@teselagen/bio-parsers 0.3.8 → 0.3.10

package/index.umd.js

@@ -6285,8 +6285,8 @@ var __async = (__this, __arguments, generator) => {
       maxRangeLength
     );
     let overlaps = [];
-    normalizedRangeA.forEach(function(nonCircularRangeA, iA) {
-      normalizedRangeB.forEach(function(nonCircularRangeB, iB) {
+    normalizedRangeA.forEach(function(nonCircularRangeA) {
+      normalizedRangeB.forEach(function(nonCircularRangeB) {
         const overlap = getOverlapOfNonCircularRanges(
           nonCircularRangeA,
           nonCircularRangeB
@@ -6298,7 +6298,7 @@ var __async = (__this, __arguments, generator) => {
     });
     if (joinIfPossible && normalizedRangeA.length === 2 && normalizedRangeB.length === 2 && maxRangeLength) {
       const joinedOverlap = {};
-      overlaps = lodashExports.flatMap(overlaps, (o, i2) => {
+      overlaps = lodashExports.flatMap(overlaps, (o) => {
         if (o.start === 0) {
           joinedOverlap.end = o.end;
           return [];
@@ -6396,12 +6396,14 @@ var __async = (__this, __arguments, generator) => {
       });
       splitRangesToBeTrimmed[index] = nonCircularRangeToBeTrimmed;
     });
-    const outputSplitRanges = splitRangesToBeTrimmed.filter(function(trimmedRange) {
-      if (trimmedRange) {
-        return true;
+    const outputSplitRanges = splitRangesToBeTrimmed.filter(
+      function(trimmedRange) {
+        if (trimmedRange) {
+          return true;
+        }
+        return false;
       }
-      return false;
-    });
+    );
     let outputTrimmedRange;
     if (outputSplitRanges.length < 0)
       ;
@@ -6451,8 +6453,14 @@ var __async = (__this, __arguments, generator) => {
   __name(normalizePositionByRangeLength, "normalizePositionByRangeLength");
   function translateRange(rangeToBeAdjusted, translateBy, rangeLength) {
     return lodashExports.assign({}, rangeToBeAdjusted, {
-      start: normalizePositionByRangeLength(rangeToBeAdjusted.start + translateBy, rangeLength),
-      end: normalizePositionByRangeLength(rangeToBeAdjusted.end + translateBy, rangeLength)
+      start: normalizePositionByRangeLength(
+        rangeToBeAdjusted.start + translateBy,
+        rangeLength
+      ),
+      end: normalizePositionByRangeLength(
+        rangeToBeAdjusted.end + translateBy,
+        rangeLength
+      )
     });
   }
   __name(translateRange, "translateRange");
@@ -10769,7 +10777,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: 1.8,
       colorByFamily: "#00FFFF",
       color: "hsl(327.3, 100%, 69%)",
-      mass: 89.1
+      mass: 71.0779
     },
     R: {
       value: "R",
@@ -10778,7 +10786,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -4.5,
       colorByFamily: "#FFC0CB",
       color: "hsl(258.1, 100%, 69%)",
-      mass: 174.2
+      mass: 156.18568
     },
     N: {
       value: "N",
@@ -10787,7 +10795,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -3.5,
       colorByFamily: "#D3D3D3",
       color: "hsl(268.9, 100%, 69%)",
-      mass: 132.1
+      mass: 114.10264
     },
     D: {
       value: "D",
@@ -10796,7 +10804,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -3.5,
       colorByFamily: "#EE82EE",
       color: "hsl(268.9, 100%, 69%)",
-      mass: 133.1
+      mass: 115.0874
     },
     C: {
       value: "C",
@@ -10805,7 +10813,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: 2.5,
       colorByFamily: "#FFFF00",
       color: "hsl(335.1, 100%, 69%)",
-      mass: 121.2
+      mass: 103.1429
     },
     E: {
       value: "E",
@@ -10814,7 +10822,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -3.5,
       colorByFamily: "#EE82EE",
       color: "hsl(268.9, 100%, 69%)",
-      mass: 147.1
+      mass: 129.11398
     },
     Q: {
       value: "Q",
@@ -10823,7 +10831,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -3.5,
       colorByFamily: "#D3D3D3",
       color: "hsl(268.9, 100%, 69%)",
-      mass: 146.2
+      mass: 128.12922
     },
     G: {
       value: "G",
@@ -10832,7 +10840,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -0.4,
       colorByFamily: "#00FFFF",
       color: "hsl(303.1, 100%, 69%)",
-      mass: 75.1
+      mass: 57.05132
     },
     H: {
       value: "H",
@@ -10841,7 +10849,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -3.2,
       colorByFamily: "#FFC0CB",
       color: "hsl(272.2, 100%, 69%)",
-      mass: 155.2
+      mass: 137.13928
     },
     I: {
       value: "I",
@@ -10850,7 +10858,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: 4.5,
       colorByFamily: "#00FFFF",
       color: "hsl(356.9, 100%, 69%)",
-      mass: 131.2
+      mass: 113.15764
     },
     L: {
       value: "L",
@@ -10859,7 +10867,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: 3.8,
       colorByFamily: "#00FFFF",
       color: "hsl(349.4, 100%, 69%)",
-      mass: 131.2
+      mass: 113.15764
     },
     K: {
       value: "K",
@@ -10868,7 +10876,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -3.9,
       colorByFamily: "#FFC0CB",
       color: "hsl(264.7, 100%, 69%)",
-      mass: 146.2
+      mass: 128.17228
     },
     M: {
       value: "M",
@@ -10877,7 +10885,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: 1.9,
       colorByFamily: "#FFFF00",
       color: "hsl(328.5, 100%, 69%)",
-      mass: 149.2
+      mass: 131.19606
     },
     F: {
       value: "F",
@@ -10886,7 +10894,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: 2.8,
       colorByFamily: "#FFA500",
       color: "hsl(338.4, 100%, 69%)",
-      mass: 165.2
+      mass: 147.17386
     },
     P: {
       value: "P",
@@ -10895,7 +10903,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -1.6,
       colorByFamily: "#00FFFF",
       color: "hsl(289.9, 100%, 69%)",
-      mass: 115.1
+      mass: 97.11518
     },
     S: {
       value: "S",
@@ -10904,7 +10912,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -0.8,
       colorByFamily: "#90EE90",
       color: "hsl(298.6, 100%, 69%)",
-      mass: 105.1
+      mass: 87.0773
     },
     T: {
       value: "T",
@@ -10913,7 +10921,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -0.7,
       colorByFamily: "#90EE90",
       color: "hsl(299.8, 100%, 69%)",
-      mass: 119.1
+      mass: 101.10388
     },
     U: {
       value: "U",
@@ -10921,7 +10929,7 @@ var __async = (__this, __arguments, generator) => {
       threeLettersName: "Sec",
       colorByFamily: "#FF0000",
       color: "hsl(0, 100%, 69%)",
-      mass: 168.1
+      mass: 150.3079
     },
     W: {
       value: "W",
@@ -10930,7 +10938,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -0.9,
       colorByFamily: "#FFA500",
       color: "hsl(297.6, 100%, 69%)",
-      mass: 204.2
+      mass: 186.2099
     },
     Y: {
       value: "Y",
@@ -10939,7 +10947,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: -1.3,
       colorByFamily: "#FFA500",
       color: "hsl(293.2, 100%, 69%)",
-      mass: 181.2
+      mass: 163.17326
     },
     V: {
       value: "V",
@@ -10948,7 +10956,7 @@ var __async = (__this, __arguments, generator) => {
       hydrophobicity: 4.2,
       colorByFamily: "#00FFFF",
       color: "hsl(353.6, 100%, 69%)",
-      mass: 117.1
+      mass: 99.13106
     },
     "*": {
       value: "*",
@@ -11393,13 +11401,13 @@ var __async = (__this, __arguments, generator) => {
       messages.push(
         "Invalid annotation start: " + location.start + " detected for " + location.name + " and set to size: " + size
       );
-      location.start = size - (isProtein ? 3 : 1);
+      location.start = Math.max(0, size - (isProtein ? 3 : 1));
     }
     if (location.end < 0 || !(location.end <= size - 1) || location.end > size - 1) {
       messages.push(
         "Invalid annotation end:  " + location.end + " detected for " + location.name + " and set to seq size: " + size
       );
-      location.end = size - 1;
+      location.end = Math.max(0, size - 1);
     }
     if (location.start > location.end && circular === false) {
       messages.push(
@@ -11412,9 +11420,9 @@ var __async = (__this, __arguments, generator) => {
   function filterAminoAcidSequenceString(sequenceString, options) {
     options = options || {};
     if (options.includeStopCodon) {
-      return sequenceString.replace(/[^xtgalmfwkqespvicyhrndu.*]/gi, "");
+      return sequenceString == null ? void 0 : sequenceString.replace(/[^xtgalmfwkqespvicyhrndu.*]/gi, "");
     }
-    return sequenceString.replace(/[^xtgalmfwkqespvicyhrndu]/gi, "");
+    return sequenceString == null ? void 0 : sequenceString.replace(/[^xtgalmfwkqespvicyhrndu]/gi, "");
   }
   __name(filterAminoAcidSequenceString, "filterAminoAcidSequenceString");
   function getDegenerateDnaStringFromAAString(aaString) {
@@ -11612,7 +11620,7 @@ var __async = (__this, __arguments, generator) => {
     calculateTemperature: function(sequence, type, A, R, C, Na) {
       if (typeof type === "undefined") {
         type = this.TABLE_BRESLAUER;
-      } else if (type != this.TABLE_BRESLAUER && (type != this.TABLE_UNIFIED && type != this.TABLE_SUGIMOTO)) {
+      } else if (type != this.TABLE_BRESLAUER && type != this.TABLE_UNIFIED && type != this.TABLE_SUGIMOTO) {
         throw new Error("Invalid table type!");
       }
       if (!A) {
@@ -19763,18 +19771,20 @@ var __async = (__this, __arguments, generator) => {
         const isKeyRunon = isKeywordRunon(line);
         const isSubKey = isSubKeyword(line);
         const isKey = isKeyword(line);
-        if (key === "LOCUS") {
-          LINETYPE = key;
-        } else if (key === "REFERENCE") {
-          LINETYPE = key;
-        } else if (key === "FEATURES") {
-          LINETYPE = key;
-        } else if (key === "ORIGIN") {
-          LINETYPE = key;
-        } else if (key === "//") {
-          LINETYPE = key;
-        } else if (isKey === true) {
-          LINETYPE = key;
+        if (!isKeyRunon) {
+          if (key === "LOCUS") {
+            LINETYPE = key;
+          } else if (key === "REFERENCE") {
+            LINETYPE = key;
+          } else if (key === "FEATURES") {
+            LINETYPE = key;
+          } else if (key === "ORIGIN") {
+            LINETYPE = key;
+          } else if (key === "//") {
+            LINETYPE = key;
+          } else if (isKey === true) {
+            LINETYPE = key;
+          }
         }
         if (line.trim() === "" || key === ";") {
           return false;
@@ -19943,7 +19953,6 @@ var __async = (__this, __arguments, generator) => {
     __name(parseOrigin, "parseOrigin");
     function parseLocus(line) {
       result = createInitialSequence(options);
-      let locusName;
       let circular;
       let gbDivision;
       let date;
@@ -19954,7 +19963,7 @@ var __async = (__this, __arguments, generator) => {
         );
         addMessage("Import Warning: Locus line contains no values: " + line);
       }
-      locusName = lineArr[1];
+      const locusName = lineArr[1];
       for (let i2 = 1; i2 < lineArr.length; i2++) {
         if (lineArr[i2].match(/circular/gi)) {
           circular = true;
@@ -20107,10 +20116,10 @@ var __async = (__this, __arguments, generator) => {
     }
     __name(parseFeatureLocation, "parseFeatureLocation");
     function parseFeatureNote(line) {
-      let newLine, lineArr;
+      let newLine;
       newLine = line.trimLeft();
       newLine = newLine.replace(/^\/|"$/g, "");
-      lineArr = newLine.split(/="|=/);
+      const lineArr = newLine.split(/="|=/);
       let val2 = lineArr.slice(1).join("=");
       if (val2) {
         val2 = val2.replace(/\\/g, " ");
@@ -29916,13 +29925,10 @@ ${seq.sequence}
             });
           }
         });
-        const toRet = lodashExports.filter(
-          resultArray,
-          (r) => {
-            var _a3, _b3;
-            return (_b3 = (_a3 = r == null ? void 0 : r.parsedSequence) == null ? void 0 : _a3.sequence) == null ? void 0 : _b3.length;
-          }
-        );
+        const toRet = lodashExports.filter(resultArray, (r) => {
+          var _a3, _b3;
+          return (_b3 = (_a3 = r == null ? void 0 : r.parsedSequence) == null ? void 0 : _a3.sequence) == null ? void 0 : _b3.length;
+        });
         if (toRet.length)
           return toRet;
         return onFileParsed(resultArray);
@@ -30027,13 +30033,10 @@ ${seq.sequence}
             messages: ["Error while parsing JBEI format"]
           });
         }
-        const toRet = lodashExports.filter(
-          resultArray,
-          (r) => {
-            var _a3, _b3;
-            return (_b3 = (_a3 = r == null ? void 0 : r.parsedSequence) == null ? void 0 : _a3.sequence) == null ? void 0 : _b3.length;
-          }
-        );
+        const toRet = lodashExports.filter(resultArray, (r) => {
+          var _a3, _b3;
+          return (_b3 = (_a3 = r == null ? void 0 : r.parsedSequence) == null ? void 0 : _a3.sequence) == null ? void 0 : _b3.length;
+        });
         if (toRet.length)
           return toRet;
         return onFileParsed(resultArray);
@@ -32417,7 +32420,6 @@ ${seq.sequence}
     if (serSeq.sequence.symbols) {
       serSeq.sequence = serSeq.sequence.symbols.split("");
     }
-    let tmp;
     let dnaType;
     if (serSeq.isProtein) {
       dnaType = "";
@@ -32434,7 +32436,7 @@ ${seq.sequence}
     line += " ";
     line += StringUtil.lpad(String(serSeq.sequence.length), " ", 11);
     line += serSeq.isProtein ? " aa " : " bp ";
-    tmp = "";
+    const tmp = "";
     line += StringUtil.lpad(tmp, " ", 3);
     line += StringUtil.rpad(dnaType, " ", 6);
     line += "  ";

package/package.json

@@ -1,9 +1,8 @@
 {
   "name": "@teselagen/bio-parsers",
-  "version": "0.3.8",
-  "type": "commonjs",
+  "version": "0.3.10",
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.7",
+    "@teselagen/sequence-utils": "0.3.8",
     "@teselagen/range-utils": "0.3.7",
     "@gmod/gff": "^1.2.1",
     "buffer": "^6.0.3",

package/src/ab1ToJson.js

@@ -10,7 +10,7 @@ async function ab1ToJson(fileObj, options = {}) {
   returnVal.parsedSequence = {
     ...returnVal.parsedSequence,
     sequence: chromatogramData.baseCalls.join(""),
-    chromatogramData,
+    chromatogramData
   };
   return [returnVal];
 }
@@ -22,7 +22,6 @@ function abConverter(inputArrayBuffer) {
   const numElements = inputArrayBuffer.getInt32(18);
   const lastEntry = dirLocation + numElements * 28;
 
-
   this.getNumber = (inOffset, numEntries) => {
     const retArray = [];
     for (let counter = 0; counter < numEntries; counter += 1) {
@@ -49,8 +48,7 @@ function abConverter(inputArrayBuffer) {
     return retArray;
   };
 
-
-  this.getTagName = (inOffset) => {
+  this.getTagName = inOffset => {
     let name = "";
     for (let loopOffset = inOffset; loopOffset < inOffset + 4; loopOffset++) {
       name += String.fromCharCode(inputArrayBuffer.getInt8(loopOffset));
@@ -58,7 +56,7 @@ function abConverter(inputArrayBuffer) {
     return name;
   };
 
-  this.getDataTag = function(inTag) {
+  this.getDataTag = function (inTag) {
     let output;
     let curElem = dirLocation;
     do {
@@ -75,7 +73,7 @@ function abConverter(inputArrayBuffer) {
     return output;
   };
 
-  this.getTraceData = function() {
+  this.getTraceData = function () {
     const traceData = {};
     traceData.aTrace = this.getDataTag(tagDict.colorDataA);
     traceData.tTrace = this.getDataTag(tagDict.colorDataT);
@@ -84,10 +82,10 @@ function abConverter(inputArrayBuffer) {
     traceData.basePos = this.getDataTag(tagDict.peakLocations);
     traceData.baseCalls = this.getDataTag(tagDict.baseCalls2);
     traceData.qualNums = this.getDataTag(tagDict.qualNums);
-    if (traceData.qualNums ) { 
+    if (traceData.qualNums) {
       //tnr if we're only getting 1's and 0's as qualNums, that means that there weren't actual qual nums attached to the file
-      if (!traceData.qualNums.filter(q => (q!==1 && q!==0)).length)  {
-        delete traceData.qualNums
+      if (!traceData.qualNums.filter(q => q !== 1 && q !== 0).length) {
+        delete traceData.qualNums;
       }
     }
     return convertBasePosTraceToPerBpTrace(traceData);
@@ -116,11 +114,10 @@ const tagDict = {
   colorDataA: { tagName: "DATA", tagNum: 10, typeToReturn: "getShort" },
   colorDataT: { tagName: "DATA", tagNum: 11, typeToReturn: "getShort" },
   colorDataG: { tagName: "DATA", tagNum: 9, typeToReturn: "getShort" },
-  colorDataC: { tagName: "DATA", tagNum: 12, typeToReturn: "getShort" },
+  colorDataC: { tagName: "DATA", tagNum: 12, typeToReturn: "getShort" }
 };
 
-
-const correctionAmount = 3
+const correctionAmount = 3;
 // tnr: this function takes in chromData which has 4 traces and a basePos (which describes where in the trace the base call lands)
 // It "normalizes" that data into a baseTraces array so that each base has its own set of that data (having a per-base trace makes insertion/deletion/copy/paste actions all easier)
 function convertBasePosTraceToPerBpTrace(chromData) {
@@ -152,15 +149,15 @@ function convertBasePosTraceToPerBpTrace(chromData) {
       "gTrace",
       "cTrace"
       // eslint-disable-next-line no-loop-func
-    ].forEach((type) => {
+    ].forEach(type => {
       const traceForType = tracesForType[type];
       const traceData = chromData[type];
       for (let j = startPos; j < endPos + correctionAmount; j++) {
         traceForType.push(traceData[j] || 0);
       }
     });
-    if (i !== basePos.length-1) {
-      startPos = endPos+correctionAmount;
+    if (i !== basePos.length - 1) {
+      startPos = endPos + correctionAmount;
       nextBasePos = basePos[i + 2];
       setEndPos();
     }
@@ -172,6 +169,4 @@ function convertBasePosTraceToPerBpTrace(chromData) {
   };
 }
 
-export {
-  convertBasePosTraceToPerBpTrace
-}
+export { convertBasePosTraceToPerBpTrace };

package/src/anyToJson.js

@@ -132,12 +132,12 @@ async function anyToJson(fileContentStringOrFileObj, options) {
 
     //try to guess the file type based on the first non-whitespace char in the filestring
     if (firstChar === ">") {
-      parsersToTry = parsersToTry.sort((a) => {
+      parsersToTry = parsersToTry.sort(a => {
         if (a.name === "Fasta Parser") return -1;
         return 1;
       });
     } else if (firstChar === "L") {
-      parsersToTry = parsersToTry.sort((a) => {
+      parsersToTry = parsersToTry.sort(a => {
         if (a.name === "Genbank Parser") return -1;
         return 1;
       });
@@ -188,10 +188,10 @@ function getUtf8StringFromFile(file, { emulateBrowser } = {}) {
   const reader = new window.FileReader();
   reader.readAsText(file, "UTF-8");
   return new Promise((resolve, reject) => {
-    reader.onload = (evt) => {
+    reader.onload = evt => {
       resolve(evt.target.result);
     };
-    reader.onerror = (err) => {
+    reader.onerror = err => {
       console.error("err:", err);
       reject(err);
     };
@@ -212,12 +212,12 @@ function getUint8ArrayFromFile(file, { emulateBrowser } = {}) {
   reader.readAsArrayBuffer(file);
 
   return new Promise((resolve, reject) => {
-    reader.onload = (evt) => {
+    reader.onload = evt => {
       const arrayBuffer = evt.target.result;
       const bytes = new Uint8Array(arrayBuffer);
       resolve(bytes);
     };
-    reader.onerror = (err) => {
+    reader.onerror = err => {
       console.error("err:", err);
       reject(err);
     };

package/src/genbankToJson.js

@@ -66,18 +66,20 @@ function genbankToJson(string, options = {}) {
       const isKey = isKeyword(line);
 
       //only set a new LINETYPE in the case that we've encountered a key that warrants it.
-      if (key === "LOCUS") {
-        LINETYPE = key;
-      } else if (key === "REFERENCE") {
-        LINETYPE = key;
-      } else if (key === "FEATURES") {
-        LINETYPE = key;
-      } else if (key === "ORIGIN") {
-        LINETYPE = key;
-      } else if (key === "//") {
-        LINETYPE = key;
-      } else if (isKey === true) {
-        LINETYPE = key;
+      if (!isKeyRunon) {
+        if (key === "LOCUS") {
+          LINETYPE = key;
+        } else if (key === "REFERENCE") {
+          LINETYPE = key;
+        } else if (key === "FEATURES") {
+          LINETYPE = key;
+        } else if (key === "ORIGIN") {
+          LINETYPE = key;
+        } else if (key === "//") {
+          LINETYPE = key;
+        } else if (isKey === true) {
+          LINETYPE = key;
+        }
       }
 
       // IGNORE LINES: DO NOT EVEN PROCESS
@@ -237,10 +239,10 @@ function genbankToJson(string, options = {}) {
   // default sequence json has primers at the top level separate from features, e.g. parsedSequence: { primers: [ {}, {} ], features: [ {}, {} ] }
   // if options.primersAsFeatures is set to true, primers are included in features with type set to primer
 
-  results.forEach((result) => {
+  results.forEach(result => {
     if (result.success) {
       const sequence = result.parsedSequence;
-      sequence.features.forEach((feat) => {
+      sequence.features.forEach(feat => {
         if (feat.type === "primer") {
           feat.type = "primer_bind";
         }
@@ -248,10 +250,10 @@ function genbankToJson(string, options = {}) {
 
       if (!options.primersAsFeatures) {
         sequence.primers = sequence.features.filter(
-          (feat) => feat.type === "primer_bind"
+          feat => feat.type === "primer_bind"
         );
         sequence.features = sequence.features.filter(
-          (feat) => feat.type !== "primer_bind"
+          feat => feat.type !== "primer_bind"
         );
       }
     }
@@ -298,7 +300,6 @@ function genbankToJson(string, options = {}) {
 
   function parseLocus(line) {
     result = createInitialSequence(options);
-    let locusName;
     let circular;
 
     let gbDivision;
@@ -312,7 +313,7 @@ function genbankToJson(string, options = {}) {
       // TODO
       addMessage("Import Warning: Locus line contains no values: " + line);
     }
-    locusName = lineArr[1];
+    const locusName = lineArr[1];
 
     // Linear vs Circular?
     for (let i = 1; i < lineArr.length; i++) {
@@ -525,13 +526,13 @@ function genbankToJson(string, options = {}) {
   }
 
   function parseFeatureNote(line) {
-    let newLine, lineArr;
+    let newLine;
 
     // only trim file formatting spaces (i.e. the left ones)
     // spaces on the right are necessary (e.g. spacing between words, etc.)
     newLine = line.trimLeft();
     newLine = newLine.replace(/^\/|"$/g, "");
-    lineArr = newLine.split(/="|=/);
+    const lineArr = newLine.split(/="|=/);
 
     let val = lineArr.slice(1).join("=");
 

package/src/geneiousXmlToJson.js

@@ -40,7 +40,7 @@ async function geneiousXmlToJson(string, options) {
         messages: ["Error: XML is not valid geneious format"]
       });
     }
-    forEach(geneiousJsonMatches, (geneiousJson) => {
+    forEach(geneiousJsonMatches, geneiousJson => {
       const response = {
         parsedSequence: null,
         messages: [],
@@ -58,10 +58,7 @@ async function geneiousXmlToJson(string, options) {
         });
       }
     });
-    const toRet = filter(
-      resultArray,
-      (r) => r?.parsedSequence?.sequence?.length
-    );
+    const toRet = filter(resultArray, r => r?.parsedSequence?.sequence?.length);
     if (toRet.length) return toRet;
     return onFileParsed(resultArray);
   } catch (e) {
@@ -105,7 +102,7 @@ function parseGeneiousJson(geneiousJson) {
           searchWholeObjByNameSimple("maximumIndex", lastInterval) - 1;
         let locations;
         if (intervals.length > 1) {
-          locations = intervals.map((i) => {
+          locations = intervals.map(i => {
             const start = searchWholeObjByNameSimple("minimumIndex", i) - 1;
             const end = searchWholeObjByNameSimple("maximumIndex", i) - 1;
             return {