@teselagen/sequence-utils 0.3.7 → 0.3.9

package/src/getLeftAndRightOfSequenceInRangeGivenPosition.js

@@ -2,7 +2,7 @@ import {
   isPositionWithinRange,
   getSequenceWithinRange,
   normalizePositionByRangeLength,
-  isPositionCloserToRangeStartThanRangeEnd,
+  isPositionCloserToRangeStartThanRangeEnd
 } from "@teselagen/range-utils";
 
 export default function getLeftAndRightOfSequenceInRangeGivenPosition(
@@ -36,4 +36,4 @@ export default function getLeftAndRightOfSequenceInRangeGivenPosition(
     }
   }
   return result;
-};
+}

package/src/getLeftAndRightOfSequenceInRangeGivenPosition.test.js

@@ -1,5 +1,3 @@
-
-
 import chai from "chai";
 import cutSequenceByRestrictionEnzyme from "./cutSequenceByRestrictionEnzyme.js";
 import enzymeList from "./aliasedEnzymesByName";

package/src/getMassOfAaString.js

@@ -20,5 +20,8 @@ export default function getMassOfAaString(
   if (divideByThree) {
     sumMass /= 3;
   }
+  if (aaString.length > 0) {
+    sumMass = sumMass + 18.0153;
+  }
   return Math.round(sumMass * 10 ** numsAfterDecimal) / 10 ** numsAfterDecimal;
-};
+}

package/src/getMassofAaString.test.js

@@ -5,14 +5,15 @@ describe("getMassOfAaString", () => {
   it("an empty string has a mass of 0", () => {
     assert.equal(getMassOfAaString(""), 0);
   });
-  it("A string with one amino acids returns the correct results", () => {
-    assert.equal(getMassOfAaString("T"), 119.1);
-    assert.equal(getMassOfAaString("A"), 89.1);
-    assert.equal(getMassOfAaString("F"), 165.2);
+  it("string with one amino acid returns the correct results", () => {
+    assert.equal(getMassOfAaString("T"), 119.12);
+    assert.equal(getMassOfAaString("A"), 89.09);
+    assert.equal(getMassOfAaString("F"), 165.19);
   });
-  it("A string a long string of amino acids returns the correct results", () => {
-    assert.equal(getMassOfAaString("TAGATAFPFPFPA"), 1510.6);
-    assert.equal(getMassOfAaString("TFPMAV"), 754.8);
-    assert.equal(getMassOfAaString("TFPMAVTAGATAFPFPFPA"), 2265.4);
+  it("a long string of amino acids returns the correct results", () => {
+    assert.equal(getMassOfAaString("TAGATAFPFPFPA"), 1294.45);
+    assert.equal(getMassOfAaString("TFPMAV"), 664.81);
+    assert.equal(getMassOfAaString("TFPMAVTAGATAFPFPFPA"), 1941.25);
+    assert.equal(getMassOfAaString("ARNDCEQGHILKMFPSTWYV"), 2395.71);
   });
 });

package/src/getOrfsFromSequence.js

@@ -1,7 +1,6 @@
 import shortid from "shortid";
 import getReverseComplementSequenceString from "./getReverseComplementSequenceString";
 
-
 /**
  * @private
  * Finds ORFs in a given DNA forward in a given frame.
@@ -121,4 +120,4 @@ export default function getOrfsFromSequence(options) {
     return false;
   });
   return nonDuplicatedOrfRanges;
-};
+}

package/src/getOrfsFromSequence.test.js

@@ -1,6 +1,4 @@
-
-
-import {expect} from "chai";
+import { expect } from "chai";
 
 import getOrfsFromSequence from "./getOrfsFromSequence.js";
 // getOrfsFromSequence(frame, sequence, minimumOrfSize, forward, circular)

package/src/getOverlapBetweenTwoSequences.js

@@ -1,4 +1,4 @@
-import {modulatePositionByRange} from "@teselagen/range-utils";
+import { modulatePositionByRange } from "@teselagen/range-utils";
 
 /**
  * This function gets the overlapping of one sequence to another based on sequence equality.
@@ -10,7 +10,7 @@ import {modulatePositionByRange} from "@teselagen/range-utils";
  */
 export default function getOverlapBetweenTwoSequences(
   sequenceToFind,
-  sequenceToSearchIn,
+  sequenceToSearchIn
 ) {
   sequenceToSearchIn = sequenceToSearchIn.toLowerCase();
   sequenceToFind = sequenceToFind.toLowerCase();
@@ -27,4 +27,4 @@ export default function getOverlapBetweenTwoSequences(
   } else {
     return null;
   }
-};
+}

package/src/getOverlapBetweenTwoSequences.test.js

@@ -1,4 +1,4 @@
-import {expect} from "chai";
+import { expect } from "chai";
 import getOverlapBetweenTwoSequences from "./getOverlapBetweenTwoSequences.js";
 describe("getOverlapBetweenTwoSequences", () => {
   it("should get the range overlap given a seq and a seq to search in", () => {

package/src/getPossiblePartsFromSequenceAndEnzymes.js

@@ -1,5 +1,5 @@
 import getComplementSequenceString from "./getComplementSequenceString";
-import {normalizePositionByRangeLength} from "@teselagen/range-utils";
+import { normalizePositionByRangeLength } from "@teselagen/range-utils";
 import cutSequenceByRestrictionEnzyme from "./cutSequenceByRestrictionEnzyme";
 
 export default function getPossiblePartsFromSequenceAndEnzyme(
@@ -67,7 +67,7 @@ export default function getPossiblePartsFromSequenceAndEnzyme(
     });
     return parts;
   }
-};
+}
 
 function getPartBetweenEnzymesWithInclusiveOverhangs(cut1, cut2, seqLen) {
   const firstCutOffset = getEnzymeRelativeOffset(cut1.restrictionEnzyme);

package/src/getReverseAminoAcidStringFromSequenceString.js

@@ -17,4 +17,4 @@ export default function getReverseAminoAcidStringFromSequenceString(
   });
   aaString = aaArray.join("");
   return aaString;
-};
+}

package/src/getReverseComplementAminoAcidStringFromSequenceString.js

@@ -1,7 +1,10 @@
+import getAminoAcidStringFromSequenceString from "./getAminoAcidStringFromSequenceString";
+import getReverseComplementSequenceString from "./getReverseComplementSequenceString";
 
-import getAminoAcidStringFromSequenceString from './getAminoAcidStringFromSequenceString';
-import getReverseComplementSequenceString from './getReverseComplementSequenceString';
-
-export default function getReverseComplementAminoAcidStringFromSequenceString(sequenceString) {
-  return getAminoAcidStringFromSequenceString(getReverseComplementSequenceString(sequenceString))
-};
+export default function getReverseComplementAminoAcidStringFromSequenceString(
+  sequenceString
+) {
+  return getAminoAcidStringFromSequenceString(
+    getReverseComplementSequenceString(sequenceString)
+  );
+}

package/src/getReverseComplementAnnotation.js

@@ -20,4 +20,4 @@ export default function getReverseComplementAnnotation(
     forward: !annotation.forward,
     strand: annotation.strand === 1 ? -1 : 1
   });
-};
+}

package/src/getReverseComplementSequenceAndAnnotations.js

@@ -1,10 +1,9 @@
 import getReverseComplementSequenceString from "./getReverseComplementSequenceString";
 import getReverseComplementAnnotation from "./getReverseComplementAnnotation";
 import { annotationTypes } from "./annotationTypes";
-import {map} from "lodash";
+import { map } from "lodash";
 import tidyUpSequenceData from "./tidyUpSequenceData";
 
-
 import getSequenceDataBetweenRange from "./getSequenceDataBetweenRange";
 
 // ac.throw([ac.string,ac.bool],arguments);
@@ -35,4 +34,4 @@ export default function getReverseComplementSequenceAndAnnoations(
     }, {})
   );
   return tidyUpSequenceData(newSeqObj, options);
-};
+}

package/src/getReverseComplementSequenceString.js

@@ -1,6 +1,5 @@
 import DNAComplementMap from "./DNAComplementMap";
 
-
 // ac.throw([ac.string,ac.bool],arguments);
 export default function getReverseComplementSequenceString(sequence) {
   // ac.throw([ac.string],arguments);
@@ -14,4 +13,4 @@ export default function getReverseComplementSequenceString(sequence) {
     reverseComplementSequenceString += revChar;
   }
   return reverseComplementSequenceString;
-};
+}

package/src/getReverseSequenceString.js

@@ -9,4 +9,4 @@ export default function getReverseSequenceString(sequence) {
     reverseSequenceString += revChar;
   }
   return reverseSequenceString;
-};
+}

package/src/getSequenceDataBetweenRange.js

@@ -1,8 +1,11 @@
-import {flatMap, extend, forEach, startCase} from "lodash";
-import {getRangeLength} from "@teselagen/range-utils";
+import { flatMap, extend, forEach, startCase } from "lodash";
+import { getRangeLength } from "@teselagen/range-utils";
 import convertDnaCaretPositionOrRangeToAa from "./convertDnaCaretPositionOrRangeToAA";
 import insertSequenceDataAtPosition from "./insertSequenceDataAtPosition";
-import {getSequenceWithinRange, getZeroedRangeOverlaps} from "@teselagen/range-utils";
+import {
+  getSequenceWithinRange,
+  getZeroedRangeOverlaps
+} from "@teselagen/range-utils";
 import tidyUpSequenceData from "./tidyUpSequenceData";
 import { annotationTypes } from "./annotationTypes";
 
@@ -79,7 +82,7 @@ export default function getSequenceDataBetweenRange(
   }
 
   return tidyUpSequenceData(seqDataToReturn, options);
-};
+}
 
 function getAnnotationsBetweenRange(
   annotationsToBeAdjusted,

package/src/getSequenceDataBetweenRange.test.js

@@ -1,6 +1,5 @@
 //tnr: half finished test.
 
-
 import chai from "chai";
 import chaiSubset from "chai-subset";
 

package/src/getVirtualDigest.js

@@ -1,8 +1,11 @@
 //UNDER CONSTRUCTION
 
-import {get} from "lodash";
+import { get } from "lodash";
 
-import {normalizePositionByRangeLength, getRangeLength} from "@teselagen/range-utils";
+import {
+  normalizePositionByRangeLength,
+  getRangeLength
+} from "@teselagen/range-utils";
 
 export default function getVirtualDigest({
   cutsites,
@@ -99,7 +102,7 @@ export default function getVirtualDigest({
     fragments,
     overlappingEnzymes
   };
-};
+}
 
 function addSizeIdName(frag, sequenceLength) {
   const size = getRangeLength(

package/src/guessIfSequenceIsDnaAndNotProtein.js

@@ -1,4 +1,4 @@
-import {ambiguous_dna_letters} from "./bioData";
+import { ambiguous_dna_letters } from "./bioData";
 
 export default function guessIfSequenceIsDnaAndNotProtein(seq, options = {}) {
   const { threshold = 0.9, loose } = options;
@@ -30,4 +30,4 @@ export default function guessIfSequenceIsDnaAndNotProtein(seq, options = {}) {
     return true; //it is DNA
   }
   return false; //it is protein
-};
+}

package/src/index.js

@@ -1,19 +1,19 @@
 import {
   autoAnnotate,
   convertApELikeRegexToRegex,
-  convertProteinSeqToDNAIupac,
-} from './autoAnnotate';
+  convertProteinSeqToDNAIupac
+} from "./autoAnnotate";
 
 import {
   genbankFeatureTypes,
   getFeatureToColorMap,
   getFeatureTypes,
-  getMergedFeatureMap,
-} from './featureTypesAndColors';
+  getMergedFeatureMap
+} from "./featureTypesAndColors";
 
-export * from './computeDigestFragments';
-export * from './diffUtils';
-export * from './annotationTypes';
+export * from "./computeDigestFragments";
+export * from "./diffUtils";
+export * from "./annotationTypes";
 
 /* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ */
 //tnr: these are deprecated exports and should no longer be used!
@@ -25,82 +25,81 @@ export {
   genbankFeatureTypes,
   getMergedFeatureMap,
   FeatureTypes,
-  featureColors,
+  featureColors
 };
 
 /* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ */
 export { autoAnnotate };
 export { convertApELikeRegexToRegex };
 export { convertProteinSeqToDNAIupac };
-export * as bioData from './bioData';
-export { default as getAllInsertionsInSeqReads } from './getAllInsertionsInSeqReads';
-export { default as annotateSingleSeq } from './annotateSingleSeq';
-export { default as getDegenerateDnaStringFromAAString } from './getDegenerateDnaStringFromAAString';
-export { default as getDegenerateRnaStringFromAAString } from './getDegenerateRnaStringFromAAString';
-export { default as getVirtualDigest } from './getVirtualDigest';
-export { default as isEnzymeType2S } from './isEnzymeType2S';
-export { default as insertGapsIntoRefSeq } from './insertGapsIntoRefSeq';
-export { default as adjustBpsToReplaceOrInsert } from './adjustBpsToReplaceOrInsert';
-export { default as calculatePercentGC } from './calculatePercentGC';
-export { default as calculateTm } from './calculateTm';
-export { default as cutSequenceByRestrictionEnzyme } from './cutSequenceByRestrictionEnzyme';
-export { default as deleteSequenceDataAtRange } from './deleteSequenceDataAtRange';
-export { default as DNAComplementMap } from './DNAComplementMap';
-export { default as doesEnzymeChopOutsideOfRecognitionSite } from './doesEnzymeChopOutsideOfRecognitionSite';
-export { default as aliasedEnzymesByName } from './aliasedEnzymesByName';
-export { default as defaultEnzymesByName } from './defaultEnzymesByName';
-export { default as generateSequenceData } from './generateSequenceData';
-export { default as generateAnnotations } from './generateAnnotations';
-export { default as filterAminoAcidSequenceString } from './filterAminoAcidSequenceString';
-export { default as filterSequenceString } from './filterSequenceString';
-export { default as findNearestRangeOfSequenceOverlapToPosition } from './findNearestRangeOfSequenceOverlapToPosition';
-export { default as findOrfsInPlasmid } from './findOrfsInPlasmid';
-export { default as findSequenceMatches } from './findSequenceMatches';
-export { default as getAminoAcidDataForEachBaseOfDna } from './getAminoAcidDataForEachBaseOfDna';
-export { default as getAminoAcidFromSequenceTriplet } from './getAminoAcidFromSequenceTriplet';
-export { default as getAminoAcidStringFromSequenceString } from './getAminoAcidStringFromSequenceString';
-export { default as getCodonRangeForAASliver } from './getCodonRangeForAASliver';
-export { default as getComplementAminoAcidStringFromSequenceString } from './getComplementAminoAcidStringFromSequenceString';
-export { default as getComplementSequenceAndAnnotations } from './getComplementSequenceAndAnnotations';
-export { default as getComplementSequenceString } from './getComplementSequenceString';
-export { default as getCutsitesFromSequence } from './getCutsitesFromSequence';
-export { default as getCutsiteType } from './getCutsiteType';
-export { default as getInsertBetweenVals } from './getInsertBetweenVals';
-export { default as getLeftAndRightOfSequenceInRangeGivenPosition } from './getLeftAndRightOfSequenceInRangeGivenPosition';
-export { default as getOrfsFromSequence } from './getOrfsFromSequence';
-export { default as getOverlapBetweenTwoSequences } from './getOverlapBetweenTwoSequences';
-export { default as getPossiblePartsFromSequenceAndEnzymes } from './getPossiblePartsFromSequenceAndEnzymes';
-export { default as getReverseAminoAcidStringFromSequenceString } from './getReverseAminoAcidStringFromSequenceString';
-export { default as getReverseComplementAminoAcidStringFromSequenceString } from './getReverseComplementAminoAcidStringFromSequenceString';
-export { default as getReverseComplementAnnotation } from './getReverseComplementAnnotation';
-export { default as getReverseComplementSequenceAndAnnotations } from './getReverseComplementSequenceAndAnnotations';
-export { default as getReverseComplementSequenceString } from './getReverseComplementSequenceString';
-export { default as getReverseSequenceString } from './getReverseSequenceString';
-export { default as getSequenceDataBetweenRange } from './getSequenceDataBetweenRange';
-export { default as guessIfSequenceIsDnaAndNotProtein } from './guessIfSequenceIsDnaAndNotProtein';
-export { default as insertSequenceDataAtPosition } from './insertSequenceDataAtPosition';
-export { default as insertSequenceDataAtPositionOrRange } from './insertSequenceDataAtPositionOrRange';
-export { default as mapAnnotationsToRows } from './mapAnnotationsToRows';
-export { default as prepareCircularViewData } from './prepareCircularViewData';
-export { default as prepareRowData } from './prepareRowData';
-export { default as proteinAlphabet } from './proteinAlphabet';
-export { default as rotateSequenceDataToPosition } from './rotateSequenceDataToPosition';
-export { default as rotateBpsToPosition } from './rotateBpsToPosition';
-export { default as threeLetterSequenceStringToAminoAcidMap } from './threeLetterSequenceStringToAminoAcidMap';
-export { default as tidyUpSequenceData } from './tidyUpSequenceData';
-export { default as tidyUpAnnotation } from './tidyUpAnnotation';
-export { default as condensePairwiseAlignmentDifferences } from './condensePairwiseAlignmentDifferences';
-export { default as addGapsToSeqReads } from './addGapsToSeqReads';
-export { default as calculateNebTm } from './calculateNebTm';
-export { default as calculateNebTa } from './calculateNebTa';
-export { default as getDigestFragmentsForCutsites } from './getDigestFragmentsForCutsites';
-export { default as getDigestFragmentsForRestrictionEnzymes } from './getDigestFragmentsForRestrictionEnzymes';
-export { default as convertDnaCaretPositionOrRangeToAA } from './convertDnaCaretPositionOrRangeToAA';
-export { default as convertAACaretPositionOrRangeToDna } from './convertAACaretPositionOrRangeToDna';
-export { default as aminoAcidToDegenerateDnaMap } from './aminoAcidToDegenerateDnaMap';
-export { default as aminoAcidToDegenerateRnaMap } from './aminoAcidToDegenerateRnaMap';
-export { default as degenerateDnaToAminoAcidMap } from './degenerateDnaToAminoAcidMap';
-export { default as degenerateRnaToAminoAcidMap } from './degenerateRnaToAminoAcidMap';
-export { default as getMassOfAaString } from './getMassOfAaString';
-export { default as shiftAnnotationsByLen } from './shiftAnnotationsByLen';
-export { default as adjustAnnotationsToInsert } from './adjustAnnotationsToInsert';
+export * as bioData from "./bioData";
+export { default as getAllInsertionsInSeqReads } from "./getAllInsertionsInSeqReads";
+export { default as annotateSingleSeq } from "./annotateSingleSeq";
+export { default as getDegenerateDnaStringFromAAString } from "./getDegenerateDnaStringFromAAString";
+export { default as getDegenerateRnaStringFromAAString } from "./getDegenerateRnaStringFromAAString";
+export { default as getVirtualDigest } from "./getVirtualDigest";
+export { default as isEnzymeType2S } from "./isEnzymeType2S";
+export { default as insertGapsIntoRefSeq } from "./insertGapsIntoRefSeq";
+export { default as adjustBpsToReplaceOrInsert } from "./adjustBpsToReplaceOrInsert";
+export { default as calculatePercentGC } from "./calculatePercentGC";
+export { default as calculateTm } from "./calculateTm";
+export { default as cutSequenceByRestrictionEnzyme } from "./cutSequenceByRestrictionEnzyme";
+export { default as deleteSequenceDataAtRange } from "./deleteSequenceDataAtRange";
+export { default as DNAComplementMap } from "./DNAComplementMap";
+export { default as doesEnzymeChopOutsideOfRecognitionSite } from "./doesEnzymeChopOutsideOfRecognitionSite";
+export { default as aliasedEnzymesByName } from "./aliasedEnzymesByName";
+export { default as defaultEnzymesByName } from "./defaultEnzymesByName";
+export { default as generateSequenceData } from "./generateSequenceData";
+export { default as generateAnnotations } from "./generateAnnotations";
+export { default as filterSequenceString } from "./filterSequenceString";
+export { default as findNearestRangeOfSequenceOverlapToPosition } from "./findNearestRangeOfSequenceOverlapToPosition";
+export { default as findOrfsInPlasmid } from "./findOrfsInPlasmid";
+export { default as findSequenceMatches } from "./findSequenceMatches";
+export { default as getAminoAcidDataForEachBaseOfDna } from "./getAminoAcidDataForEachBaseOfDna";
+export { default as getAminoAcidFromSequenceTriplet } from "./getAminoAcidFromSequenceTriplet";
+export { default as getAminoAcidStringFromSequenceString } from "./getAminoAcidStringFromSequenceString";
+export { default as getCodonRangeForAASliver } from "./getCodonRangeForAASliver";
+export { default as getComplementAminoAcidStringFromSequenceString } from "./getComplementAminoAcidStringFromSequenceString";
+export { default as getComplementSequenceAndAnnotations } from "./getComplementSequenceAndAnnotations";
+export { default as getComplementSequenceString } from "./getComplementSequenceString";
+export { default as getCutsitesFromSequence } from "./getCutsitesFromSequence";
+export { default as getCutsiteType } from "./getCutsiteType";
+export { default as getInsertBetweenVals } from "./getInsertBetweenVals";
+export { default as getLeftAndRightOfSequenceInRangeGivenPosition } from "./getLeftAndRightOfSequenceInRangeGivenPosition";
+export { default as getOrfsFromSequence } from "./getOrfsFromSequence";
+export { default as getOverlapBetweenTwoSequences } from "./getOverlapBetweenTwoSequences";
+export { default as getPossiblePartsFromSequenceAndEnzymes } from "./getPossiblePartsFromSequenceAndEnzymes";
+export { default as getReverseAminoAcidStringFromSequenceString } from "./getReverseAminoAcidStringFromSequenceString";
+export { default as getReverseComplementAminoAcidStringFromSequenceString } from "./getReverseComplementAminoAcidStringFromSequenceString";
+export { default as getReverseComplementAnnotation } from "./getReverseComplementAnnotation";
+export { default as getReverseComplementSequenceAndAnnotations } from "./getReverseComplementSequenceAndAnnotations";
+export { default as getReverseComplementSequenceString } from "./getReverseComplementSequenceString";
+export { default as getReverseSequenceString } from "./getReverseSequenceString";
+export { default as getSequenceDataBetweenRange } from "./getSequenceDataBetweenRange";
+export { default as guessIfSequenceIsDnaAndNotProtein } from "./guessIfSequenceIsDnaAndNotProtein";
+export { default as insertSequenceDataAtPosition } from "./insertSequenceDataAtPosition";
+export { default as insertSequenceDataAtPositionOrRange } from "./insertSequenceDataAtPositionOrRange";
+export { default as mapAnnotationsToRows } from "./mapAnnotationsToRows";
+export { default as prepareCircularViewData } from "./prepareCircularViewData";
+export { default as prepareRowData } from "./prepareRowData";
+export { default as proteinAlphabet } from "./proteinAlphabet";
+export { default as rotateSequenceDataToPosition } from "./rotateSequenceDataToPosition";
+export { default as rotateBpsToPosition } from "./rotateBpsToPosition";
+export { default as threeLetterSequenceStringToAminoAcidMap } from "./threeLetterSequenceStringToAminoAcidMap";
+export { default as tidyUpSequenceData } from "./tidyUpSequenceData";
+export { default as tidyUpAnnotation } from "./tidyUpAnnotation";
+export { default as condensePairwiseAlignmentDifferences } from "./condensePairwiseAlignmentDifferences";
+export { default as addGapsToSeqReads } from "./addGapsToSeqReads";
+export { default as calculateNebTm } from "./calculateNebTm";
+export { default as calculateNebTa } from "./calculateNebTa";
+export { default as getDigestFragmentsForCutsites } from "./getDigestFragmentsForCutsites";
+export { default as getDigestFragmentsForRestrictionEnzymes } from "./getDigestFragmentsForRestrictionEnzymes";
+export { default as convertDnaCaretPositionOrRangeToAA } from "./convertDnaCaretPositionOrRangeToAA";
+export { default as convertAACaretPositionOrRangeToDna } from "./convertAACaretPositionOrRangeToDna";
+export { default as aminoAcidToDegenerateDnaMap } from "./aminoAcidToDegenerateDnaMap";
+export { default as aminoAcidToDegenerateRnaMap } from "./aminoAcidToDegenerateRnaMap";
+export { default as degenerateDnaToAminoAcidMap } from "./degenerateDnaToAminoAcidMap";
+export { default as degenerateRnaToAminoAcidMap } from "./degenerateRnaToAminoAcidMap";
+export { default as getMassOfAaString } from "./getMassOfAaString";
+export { default as shiftAnnotationsByLen } from "./shiftAnnotationsByLen";
+export { default as adjustAnnotationsToInsert } from "./adjustAnnotationsToInsert";

package/src/index.test.js

@@ -3,8 +3,7 @@ import fs from "fs";
 
 describe("index.js", () => {
   it(`should export all functions defined`, () => {
-    return new Promise((resolve) => {
-
+    return new Promise(resolve => {
       fs.readdir(__dirname, (err, files) => {
         let passes = true;
         files.forEach(file => {
@@ -29,10 +28,12 @@ describe("index.js", () => {
           }
         });
         if (!passes) {
-          throw new Error("Please make sure to export (or ignore) each file! Update index.js to export the file");
+          throw new Error(
+            "Please make sure to export (or ignore) each file! Update index.js to export the file"
+          );
         }
         resolve();
       });
-    })
+    });
   });
 });

package/src/insertGapsIntoRefSeq.js

@@ -21,7 +21,7 @@ export default function insertGapsIntoRefSeq(refSeq, seqReads) {
   }
   // refSeqWithGaps is a string "GGGA--GA-C--ACC"
   return refSeqWithGaps.join("");
-};
+}
 
 // allInsertionsInSeqReads.forEach(insertion => {
 //       // adding gap at the bp pos of insertion

package/src/insertSequenceDataAtPosition.test.js

@@ -1,6 +1,5 @@
 //tnr: half finished test.
 
-
 import chai from "chai";
 import chaiSubset from "chai-subset";
 
@@ -40,7 +39,10 @@ describe("insertSequenceData", () => {
         {
           start: 0,
           end: 9,
-          locations: [{ start: 0, end: 3 }, { start: 5, end: 9 }]
+          locations: [
+            { start: 0, end: 3 },
+            { start: 5, end: 9 }
+          ]
         }
       ]
     };

package/src/insertSequenceDataAtPositionOrRange.js

@@ -1,10 +1,10 @@
-import {getRangeLength} from "@teselagen/range-utils";
-import {map, cloneDeep} from "lodash";
+import { getRangeLength } from "@teselagen/range-utils";
+import { map, cloneDeep } from "lodash";
 import convertDnaCaretPositionOrRangeToAa from "./convertDnaCaretPositionOrRangeToAA";
 import rotateSequenceDataToPosition from "./rotateSequenceDataToPosition";
-import {adjustRangeToDeletionOfAnotherRange} from "@teselagen/range-utils";
+import { adjustRangeToDeletionOfAnotherRange } from "@teselagen/range-utils";
 import tidyUpSequenceData from "./tidyUpSequenceData";
-import {modifiableTypes} from "./annotationTypes";
+import { modifiableTypes } from "./annotationTypes";
 import adjustBpsToReplaceOrInsert from "./adjustBpsToReplaceOrInsert";
 import adjustAnnotationsToInsert from "./adjustAnnotationsToInsert";
 
@@ -164,7 +164,7 @@ export default function insertSequenceDataAtPositionOrRange(
     );
   }
   return newSequenceData;
-};
+}
 
 function adjustAnnotationsToDelete(annotationsToBeAdjusted, range, maxLength) {
   return map(annotationsToBeAdjusted, annotation => {

package/src/insertSequenceDataAtPositionOrRange.test.js

@@ -1,9 +1,8 @@
 //tnr: half finished test.
 
-
 import chai from "chai";
 
-import {getRangeLength} from "@teselagen/range-utils";
+import { getRangeLength } from "@teselagen/range-utils";
 import assert from "assert";
 import chaiSubset from "chai-subset";
 
@@ -452,17 +451,7 @@ describe("insertSequenceData", () => {
     postInsertSeq.chromatogramData.baseCalls.length.should.equal(8);
     postInsertSeq.chromatogramData.baseTraces.length.should.equal(8);
     postInsertSeq.chromatogramData.baseTraces[4].aTrace.should.deep.equal([
-      0,
-      0,
-      0,
-      0,
-      0,
-      0,
-      0,
-      0,
-      0,
-      0,
-      0
+      0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
     ]);
   });
   it("properly inserts into chromatogramData, keeping the chromatogramData intact if the insert length is the same length as the selection range", () => {
@@ -538,10 +527,7 @@ describe("insertSequenceData", () => {
     ]);
     postInsertSeq.chromatogramData.baseTraces.length.should.equal(7);
     postInsertSeq.chromatogramData.baseTraces[4].aTrace.should.deep.equal([
-      0,
-      2,
-      6,
-      8
+      0, 2, 6, 8
     ]);
   });
 });

package/src/isEnzymeType2S.js

@@ -1,3 +1,3 @@
 export default function isEnzymeType2S(e) {
   return e.site.length < e.topSnipOffset || e.site.length < e.bottomSnipOffset;
-};
+}

package/src/mapAnnotationsToRows.js

@@ -1,8 +1,8 @@
-import {each, forEach, startsWith, filter} from "lodash";
+import { each, forEach, startsWith, filter } from "lodash";
 
 import {
   getYOffsetForPotentiallyCircularRange,
-  splitRangeIntoTwoPartsIfItIsCircular,
+  splitRangeIntoTwoPartsIfItIsCircular
 } from "@teselagen/range-utils";
 
 export default function mapAnnotationsToRows(
@@ -72,7 +72,7 @@ export default function mapAnnotationsToRows(
     );
   });
   return annotationsToRowsMap;
-};
+}
 
 function mapAnnotationToRows({
   annotation,

package/src/mapAnnotationsToRows.test.js

@@ -1,8 +1,6 @@
-
-
 import chai from "chai";
 
-import {expect} from "chai";
+import { expect } from "chai";
 import chaiSubset from "chai-subset";
 import mapAnnotationsToRows from "./mapAnnotationsToRows.js";
 chai.use(chaiSubset);