@teselagen/bio-parsers 0.4.2 → 0.4.3

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Files changed (5) hide show
  1. package/index.js +7 -4
  2. package/index.mjs +7 -4
  3. package/index.umd.js +7 -4
  4. package/package.json +2 -2
  5. package/src/utils/validateSequence.js +2 -2
package/index.js CHANGED
@@ -6170,7 +6170,7 @@ lodash.exports;
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  })(lodash, lodash.exports);
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  var lodashExports = lodash.exports;
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  const _ = /* @__PURE__ */ getDefaultExportFromCjs(lodashExports);
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- const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO*";
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+ const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO";
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  const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
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  const ambiguous_rna_letters = "GAUCRYWSMKHBVDN";
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  const aminoAcidToDegenerateDnaMap = {
@@ -11351,9 +11351,12 @@ function getReplaceChars({
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  isRna,
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  isMixedRnaAndDna
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  } = {}) {
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- return isProtein ? {} : isOligo ? {} : isRna ? { t: "u" } : isMixedRnaAndDna ? {} : (
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- //just plain old dna
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- {}
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+ return isProtein ? {} : (
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+ // {".": "*"}
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+ isOligo ? {} : isRna ? { t: "u" } : isMixedRnaAndDna ? {} : (
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+ //just plain old dna
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+ {}
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+ )
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  );
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  }
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  __name(getReplaceChars, "getReplaceChars");
package/index.mjs CHANGED
@@ -6168,7 +6168,7 @@ lodash.exports;
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  })(lodash, lodash.exports);
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  var lodashExports = lodash.exports;
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  const _ = /* @__PURE__ */ getDefaultExportFromCjs(lodashExports);
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- const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO*";
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+ const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO";
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  const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
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  const ambiguous_rna_letters = "GAUCRYWSMKHBVDN";
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  const aminoAcidToDegenerateDnaMap = {
@@ -11349,9 +11349,12 @@ function getReplaceChars({
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  isRna,
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  isMixedRnaAndDna
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  } = {}) {
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- return isProtein ? {} : isOligo ? {} : isRna ? { t: "u" } : isMixedRnaAndDna ? {} : (
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- //just plain old dna
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- {}
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+ return isProtein ? {} : (
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+ // {".": "*"}
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+ isOligo ? {} : isRna ? { t: "u" } : isMixedRnaAndDna ? {} : (
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+ //just plain old dna
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+ {}
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+ )
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  );
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  }
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  __name(getReplaceChars, "getReplaceChars");
package/index.umd.js CHANGED
@@ -6172,7 +6172,7 @@ var __async = (__this, __arguments, generator) => {
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  })(lodash, lodash.exports);
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  var lodashExports = lodash.exports;
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  const _ = /* @__PURE__ */ getDefaultExportFromCjs(lodashExports);
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- const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO*";
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+ const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO";
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  const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
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  const ambiguous_rna_letters = "GAUCRYWSMKHBVDN";
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  const aminoAcidToDegenerateDnaMap = {
@@ -11353,9 +11353,12 @@ var __async = (__this, __arguments, generator) => {
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  isRna,
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  isMixedRnaAndDna
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  } = {}) {
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- return isProtein ? {} : isOligo ? {} : isRna ? { t: "u" } : isMixedRnaAndDna ? {} : (
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- //just plain old dna
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- {}
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+ return isProtein ? {} : (
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+ // {".": "*"}
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+ isOligo ? {} : isRna ? { t: "u" } : isMixedRnaAndDna ? {} : (
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+ //just plain old dna
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+ {}
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+ )
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  );
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  }
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  __name(getReplaceChars, "getReplaceChars");
package/package.json CHANGED
@@ -1,8 +1,8 @@
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  {
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  "name": "@teselagen/bio-parsers",
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- "version": "0.4.2",
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+ "version": "0.4.3",
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  "dependencies": {
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- "@teselagen/sequence-utils": "0.3.10",
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+ "@teselagen/sequence-utils": "0.3.11",
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  "@teselagen/range-utils": "0.3.7",
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  "@gmod/gff": "^1.2.1",
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  "buffer": "^6.0.3",
package/src/utils/validateSequence.js CHANGED
@@ -29,7 +29,7 @@ export default function validateSequence(sequence, options = {}) {
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  inclusive1BasedEnd,
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  additionalValidChars,
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  allowOverflowAnnotations,
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- coerceFeatureTypes,
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+ coerceFeatureTypes
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  } = options;
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  [
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  "isDNA",
@@ -95,7 +95,7 @@ export default function validateSequence(sequence, options = {}) {
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  const [validChars, warnings] = filterSequenceString(sequence.sequence, {
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  name: sequence.name,
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  isProtein: true,
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- additionalValidChars,
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+ additionalValidChars
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  });
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  if (validChars !== sequence.sequence) {
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  sequence.sequence = validChars;