
|
86
86
|
while ((block = parsePairwiseBlock(arr))) {
|
|
87
87
|
for (let i = 0; i < block.seqs.length; i++) {
|
|
88
|
-
res.seqs[i]
|
|
88
|
+
res.seqs[i] += block.seqs[i]!
|
|
89
89
|
}
|
|
90
90
|
res.consensus += block.consensus
|
|
91
91
|
}
|
package/src/util.ts
CHANGED
|
@@ -22,7 +22,7 @@ export function getFirstNonEmptyLine(arr: Iterator<string>): string {
|
|
|
22
22
|
while (!line.done && line.value.trim() === '') {
|
|
23
23
|
line = arr.next()
|
|
24
24
|
}
|
|
25
|
-
return line.value
|
|
25
|
+
return line.value!
|
|
26
26
|
}
|
|
27
27
|
|
|
28
28
|
export function getSeqBounds(line: string) {
|
|
@@ -74,7 +74,7 @@ export function parseBlocks(arr: Iterator<string>) {
|
|
|
74
74
|
if (res !== undefined) {
|
|
75
75
|
while ((block = parseBlock(arr))) {
|
|
76
76
|
for (let i = 0; i < block.seqs.length; i++) {
|
|
77
|
-
res.seqs[i]
|
|
77
|
+
res.seqs[i] += block.seqs[i]!
|
|
78
78
|
}
|
|
79
79
|
res.consensus += block.consensus
|
|
80
80
|
}
|
package/CHANGELOG.md
DELETED
|
@@ -1,27 +0,0 @@
|
|
|
1
|
-
# v2.0.1
|
|
2
|
-
|
|
3
|
-
- Fix preversion build script
|
|
4
|
-
|
|
5
|
-
# v2.0.0
|
|
6
|
-
|
|
7
|
-
- Parse pairwise format, outputted by e.g. EMBOSS needle, etc
|
|
8
|
-
|
|
9
|
-
# v1.0.4
|
|
10
|
-
|
|
11
|
-
- Fix package name in README
|
|
12
|
-
|
|
13
|
-
# v1.0.3
|
|
14
|
-
|
|
15
|
-
- Add generated typescript declarations to output
|
|
16
|
-
|
|
17
|
-
## v1.0.2
|
|
18
|
-
|
|
19
|
-
- Add dist folder to package.json
|
|
20
|
-
|
|
21
|
-
## v1.0.1
|
|
22
|
-
|
|
23
|
-
Remove unused dependency on @babel/runtime
|
|
24
|
-
|
|
25
|
-
## v1.0.0
|
|
26
|
-
|
|
27
|
-
- Initial version parses .aln CLUSTAL files
|