@teselagen/sequence-utils 0.3.27 → 0.3.28-beta.1

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Files changed (7) hide show
  1. package/getAminoAcidDataForEachBaseOfDna.d.ts +1 -1
  2. package/index.cjs +9 -7
  3. package/index.js +9 -7
  4. package/index.umd.cjs +9 -7
  5. package/package.json +9 -2
  6. package/src/defaultEnzymesByName.js +1 -0
  7. package/src/getAminoAcidDataForEachBaseOfDna.js +12 -10
package/getAminoAcidDataForEachBaseOfDna.d.ts CHANGED
@@ -24,7 +24,7 @@ export default function getAminoAcidDataForEachBaseOfDna(originalSequenceString:
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  aminoAcid: null;
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  positionInCodon: null;
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  aminoAcidIndex: null;
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- sequenceIndex: number;
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+ sequenceIndex: any;
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  codonRange: null;
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  fullCodon: null;
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  })[];
package/index.cjs CHANGED
@@ -8715,12 +8715,18 @@ function getAminoAcidDataForEachBaseOfDna(originalSequenceString, forward, optio
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  let positionInCodon = 0;
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  for (let i = 0; i < basesRead; i++) {
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  const posInCds = i + index;
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+ const sequenceIndex = codonPositionsInCDS.includes(posInCds) ? absoluteCodonPositions[codonPositionsInCDS.indexOf(posInCds)] : positionInCdsToPositionInMainSequence(
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+ posInCds,
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+ forward,
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+ translationRange,
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+ originalSequenceStringLength
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+ );
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  if (codonPositionsInCDS.includes(posInCds)) {
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  aminoAcidDataForEachBaseOfDNA.push({
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  aminoAcid,
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  positionInCodon,
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  aminoAcidIndex,
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- sequenceIndex: absoluteCodonPositions[i],
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+ sequenceIndex,
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  codonRange,
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  fullCodon: codonPositionsInCDS.length === 3
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  });
@@ -8730,12 +8736,7 @@ function getAminoAcidDataForEachBaseOfDna(originalSequenceString, forward, optio
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  aminoAcid: null,
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  positionInCodon: null,
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  aminoAcidIndex: null,
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- sequenceIndex: positionInCdsToPositionInMainSequence(
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- posInCds,
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- forward,
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- translationRange,
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- originalSequenceStringLength
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- ),
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+ sequenceIndex,
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  codonRange: null,
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  fullCodon: null
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  });
@@ -17427,6 +17428,7 @@ const defaultEnzymes = [
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  "banii",
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  "bari",
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  "baui",
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+ "bbsi",
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  "bbvbi",
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  "bcni",
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  "bcoki",
package/index.js CHANGED
@@ -8713,12 +8713,18 @@ function getAminoAcidDataForEachBaseOfDna(originalSequenceString, forward, optio
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  let positionInCodon = 0;
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  for (let i = 0; i < basesRead; i++) {
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  const posInCds = i + index;
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+ const sequenceIndex = codonPositionsInCDS.includes(posInCds) ? absoluteCodonPositions[codonPositionsInCDS.indexOf(posInCds)] : positionInCdsToPositionInMainSequence(
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+ posInCds,
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+ forward,
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+ translationRange,
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+ originalSequenceStringLength
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+ );
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  if (codonPositionsInCDS.includes(posInCds)) {
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  aminoAcidDataForEachBaseOfDNA.push({
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  aminoAcid,
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  positionInCodon,
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  aminoAcidIndex,
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- sequenceIndex: absoluteCodonPositions[i],
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+ sequenceIndex,
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  codonRange,
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  fullCodon: codonPositionsInCDS.length === 3
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  });
@@ -8728,12 +8734,7 @@ function getAminoAcidDataForEachBaseOfDna(originalSequenceString, forward, optio
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  aminoAcid: null,
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  positionInCodon: null,
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  aminoAcidIndex: null,
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- sequenceIndex: positionInCdsToPositionInMainSequence(
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- posInCds,
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- forward,
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- translationRange,
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- originalSequenceStringLength
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- ),
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+ sequenceIndex,
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  codonRange: null,
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  fullCodon: null
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  });
@@ -17425,6 +17426,7 @@ const defaultEnzymes = [
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  "banii",
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  "bari",
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  "baui",
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+ "bbsi",
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  "bbvbi",
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  "bcni",
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  "bcoki",
package/index.umd.cjs CHANGED
@@ -8717,12 +8717,18 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
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  let positionInCodon = 0;
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  for (let i = 0; i < basesRead; i++) {
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  const posInCds = i + index;
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+ const sequenceIndex = codonPositionsInCDS.includes(posInCds) ? absoluteCodonPositions[codonPositionsInCDS.indexOf(posInCds)] : positionInCdsToPositionInMainSequence(
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+ posInCds,
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+ forward,
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+ translationRange,
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+ originalSequenceStringLength
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+ );
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  if (codonPositionsInCDS.includes(posInCds)) {
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  aminoAcidDataForEachBaseOfDNA.push({
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  aminoAcid,
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  positionInCodon,
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  aminoAcidIndex,
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- sequenceIndex: absoluteCodonPositions[i],
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+ sequenceIndex,
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  codonRange,
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  fullCodon: codonPositionsInCDS.length === 3
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  });
@@ -8732,12 +8738,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
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  aminoAcid: null,
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  positionInCodon: null,
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  aminoAcidIndex: null,
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- sequenceIndex: positionInCdsToPositionInMainSequence(
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- posInCds,
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- forward,
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- translationRange,
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- originalSequenceStringLength
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- ),
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+ sequenceIndex,
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  codonRange: null,
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  fullCodon: null
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  });
@@ -17429,6 +17430,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
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  "banii",
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  "bari",
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  "baui",
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+ "bbsi",
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  "bbvbi",
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  "bcni",
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  "bcoki",
package/package.json CHANGED
@@ -1,12 +1,19 @@
1
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  {
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  "name": "@teselagen/sequence-utils",
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- "version": "0.3.27",
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+ "version": "0.3.28-beta.1",
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+ "type": "module",
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  "dependencies": {
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- "@teselagen/range-utils": "0.3.7",
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+ "@teselagen/range-utils": "0.3.10",
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  "bson-objectid": "^2.0.4",
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  "escape-string-regexp": "^5.0.0",
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  "jsondiffpatch": "0.4.1",
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  "string-splice": "^1.3.0"
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  },
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+ "exports": {
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+ ".": {
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+ "import": "./index.js",
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+ "require": "./index.cjs"
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+ }
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+ },
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  "license": "MIT"
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  }
package/src/defaultEnzymesByName.js CHANGED
@@ -31,6 +31,7 @@ const defaultEnzymes = [
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  "banii",
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  "bari",
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  "baui",
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+ "bbsi",
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  "bbvbi",
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  "bcni",
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  "bcoki",
package/src/getAminoAcidDataForEachBaseOfDna.js CHANGED
@@ -28,8 +28,7 @@ function getNextTriplet(index, sequenceString, exonRange) {
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  // including introns.
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  const codonPositions = [];
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- // A function to check if a base is within an exon, defined here
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- // to avoid function creation in the loop (linter error)
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+ // A function to check if a base is within an exon
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  const isBaseInExon = baseIndex =>
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  exonRange.some(r =>
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  isPositionWithinRange(baseIndex, r, sequenceString.length, true, false)
@@ -251,28 +250,31 @@ export default function getAminoAcidDataForEachBaseOfDna(
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  let positionInCodon = 0;
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  for (let i = 0; i < basesRead; i++) {
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  const posInCds = i + index;
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+ const sequenceIndex = codonPositionsInCDS.includes(posInCds)
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+ ? absoluteCodonPositions[codonPositionsInCDS.indexOf(posInCds)]
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+ : positionInCdsToPositionInMainSequence(
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+ posInCds,
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+ forward,
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+ translationRange,
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+ originalSequenceStringLength
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+ );
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  if (codonPositionsInCDS.includes(posInCds)) {
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  aminoAcidDataForEachBaseOfDNA.push({
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  aminoAcid,
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  positionInCodon,
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  aminoAcidIndex,
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- sequenceIndex: absoluteCodonPositions[i],
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+ sequenceIndex,
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  codonRange,
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  fullCodon: codonPositionsInCDS.length === 3
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  });
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  positionInCodon++;
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  } else {
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- // TODO: what should we insert here?
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+ // push a null object for intron bases
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  aminoAcidDataForEachBaseOfDNA.push({
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  aminoAcid: null,
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  positionInCodon: null,
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  aminoAcidIndex: null,
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- sequenceIndex: positionInCdsToPositionInMainSequence(
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- posInCds,
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- forward,
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- translationRange,
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- originalSequenceStringLength
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- ),
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+ sequenceIndex,
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  codonRange: null,
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  fullCodon: null
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  });