@teselagen/bio-parsers 0.3.8 → 0.3.9

package/index.mjs

@@ -6281,8 +6281,8 @@ function getOverlapsOfPotentiallyCircularRanges(rangeA, rangeB, maxRangeLength,
     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
@@ -6294,7 +6294,7 @@ function getOverlapsOfPotentiallyCircularRanges(rangeA, rangeB, maxRangeLength,
   });
   if (joinIfPossible && normalizedRangeA.length === 2 && normalizedRangeB.length === 2 && maxRangeLength) {
     const joinedOverlap = {};
-    overlaps = lodashExports.flatMap(overlaps, (o, i) => {
+    overlaps = lodashExports.flatMap(overlaps, (o) => {
       if (o.start === 0) {
         joinedOverlap.end = o.end;
         return [];
@@ -6392,12 +6392,14 @@ function trimRangeByAnotherRange(rangeToBeTrimmed, trimmingRange, sequenceLength
     });
     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)
     ;
@@ -6447,8 +6449,14 @@ function normalizePositionByRangeLength(pPosition, sequenceLength, isInBetweenPo
 __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");
@@ -11389,13 +11397,13 @@ function coerceLocation({
     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(
@@ -11408,9 +11416,9 @@ __name(coerceLocation, "coerceLocation");
 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) {
@@ -11608,7 +11616,7 @@ const calcTmMethods = {
   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) {
@@ -19759,18 +19767,20 @@ function genbankToJson(string, options = {}) {
       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;
@@ -19939,7 +19949,6 @@ function genbankToJson(string, options = {}) {
   __name(parseOrigin, "parseOrigin");
   function parseLocus(line) {
     result = createInitialSequence(options);
-    let locusName;
     let circular;
     let gbDivision;
     let date;
@@ -19950,7 +19959,7 @@ function genbankToJson(string, options = {}) {
       );
       addMessage("Import Warning: Locus line contains no values: " + line);
     }
-    locusName = lineArr[1];
+    const locusName = lineArr[1];
     for (let i = 1; i < lineArr.length; i++) {
       if (lineArr[i].match(/circular/gi)) {
         circular = true;
@@ -20103,10 +20112,10 @@ function genbankToJson(string, options = {}) {
   }
   __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, " ");
@@ -29912,13 +29921,10 @@ function geneiousXmlToJson(string, options) {
           });
         }
       });
-      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);
@@ -30023,13 +30029,10 @@ function jbeiXmlToJson(string, options) {
           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);
@@ -32413,7 +32416,6 @@ function createGenbankLocus(serSeq, options) {
   if (serSeq.sequence.symbols) {
     serSeq.sequence = serSeq.sequence.symbols.split("");
   }
-  let tmp;
   let dnaType;
   if (serSeq.isProtein) {
     dnaType = "";
@@ -32430,7 +32432,7 @@ function createGenbankLocus(serSeq, options) {
   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/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");
@@ -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

@@ -1,7 +1,6 @@
 {
   "name": "@teselagen/bio-parsers",
-  "version": "0.3.8",
-  "type": "commonjs",
+  "version": "0.3.9",
   "dependencies": {
     "@teselagen/sequence-utils": "0.3.7",
     "@teselagen/range-utils": "0.3.7",

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("=");