@teselagen/sequence-utils 0.3.32-beta.1 → 0.3.32-beta.2

package/findOrfsInPlasmid.d.ts

@@ -7,5 +7,5 @@ export default function findOrfsInPlasmid(sequence: any, circular: any, minimumO
     forward: any;
     annotationTypePlural: string;
     isOrf: boolean;
-    id: any;
+    id: string;
 }[];

package/getOrfsFromSequence.d.ts

@@ -16,5 +16,5 @@ export default function getOrfsFromSequence(options: any): {
     forward: any;
     annotationTypePlural: string;
     isOrf: boolean;
-    id: any;
+    id: string;
 }[];

package/index.cjs

@@ -3667,307 +3667,15 @@ const getFeatureToColorMap = /* @__PURE__ */ __name(({ includeHidden } = {}) =>
 const getFeatureTypes = /* @__PURE__ */ __name(({ includeHidden } = {}) => filter(getMergedFeatureMap(), (f) => includeHidden ? true : !f.isHidden).map(
   (f) => f.name
 ), "getFeatureTypes");
-function getDefaultExportFromCjs(x) {
-  return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
-}
-__name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
-var lib = { exports: {} };
-var randomFromSeed;
-var hasRequiredRandomFromSeed;
-function requireRandomFromSeed() {
-  if (hasRequiredRandomFromSeed) return randomFromSeed;
-  hasRequiredRandomFromSeed = 1;
-  var seed = 1;
-  function getNextValue() {
-    seed = (seed * 9301 + 49297) % 233280;
-    return seed / 233280;
-  }
-  __name(getNextValue, "getNextValue");
-  function setSeed(_seed_) {
-    seed = _seed_;
-  }
-  __name(setSeed, "setSeed");
-  randomFromSeed = {
-    nextValue: getNextValue,
-    seed: setSeed
-  };
-  return randomFromSeed;
-}
-__name(requireRandomFromSeed, "requireRandomFromSeed");
-var alphabet_1;
-var hasRequiredAlphabet;
-function requireAlphabet() {
-  if (hasRequiredAlphabet) return alphabet_1;
-  hasRequiredAlphabet = 1;
-  var randomFromSeed2 = requireRandomFromSeed();
-  var ORIGINAL = "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ_-";
-  var alphabet;
-  var previousSeed;
-  var shuffled;
-  function reset() {
-    shuffled = false;
-  }
-  __name(reset, "reset");
-  function setCharacters(_alphabet_) {
-    if (!_alphabet_) {
-      if (alphabet !== ORIGINAL) {
-        alphabet = ORIGINAL;
-        reset();
-      }
-      return;
-    }
-    if (_alphabet_ === alphabet) {
-      return;
-    }
-    if (_alphabet_.length !== ORIGINAL.length) {
-      throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. You submitted " + _alphabet_.length + " characters: " + _alphabet_);
-    }
-    var unique = _alphabet_.split("").filter(function(item, ind, arr) {
-      return ind !== arr.lastIndexOf(item);
-    });
-    if (unique.length) {
-      throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. These characters were not unique: " + unique.join(", "));
-    }
-    alphabet = _alphabet_;
-    reset();
-  }
-  __name(setCharacters, "setCharacters");
-  function characters(_alphabet_) {
-    setCharacters(_alphabet_);
-    return alphabet;
-  }
-  __name(characters, "characters");
-  function setSeed(seed) {
-    randomFromSeed2.seed(seed);
-    if (previousSeed !== seed) {
-      reset();
-      previousSeed = seed;
-    }
-  }
-  __name(setSeed, "setSeed");
-  function shuffle() {
-    if (!alphabet) {
-      setCharacters(ORIGINAL);
-    }
-    var sourceArray = alphabet.split("");
-    var targetArray = [];
-    var r = randomFromSeed2.nextValue();
-    var characterIndex;
-    while (sourceArray.length > 0) {
-      r = randomFromSeed2.nextValue();
-      characterIndex = Math.floor(r * sourceArray.length);
-      targetArray.push(sourceArray.splice(characterIndex, 1)[0]);
-    }
-    return targetArray.join("");
-  }
-  __name(shuffle, "shuffle");
-  function getShuffled() {
-    if (shuffled) {
-      return shuffled;
-    }
-    shuffled = shuffle();
-    return shuffled;
-  }
-  __name(getShuffled, "getShuffled");
-  function lookup(index) {
-    var alphabetShuffled = getShuffled();
-    return alphabetShuffled[index];
-  }
-  __name(lookup, "lookup");
-  function get2() {
-    return alphabet || ORIGINAL;
-  }
-  __name(get2, "get");
-  alphabet_1 = {
-    get: get2,
-    characters,
-    seed: setSeed,
-    lookup,
-    shuffled: getShuffled
-  };
-  return alphabet_1;
-}
-__name(requireAlphabet, "requireAlphabet");
-var randomByteBrowser;
-var hasRequiredRandomByteBrowser;
-function requireRandomByteBrowser() {
-  if (hasRequiredRandomByteBrowser) return randomByteBrowser;
-  hasRequiredRandomByteBrowser = 1;
-  var crypto = typeof window === "object" && (window.crypto || window.msCrypto);
-  var randomByte;
-  if (!crypto || !crypto.getRandomValues) {
-    randomByte = /* @__PURE__ */ __name(function(size) {
-      var bytes = [];
-      for (var i = 0; i < size; i++) {
-        bytes.push(Math.floor(Math.random() * 256));
-      }
-      return bytes;
-    }, "randomByte");
-  } else {
-    randomByte = /* @__PURE__ */ __name(function(size) {
-      return crypto.getRandomValues(new Uint8Array(size));
-    }, "randomByte");
-  }
-  randomByteBrowser = randomByte;
-  return randomByteBrowser;
-}
-__name(requireRandomByteBrowser, "requireRandomByteBrowser");
-var format_browser;
-var hasRequiredFormat_browser;
-function requireFormat_browser() {
-  if (hasRequiredFormat_browser) return format_browser;
-  hasRequiredFormat_browser = 1;
-  format_browser = /* @__PURE__ */ __name(function(random, alphabet, size) {
-    var mask = (2 << Math.log(alphabet.length - 1) / Math.LN2) - 1;
-    var step = -~(1.6 * mask * size / alphabet.length);
-    var id = "";
-    while (true) {
-      var bytes = random(step);
-      var i = step;
-      while (i--) {
-        id += alphabet[bytes[i] & mask] || "";
-        if (id.length === +size) return id;
-      }
-    }
-  }, "format_browser");
-  return format_browser;
-}
-__name(requireFormat_browser, "requireFormat_browser");
-var generate_1;
-var hasRequiredGenerate;
-function requireGenerate() {
-  if (hasRequiredGenerate) return generate_1;
-  hasRequiredGenerate = 1;
-  var alphabet = requireAlphabet();
-  var random = requireRandomByteBrowser();
-  var format = /* @__PURE__ */ requireFormat_browser();
-  function generate(number) {
-    var loopCounter = 0;
-    var done;
-    var str = "";
-    while (!done) {
-      str = str + format(random, alphabet.get(), 1);
-      done = number < Math.pow(16, loopCounter + 1);
-      loopCounter++;
-    }
-    return str;
-  }
-  __name(generate, "generate");
-  generate_1 = generate;
-  return generate_1;
-}
-__name(requireGenerate, "requireGenerate");
-var build_1;
-var hasRequiredBuild;
-function requireBuild() {
-  if (hasRequiredBuild) return build_1;
-  hasRequiredBuild = 1;
-  var generate = requireGenerate();
-  requireAlphabet();
-  var REDUCE_TIME = 1567752802062;
-  var version = 7;
-  var counter;
-  var previousSeconds;
-  function build(clusterWorkerId) {
-    var str = "";
-    var seconds = Math.floor((Date.now() - REDUCE_TIME) * 1e-3);
-    if (seconds === previousSeconds) {
-      counter++;
-    } else {
-      counter = 0;
-      previousSeconds = seconds;
-    }
-    str = str + generate(version);
-    str = str + generate(clusterWorkerId);
-    if (counter > 0) {
-      str = str + generate(counter);
-    }
-    str = str + generate(seconds);
-    return str;
-  }
-  __name(build, "build");
-  build_1 = build;
-  return build_1;
-}
-__name(requireBuild, "requireBuild");
-var isValid;
-var hasRequiredIsValid;
-function requireIsValid() {
-  if (hasRequiredIsValid) return isValid;
-  hasRequiredIsValid = 1;
-  var alphabet = requireAlphabet();
-  function isShortId(id) {
-    if (!id || typeof id !== "string" || id.length < 6) {
-      return false;
-    }
-    var nonAlphabetic = new RegExp("[^" + alphabet.get().replace(/[|\\{}()[\]^$+*?.-]/g, "\\$&") + "]");
-    return !nonAlphabetic.test(id);
-  }
-  __name(isShortId, "isShortId");
-  isValid = isShortId;
-  return isValid;
-}
-__name(requireIsValid, "requireIsValid");
-var clusterWorkerIdBrowser;
-var hasRequiredClusterWorkerIdBrowser;
-function requireClusterWorkerIdBrowser() {
-  if (hasRequiredClusterWorkerIdBrowser) return clusterWorkerIdBrowser;
-  hasRequiredClusterWorkerIdBrowser = 1;
-  clusterWorkerIdBrowser = 0;
-  return clusterWorkerIdBrowser;
-}
-__name(requireClusterWorkerIdBrowser, "requireClusterWorkerIdBrowser");
-var hasRequiredLib;
-function requireLib() {
-  if (hasRequiredLib) return lib.exports;
-  hasRequiredLib = 1;
-  (function(module2) {
-    var alphabet = requireAlphabet();
-    var build = requireBuild();
-    var isValid2 = requireIsValid();
-    var clusterWorkerId = requireClusterWorkerIdBrowser() || 0;
-    function seed(seedValue) {
-      alphabet.seed(seedValue);
-      return module2.exports;
-    }
-    __name(seed, "seed");
-    function worker(workerId) {
-      clusterWorkerId = workerId;
-      return module2.exports;
-    }
-    __name(worker, "worker");
-    function characters(newCharacters) {
-      if (newCharacters !== void 0) {
-        alphabet.characters(newCharacters);
-      }
-      return alphabet.shuffled();
-    }
-    __name(characters, "characters");
-    function generate() {
-      return build(clusterWorkerId);
-    }
-    __name(generate, "generate");
-    module2.exports = generate;
-    module2.exports.generate = generate;
-    module2.exports.seed = seed;
-    module2.exports.worker = worker;
-    module2.exports.characters = characters;
-    module2.exports.isValid = isValid2;
-  })(lib);
-  return lib.exports;
-}
-__name(requireLib, "requireLib");
-var shortid$1;
-var hasRequiredShortid;
-function requireShortid() {
-  if (hasRequiredShortid) return shortid$1;
-  hasRequiredShortid = 1;
-  shortid$1 = requireLib();
-  return shortid$1;
-}
-__name(requireShortid, "requireShortid");
-var shortidExports = requireShortid();
-const shortid = /* @__PURE__ */ getDefaultExportFromCjs(shortidExports);
+const urlAlphabet = "useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict";
+let nanoid = /* @__PURE__ */ __name((size = 21) => {
+  let id = "";
+  let bytes = crypto.getRandomValues(new Uint8Array(size |= 0));
+  while (size--) {
+    id += urlAlphabet[bytes[size] & 63];
+  }
+  return id;
+}, "nanoid");
 function cutSequenceByRestrictionEnzyme(pSequence, circular, restrictionEnzyme) {
   if (restrictionEnzyme.forwardRegex.length === 0 || restrictionEnzyme.reverseRegex.length === 0) {
     const returnArray = [];
@@ -4175,7 +3883,7 @@ function cutSequence(forwardRegExpPattern, restrictionEnzyme, sequence, circular
       }
       const overhangBps = getSequenceWithinRange(cutRange, originalSequence);
       restrictionCutSite = {
-        id: shortid(),
+        id: nanoid(),
         start,
         end,
         topSnipPosition,
@@ -4233,7 +3941,7 @@ function computeDigestFragments({
   });
   if (!circular && cutsites.length) {
     sortedCutsites.push({
-      id: "seqTerm_" + shortid(),
+      id: "seqTerm_" + nanoid(),
       start: 0,
       end: 0,
       overhangBps: "",
@@ -4367,6 +4075,10 @@ function getDigestFragsForSeqAndEnzymes({
   });
 }
 __name(getDigestFragsForSeqAndEnzymes, "getDigestFragsForSeqAndEnzymes");
+function getDefaultExportFromCjs(x) {
+  return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
+}
+__name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
 var jsondiffpatch_umd$1 = { exports: {} };
 var empty = {};
 var hasRequiredEmpty;
@@ -8965,10 +8677,10 @@ function tidyUpAnnotation(_annotation, {
     annotation.name = "Untitled annotation";
   }
   if (provideNewIdsForAnnotations) {
-    annotation.id = shortid();
+    annotation.id = nanoid();
   }
   if (!annotation.id && annotation.id !== 0 && !doNotProvideIdsForAnnotations) {
-    annotation.id = shortid();
+    annotation.id = nanoid();
     messages.push(
       "Unable to detect valid ID for annotation, setting ID to " + annotation.id
     );
@@ -9212,7 +8924,7 @@ function tidyUpSequenceData(pSeqData, options = {}) {
         if (item.id || item.id === 0) {
           itemId = item.id;
         } else {
-          itemId = shortid();
+          itemId = nanoid();
           if (!doNotProvideIdsForAnnotations) {
             item.id = itemId;
           }
@@ -17782,7 +17494,7 @@ function generateAnnotation(start, end, maxLength) {
   return __spreadProps(__spreadValues({}, range), {
     name: getRandomInt(0, 1e5).toString(),
     type: "misc_feature",
-    id: shortid(),
+    id: nanoid(),
     forward: Math.random() > 0.5,
     notes: {}
   });
@@ -17905,7 +17617,7 @@ function getOrfsFromSequence(options) {
           forward,
           annotationTypePlural: "orfs",
           isOrf: true,
-          id: shortid()
+          id: nanoid()
         });
       }
     }

package/index.js

@@ -3665,307 +3665,15 @@ const getFeatureToColorMap = /* @__PURE__ */ __name(({ includeHidden } = {}) =>
 const getFeatureTypes = /* @__PURE__ */ __name(({ includeHidden } = {}) => filter(getMergedFeatureMap(), (f) => includeHidden ? true : !f.isHidden).map(
   (f) => f.name
 ), "getFeatureTypes");
-function getDefaultExportFromCjs(x) {
-  return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
-}
-__name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
-var lib = { exports: {} };
-var randomFromSeed;
-var hasRequiredRandomFromSeed;
-function requireRandomFromSeed() {
-  if (hasRequiredRandomFromSeed) return randomFromSeed;
-  hasRequiredRandomFromSeed = 1;
-  var seed = 1;
-  function getNextValue() {
-    seed = (seed * 9301 + 49297) % 233280;
-    return seed / 233280;
-  }
-  __name(getNextValue, "getNextValue");
-  function setSeed(_seed_) {
-    seed = _seed_;
-  }
-  __name(setSeed, "setSeed");
-  randomFromSeed = {
-    nextValue: getNextValue,
-    seed: setSeed
-  };
-  return randomFromSeed;
-}
-__name(requireRandomFromSeed, "requireRandomFromSeed");
-var alphabet_1;
-var hasRequiredAlphabet;
-function requireAlphabet() {
-  if (hasRequiredAlphabet) return alphabet_1;
-  hasRequiredAlphabet = 1;
-  var randomFromSeed2 = requireRandomFromSeed();
-  var ORIGINAL = "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ_-";
-  var alphabet;
-  var previousSeed;
-  var shuffled;
-  function reset() {
-    shuffled = false;
-  }
-  __name(reset, "reset");
-  function setCharacters(_alphabet_) {
-    if (!_alphabet_) {
-      if (alphabet !== ORIGINAL) {
-        alphabet = ORIGINAL;
-        reset();
-      }
-      return;
-    }
-    if (_alphabet_ === alphabet) {
-      return;
-    }
-    if (_alphabet_.length !== ORIGINAL.length) {
-      throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. You submitted " + _alphabet_.length + " characters: " + _alphabet_);
-    }
-    var unique = _alphabet_.split("").filter(function(item, ind, arr) {
-      return ind !== arr.lastIndexOf(item);
-    });
-    if (unique.length) {
-      throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. These characters were not unique: " + unique.join(", "));
-    }
-    alphabet = _alphabet_;
-    reset();
-  }
-  __name(setCharacters, "setCharacters");
-  function characters(_alphabet_) {
-    setCharacters(_alphabet_);
-    return alphabet;
-  }
-  __name(characters, "characters");
-  function setSeed(seed) {
-    randomFromSeed2.seed(seed);
-    if (previousSeed !== seed) {
-      reset();
-      previousSeed = seed;
-    }
-  }
-  __name(setSeed, "setSeed");
-  function shuffle() {
-    if (!alphabet) {
-      setCharacters(ORIGINAL);
-    }
-    var sourceArray = alphabet.split("");
-    var targetArray = [];
-    var r = randomFromSeed2.nextValue();
-    var characterIndex;
-    while (sourceArray.length > 0) {
-      r = randomFromSeed2.nextValue();
-      characterIndex = Math.floor(r * sourceArray.length);
-      targetArray.push(sourceArray.splice(characterIndex, 1)[0]);
-    }
-    return targetArray.join("");
-  }
-  __name(shuffle, "shuffle");
-  function getShuffled() {
-    if (shuffled) {
-      return shuffled;
-    }
-    shuffled = shuffle();
-    return shuffled;
-  }
-  __name(getShuffled, "getShuffled");
-  function lookup(index) {
-    var alphabetShuffled = getShuffled();
-    return alphabetShuffled[index];
-  }
-  __name(lookup, "lookup");
-  function get2() {
-    return alphabet || ORIGINAL;
-  }
-  __name(get2, "get");
-  alphabet_1 = {
-    get: get2,
-    characters,
-    seed: setSeed,
-    lookup,
-    shuffled: getShuffled
-  };
-  return alphabet_1;
-}
-__name(requireAlphabet, "requireAlphabet");
-var randomByteBrowser;
-var hasRequiredRandomByteBrowser;
-function requireRandomByteBrowser() {
-  if (hasRequiredRandomByteBrowser) return randomByteBrowser;
-  hasRequiredRandomByteBrowser = 1;
-  var crypto = typeof window === "object" && (window.crypto || window.msCrypto);
-  var randomByte;
-  if (!crypto || !crypto.getRandomValues) {
-    randomByte = /* @__PURE__ */ __name(function(size) {
-      var bytes = [];
-      for (var i = 0; i < size; i++) {
-        bytes.push(Math.floor(Math.random() * 256));
-      }
-      return bytes;
-    }, "randomByte");
-  } else {
-    randomByte = /* @__PURE__ */ __name(function(size) {
-      return crypto.getRandomValues(new Uint8Array(size));
-    }, "randomByte");
-  }
-  randomByteBrowser = randomByte;
-  return randomByteBrowser;
-}
-__name(requireRandomByteBrowser, "requireRandomByteBrowser");
-var format_browser;
-var hasRequiredFormat_browser;
-function requireFormat_browser() {
-  if (hasRequiredFormat_browser) return format_browser;
-  hasRequiredFormat_browser = 1;
-  format_browser = /* @__PURE__ */ __name(function(random, alphabet, size) {
-    var mask = (2 << Math.log(alphabet.length - 1) / Math.LN2) - 1;
-    var step = -~(1.6 * mask * size / alphabet.length);
-    var id = "";
-    while (true) {
-      var bytes = random(step);
-      var i = step;
-      while (i--) {
-        id += alphabet[bytes[i] & mask] || "";
-        if (id.length === +size) return id;
-      }
-    }
-  }, "format_browser");
-  return format_browser;
-}
-__name(requireFormat_browser, "requireFormat_browser");
-var generate_1;
-var hasRequiredGenerate;
-function requireGenerate() {
-  if (hasRequiredGenerate) return generate_1;
-  hasRequiredGenerate = 1;
-  var alphabet = requireAlphabet();
-  var random = requireRandomByteBrowser();
-  var format = /* @__PURE__ */ requireFormat_browser();
-  function generate(number) {
-    var loopCounter = 0;
-    var done;
-    var str = "";
-    while (!done) {
-      str = str + format(random, alphabet.get(), 1);
-      done = number < Math.pow(16, loopCounter + 1);
-      loopCounter++;
-    }
-    return str;
-  }
-  __name(generate, "generate");
-  generate_1 = generate;
-  return generate_1;
-}
-__name(requireGenerate, "requireGenerate");
-var build_1;
-var hasRequiredBuild;
-function requireBuild() {
-  if (hasRequiredBuild) return build_1;
-  hasRequiredBuild = 1;
-  var generate = requireGenerate();
-  requireAlphabet();
-  var REDUCE_TIME = 1567752802062;
-  var version = 7;
-  var counter;
-  var previousSeconds;
-  function build(clusterWorkerId) {
-    var str = "";
-    var seconds = Math.floor((Date.now() - REDUCE_TIME) * 1e-3);
-    if (seconds === previousSeconds) {
-      counter++;
-    } else {
-      counter = 0;
-      previousSeconds = seconds;
-    }
-    str = str + generate(version);
-    str = str + generate(clusterWorkerId);
-    if (counter > 0) {
-      str = str + generate(counter);
-    }
-    str = str + generate(seconds);
-    return str;
-  }
-  __name(build, "build");
-  build_1 = build;
-  return build_1;
-}
-__name(requireBuild, "requireBuild");
-var isValid;
-var hasRequiredIsValid;
-function requireIsValid() {
-  if (hasRequiredIsValid) return isValid;
-  hasRequiredIsValid = 1;
-  var alphabet = requireAlphabet();
-  function isShortId(id) {
-    if (!id || typeof id !== "string" || id.length < 6) {
-      return false;
-    }
-    var nonAlphabetic = new RegExp("[^" + alphabet.get().replace(/[|\\{}()[\]^$+*?.-]/g, "\\$&") + "]");
-    return !nonAlphabetic.test(id);
-  }
-  __name(isShortId, "isShortId");
-  isValid = isShortId;
-  return isValid;
-}
-__name(requireIsValid, "requireIsValid");
-var clusterWorkerIdBrowser;
-var hasRequiredClusterWorkerIdBrowser;
-function requireClusterWorkerIdBrowser() {
-  if (hasRequiredClusterWorkerIdBrowser) return clusterWorkerIdBrowser;
-  hasRequiredClusterWorkerIdBrowser = 1;
-  clusterWorkerIdBrowser = 0;
-  return clusterWorkerIdBrowser;
-}
-__name(requireClusterWorkerIdBrowser, "requireClusterWorkerIdBrowser");
-var hasRequiredLib;
-function requireLib() {
-  if (hasRequiredLib) return lib.exports;
-  hasRequiredLib = 1;
-  (function(module2) {
-    var alphabet = requireAlphabet();
-    var build = requireBuild();
-    var isValid2 = requireIsValid();
-    var clusterWorkerId = requireClusterWorkerIdBrowser() || 0;
-    function seed(seedValue) {
-      alphabet.seed(seedValue);
-      return module2.exports;
-    }
-    __name(seed, "seed");
-    function worker(workerId) {
-      clusterWorkerId = workerId;
-      return module2.exports;
-    }
-    __name(worker, "worker");
-    function characters(newCharacters) {
-      if (newCharacters !== void 0) {
-        alphabet.characters(newCharacters);
-      }
-      return alphabet.shuffled();
-    }
-    __name(characters, "characters");
-    function generate() {
-      return build(clusterWorkerId);
-    }
-    __name(generate, "generate");
-    module2.exports = generate;
-    module2.exports.generate = generate;
-    module2.exports.seed = seed;
-    module2.exports.worker = worker;
-    module2.exports.characters = characters;
-    module2.exports.isValid = isValid2;
-  })(lib);
-  return lib.exports;
-}
-__name(requireLib, "requireLib");
-var shortid$1;
-var hasRequiredShortid;
-function requireShortid() {
-  if (hasRequiredShortid) return shortid$1;
-  hasRequiredShortid = 1;
-  shortid$1 = requireLib();
-  return shortid$1;
-}
-__name(requireShortid, "requireShortid");
-var shortidExports = requireShortid();
-const shortid = /* @__PURE__ */ getDefaultExportFromCjs(shortidExports);
+const urlAlphabet = "useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict";
+let nanoid = /* @__PURE__ */ __name((size = 21) => {
+  let id = "";
+  let bytes = crypto.getRandomValues(new Uint8Array(size |= 0));
+  while (size--) {
+    id += urlAlphabet[bytes[size] & 63];
+  }
+  return id;
+}, "nanoid");
 function cutSequenceByRestrictionEnzyme(pSequence, circular, restrictionEnzyme) {
   if (restrictionEnzyme.forwardRegex.length === 0 || restrictionEnzyme.reverseRegex.length === 0) {
     const returnArray = [];
@@ -4173,7 +3881,7 @@ function cutSequence(forwardRegExpPattern, restrictionEnzyme, sequence, circular
       }
       const overhangBps = getSequenceWithinRange(cutRange, originalSequence);
       restrictionCutSite = {
-        id: shortid(),
+        id: nanoid(),
         start,
         end,
         topSnipPosition,
@@ -4231,7 +3939,7 @@ function computeDigestFragments({
   });
   if (!circular && cutsites.length) {
     sortedCutsites.push({
-      id: "seqTerm_" + shortid(),
+      id: "seqTerm_" + nanoid(),
       start: 0,
       end: 0,
       overhangBps: "",
@@ -4365,6 +4073,10 @@ function getDigestFragsForSeqAndEnzymes({
   });
 }
 __name(getDigestFragsForSeqAndEnzymes, "getDigestFragsForSeqAndEnzymes");
+function getDefaultExportFromCjs(x) {
+  return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
+}
+__name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
 var jsondiffpatch_umd$1 = { exports: {} };
 var empty = {};
 var hasRequiredEmpty;
@@ -8963,10 +8675,10 @@ function tidyUpAnnotation(_annotation, {
     annotation.name = "Untitled annotation";
   }
   if (provideNewIdsForAnnotations) {
-    annotation.id = shortid();
+    annotation.id = nanoid();
   }
   if (!annotation.id && annotation.id !== 0 && !doNotProvideIdsForAnnotations) {
-    annotation.id = shortid();
+    annotation.id = nanoid();
     messages.push(
       "Unable to detect valid ID for annotation, setting ID to " + annotation.id
     );
@@ -9210,7 +8922,7 @@ function tidyUpSequenceData(pSeqData, options = {}) {
         if (item.id || item.id === 0) {
           itemId = item.id;
         } else {
-          itemId = shortid();
+          itemId = nanoid();
           if (!doNotProvideIdsForAnnotations) {
             item.id = itemId;
           }
@@ -17780,7 +17492,7 @@ function generateAnnotation(start, end, maxLength) {
   return __spreadProps(__spreadValues({}, range), {
     name: getRandomInt(0, 1e5).toString(),
     type: "misc_feature",
-    id: shortid(),
+    id: nanoid(),
     forward: Math.random() > 0.5,
     notes: {}
   });
@@ -17903,7 +17615,7 @@ function getOrfsFromSequence(options) {
           forward,
           annotationTypePlural: "orfs",
           isOrf: true,
-          id: shortid()
+          id: nanoid()
         });
       }
     }

package/index.umd.cjs

@@ -3669,307 +3669,15 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   const getFeatureTypes = /* @__PURE__ */ __name(({ includeHidden } = {}) => filter(getMergedFeatureMap(), (f) => includeHidden ? true : !f.isHidden).map(
     (f) => f.name
   ), "getFeatureTypes");
-  function getDefaultExportFromCjs(x) {
-    return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
-  }
-  __name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
-  var lib = { exports: {} };
-  var randomFromSeed;
-  var hasRequiredRandomFromSeed;
-  function requireRandomFromSeed() {
-    if (hasRequiredRandomFromSeed) return randomFromSeed;
-    hasRequiredRandomFromSeed = 1;
-    var seed = 1;
-    function getNextValue() {
-      seed = (seed * 9301 + 49297) % 233280;
-      return seed / 233280;
-    }
-    __name(getNextValue, "getNextValue");
-    function setSeed(_seed_) {
-      seed = _seed_;
-    }
-    __name(setSeed, "setSeed");
-    randomFromSeed = {
-      nextValue: getNextValue,
-      seed: setSeed
-    };
-    return randomFromSeed;
-  }
-  __name(requireRandomFromSeed, "requireRandomFromSeed");
-  var alphabet_1;
-  var hasRequiredAlphabet;
-  function requireAlphabet() {
-    if (hasRequiredAlphabet) return alphabet_1;
-    hasRequiredAlphabet = 1;
-    var randomFromSeed2 = requireRandomFromSeed();
-    var ORIGINAL = "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ_-";
-    var alphabet;
-    var previousSeed;
-    var shuffled;
-    function reset() {
-      shuffled = false;
-    }
-    __name(reset, "reset");
-    function setCharacters(_alphabet_) {
-      if (!_alphabet_) {
-        if (alphabet !== ORIGINAL) {
-          alphabet = ORIGINAL;
-          reset();
-        }
-        return;
-      }
-      if (_alphabet_ === alphabet) {
-        return;
-      }
-      if (_alphabet_.length !== ORIGINAL.length) {
-        throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. You submitted " + _alphabet_.length + " characters: " + _alphabet_);
-      }
-      var unique = _alphabet_.split("").filter(function(item, ind, arr) {
-        return ind !== arr.lastIndexOf(item);
-      });
-      if (unique.length) {
-        throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. These characters were not unique: " + unique.join(", "));
-      }
-      alphabet = _alphabet_;
-      reset();
-    }
-    __name(setCharacters, "setCharacters");
-    function characters(_alphabet_) {
-      setCharacters(_alphabet_);
-      return alphabet;
-    }
-    __name(characters, "characters");
-    function setSeed(seed) {
-      randomFromSeed2.seed(seed);
-      if (previousSeed !== seed) {
-        reset();
-        previousSeed = seed;
-      }
-    }
-    __name(setSeed, "setSeed");
-    function shuffle() {
-      if (!alphabet) {
-        setCharacters(ORIGINAL);
-      }
-      var sourceArray = alphabet.split("");
-      var targetArray = [];
-      var r = randomFromSeed2.nextValue();
-      var characterIndex;
-      while (sourceArray.length > 0) {
-        r = randomFromSeed2.nextValue();
-        characterIndex = Math.floor(r * sourceArray.length);
-        targetArray.push(sourceArray.splice(characterIndex, 1)[0]);
-      }
-      return targetArray.join("");
-    }
-    __name(shuffle, "shuffle");
-    function getShuffled() {
-      if (shuffled) {
-        return shuffled;
-      }
-      shuffled = shuffle();
-      return shuffled;
-    }
-    __name(getShuffled, "getShuffled");
-    function lookup(index) {
-      var alphabetShuffled = getShuffled();
-      return alphabetShuffled[index];
-    }
-    __name(lookup, "lookup");
-    function get2() {
-      return alphabet || ORIGINAL;
-    }
-    __name(get2, "get");
-    alphabet_1 = {
-      get: get2,
-      characters,
-      seed: setSeed,
-      lookup,
-      shuffled: getShuffled
-    };
-    return alphabet_1;
-  }
-  __name(requireAlphabet, "requireAlphabet");
-  var randomByteBrowser;
-  var hasRequiredRandomByteBrowser;
-  function requireRandomByteBrowser() {
-    if (hasRequiredRandomByteBrowser) return randomByteBrowser;
-    hasRequiredRandomByteBrowser = 1;
-    var crypto = typeof window === "object" && (window.crypto || window.msCrypto);
-    var randomByte;
-    if (!crypto || !crypto.getRandomValues) {
-      randomByte = /* @__PURE__ */ __name(function(size) {
-        var bytes = [];
-        for (var i = 0; i < size; i++) {
-          bytes.push(Math.floor(Math.random() * 256));
-        }
-        return bytes;
-      }, "randomByte");
-    } else {
-      randomByte = /* @__PURE__ */ __name(function(size) {
-        return crypto.getRandomValues(new Uint8Array(size));
-      }, "randomByte");
-    }
-    randomByteBrowser = randomByte;
-    return randomByteBrowser;
-  }
-  __name(requireRandomByteBrowser, "requireRandomByteBrowser");
-  var format_browser;
-  var hasRequiredFormat_browser;
-  function requireFormat_browser() {
-    if (hasRequiredFormat_browser) return format_browser;
-    hasRequiredFormat_browser = 1;
-    format_browser = /* @__PURE__ */ __name(function(random, alphabet, size) {
-      var mask = (2 << Math.log(alphabet.length - 1) / Math.LN2) - 1;
-      var step = -~(1.6 * mask * size / alphabet.length);
-      var id = "";
-      while (true) {
-        var bytes = random(step);
-        var i = step;
-        while (i--) {
-          id += alphabet[bytes[i] & mask] || "";
-          if (id.length === +size) return id;
-        }
-      }
-    }, "format_browser");
-    return format_browser;
-  }
-  __name(requireFormat_browser, "requireFormat_browser");
-  var generate_1;
-  var hasRequiredGenerate;
-  function requireGenerate() {
-    if (hasRequiredGenerate) return generate_1;
-    hasRequiredGenerate = 1;
-    var alphabet = requireAlphabet();
-    var random = requireRandomByteBrowser();
-    var format = /* @__PURE__ */ requireFormat_browser();
-    function generate(number) {
-      var loopCounter = 0;
-      var done;
-      var str = "";
-      while (!done) {
-        str = str + format(random, alphabet.get(), 1);
-        done = number < Math.pow(16, loopCounter + 1);
-        loopCounter++;
-      }
-      return str;
-    }
-    __name(generate, "generate");
-    generate_1 = generate;
-    return generate_1;
-  }
-  __name(requireGenerate, "requireGenerate");
-  var build_1;
-  var hasRequiredBuild;
-  function requireBuild() {
-    if (hasRequiredBuild) return build_1;
-    hasRequiredBuild = 1;
-    var generate = requireGenerate();
-    requireAlphabet();
-    var REDUCE_TIME = 1567752802062;
-    var version = 7;
-    var counter;
-    var previousSeconds;
-    function build(clusterWorkerId) {
-      var str = "";
-      var seconds = Math.floor((Date.now() - REDUCE_TIME) * 1e-3);
-      if (seconds === previousSeconds) {
-        counter++;
-      } else {
-        counter = 0;
-        previousSeconds = seconds;
-      }
-      str = str + generate(version);
-      str = str + generate(clusterWorkerId);
-      if (counter > 0) {
-        str = str + generate(counter);
-      }
-      str = str + generate(seconds);
-      return str;
-    }
-    __name(build, "build");
-    build_1 = build;
-    return build_1;
-  }
-  __name(requireBuild, "requireBuild");
-  var isValid;
-  var hasRequiredIsValid;
-  function requireIsValid() {
-    if (hasRequiredIsValid) return isValid;
-    hasRequiredIsValid = 1;
-    var alphabet = requireAlphabet();
-    function isShortId(id) {
-      if (!id || typeof id !== "string" || id.length < 6) {
-        return false;
-      }
-      var nonAlphabetic = new RegExp("[^" + alphabet.get().replace(/[|\\{}()[\]^$+*?.-]/g, "\\$&") + "]");
-      return !nonAlphabetic.test(id);
-    }
-    __name(isShortId, "isShortId");
-    isValid = isShortId;
-    return isValid;
-  }
-  __name(requireIsValid, "requireIsValid");
-  var clusterWorkerIdBrowser;
-  var hasRequiredClusterWorkerIdBrowser;
-  function requireClusterWorkerIdBrowser() {
-    if (hasRequiredClusterWorkerIdBrowser) return clusterWorkerIdBrowser;
-    hasRequiredClusterWorkerIdBrowser = 1;
-    clusterWorkerIdBrowser = 0;
-    return clusterWorkerIdBrowser;
-  }
-  __name(requireClusterWorkerIdBrowser, "requireClusterWorkerIdBrowser");
-  var hasRequiredLib;
-  function requireLib() {
-    if (hasRequiredLib) return lib.exports;
-    hasRequiredLib = 1;
-    (function(module2) {
-      var alphabet = requireAlphabet();
-      var build = requireBuild();
-      var isValid2 = requireIsValid();
-      var clusterWorkerId = requireClusterWorkerIdBrowser() || 0;
-      function seed(seedValue) {
-        alphabet.seed(seedValue);
-        return module2.exports;
-      }
-      __name(seed, "seed");
-      function worker(workerId) {
-        clusterWorkerId = workerId;
-        return module2.exports;
-      }
-      __name(worker, "worker");
-      function characters(newCharacters) {
-        if (newCharacters !== void 0) {
-          alphabet.characters(newCharacters);
-        }
-        return alphabet.shuffled();
-      }
-      __name(characters, "characters");
-      function generate() {
-        return build(clusterWorkerId);
-      }
-      __name(generate, "generate");
-      module2.exports = generate;
-      module2.exports.generate = generate;
-      module2.exports.seed = seed;
-      module2.exports.worker = worker;
-      module2.exports.characters = characters;
-      module2.exports.isValid = isValid2;
-    })(lib);
-    return lib.exports;
-  }
-  __name(requireLib, "requireLib");
-  var shortid$1;
-  var hasRequiredShortid;
-  function requireShortid() {
-    if (hasRequiredShortid) return shortid$1;
-    hasRequiredShortid = 1;
-    shortid$1 = requireLib();
-    return shortid$1;
-  }
-  __name(requireShortid, "requireShortid");
-  var shortidExports = requireShortid();
-  const shortid = /* @__PURE__ */ getDefaultExportFromCjs(shortidExports);
+  const urlAlphabet = "useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict";
+  let nanoid = /* @__PURE__ */ __name((size = 21) => {
+    let id = "";
+    let bytes = crypto.getRandomValues(new Uint8Array(size |= 0));
+    while (size--) {
+      id += urlAlphabet[bytes[size] & 63];
+    }
+    return id;
+  }, "nanoid");
   function cutSequenceByRestrictionEnzyme(pSequence, circular, restrictionEnzyme) {
     if (restrictionEnzyme.forwardRegex.length === 0 || restrictionEnzyme.reverseRegex.length === 0) {
       const returnArray = [];
@@ -4177,7 +3885,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
         }
         const overhangBps = getSequenceWithinRange(cutRange, originalSequence);
         restrictionCutSite = {
-          id: shortid(),
+          id: nanoid(),
           start,
           end,
           topSnipPosition,
@@ -4235,7 +3943,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     });
     if (!circular && cutsites.length) {
       sortedCutsites.push({
-        id: "seqTerm_" + shortid(),
+        id: "seqTerm_" + nanoid(),
         start: 0,
         end: 0,
         overhangBps: "",
@@ -4369,6 +4077,10 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     });
   }
   __name(getDigestFragsForSeqAndEnzymes, "getDigestFragsForSeqAndEnzymes");
+  function getDefaultExportFromCjs(x) {
+    return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
+  }
+  __name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
   var jsondiffpatch_umd$1 = { exports: {} };
   var empty = {};
   var hasRequiredEmpty;
@@ -8967,10 +8679,10 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       annotation.name = "Untitled annotation";
     }
     if (provideNewIdsForAnnotations) {
-      annotation.id = shortid();
+      annotation.id = nanoid();
     }
     if (!annotation.id && annotation.id !== 0 && !doNotProvideIdsForAnnotations) {
-      annotation.id = shortid();
+      annotation.id = nanoid();
       messages.push(
         "Unable to detect valid ID for annotation, setting ID to " + annotation.id
       );
@@ -9214,7 +8926,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
           if (item.id || item.id === 0) {
             itemId = item.id;
           } else {
-            itemId = shortid();
+            itemId = nanoid();
             if (!doNotProvideIdsForAnnotations) {
               item.id = itemId;
             }
@@ -17784,7 +17496,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     return __spreadProps(__spreadValues({}, range), {
       name: getRandomInt(0, 1e5).toString(),
       type: "misc_feature",
-      id: shortid(),
+      id: nanoid(),
       forward: Math.random() > 0.5,
       notes: {}
     });
@@ -17907,7 +17619,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
             forward,
             annotationTypePlural: "orfs",
             isOrf: true,
-            id: shortid()
+            id: nanoid()
           });
         }
       }

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.32-beta.1",
+  "version": "0.3.32-beta.2",
   "type": "module",
   "dependencies": {
+    "@teselagen/range-utils": "0.3.14-beta.1",
     "escape-string-regexp": "5.0.0",
     "jsondiffpatch": "0.4.1",
-    "string-splice": "^1.3.0",
     "lodash-es": "^4.17.21",
-    "shortid": "2.2.16",
-    "@teselagen/range-utils": "0.3.13"
+    "nanoid": "^5.1.5",
+    "string-splice": "^1.3.0"
   },
   "exports": {
     ".": {
@@ -16,5 +16,9 @@
       "require": "./index.cjs"
     }
   },
+  "volta": {
+    "node": "18.18.0",
+    "yarn": "1.22.22"
+  },
   "license": "MIT"
 }

package/src/computeDigestFragments.js

@@ -1,4 +1,4 @@
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 import { flatMap, cloneDeep } from "lodash-es";
 import {
   normalizePositionByRangeLength,
@@ -27,7 +27,7 @@ function computeDigestFragments({
   });
   if (!circular && cutsites.length) {
     sortedCutsites.push({
-      id: "seqTerm_" + shortid(),
+      id: "seqTerm_" + nanoid(),
       start: 0,
       end: 0,
       overhangBps: "",

package/src/cutSequenceByRestrictionEnzyme.js

@@ -1,5 +1,5 @@
 import { assign } from "lodash-es";
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 import getReverseComplementSequenceString from "./getReverseComplementSequenceString";
 
 import {
@@ -268,7 +268,7 @@ function cutSequence(
       const overhangBps = getSequenceWithinRange(cutRange, originalSequence);
 
       restrictionCutSite = {
-        id: shortid(),
+        id: nanoid(),
         start,
         end,
         topSnipPosition,

package/src/generateAnnotations.js

@@ -1,5 +1,5 @@
 import { generateRandomRange } from "@teselagen/range-utils";
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 
 function generateAnnotations(
   numberOfAnnotationsToGenerate,
@@ -21,7 +21,7 @@ function generateAnnotation(start, end, maxLength) {
     ...range,
     name: getRandomInt(0, 100000).toString(),
     type: "misc_feature",
-    id: shortid(),
+    id: nanoid(),
     forward: Math.random() > 0.5,
     notes: {}
   };

package/src/getOrfsFromSequence.js

@@ -1,4 +1,4 @@
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 import getReverseComplementSequenceString from "./getReverseComplementSequenceString";
 
 /**
@@ -61,7 +61,7 @@ export default function getOrfsFromSequence(options) {
           forward: forward,
           annotationTypePlural: "orfs",
           isOrf: true,
-          id: shortid()
+          id: nanoid()
         });
       }
     }

package/src/tidyUpAnnotation.js

@@ -1,6 +1,6 @@
 import { cloneDeep, get, some } from "lodash-es";
 import { getFeatureToColorMap, getFeatureTypes } from "./featureTypesAndColors";
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 
 export default function tidyUpAnnotation(
   _annotation,
@@ -34,10 +34,10 @@ export default function tidyUpAnnotation(
     annotation.name = "Untitled annotation";
   }
   if (provideNewIdsForAnnotations) {
-    annotation.id = shortid();
+    annotation.id = nanoid();
   }
   if (!annotation.id && annotation.id !== 0 && !doNotProvideIdsForAnnotations) {
-    annotation.id = shortid();
+    annotation.id = nanoid();
     messages.push(
       "Unable to detect valid ID for annotation, setting ID to " + annotation.id
     );

package/src/tidyUpSequenceData.js

@@ -1,5 +1,5 @@
 // tnrtodo: figure out where to insert this validation exactly..
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 
 import getAminoAcidDataForEachBaseOfDna from "./getAminoAcidDataForEachBaseOfDna";
 import { cloneDeep, flatMap } from "lodash-es";
@@ -155,7 +155,7 @@ export default function tidyUpSequenceData(pSeqData, options = {}) {
         if (item.id || item.id === 0) {
           itemId = item.id;
         } else {
-          itemId = shortid();
+          itemId = nanoid();
           if (!doNotProvideIdsForAnnotations) {
             item.id = itemId; //assign the newly created id to the item
           }