@teselagen/sequence-utils 0.3.11 → 0.3.12

package/index.js

@@ -12675,11 +12675,13 @@ __name(tidyUpSequenceData, "tidyUpSequenceData");
 const getDiffFromSeqs = /* @__PURE__ */ __name((oldData, newData, { ignoreKeys = [] } = {}) => {
   oldData = tidyUpSequenceData(oldData, {
     annotationsAsObjects: true,
-    noTranslationData: true
+    noTranslationData: true,
+    doNotRemoveInvalidChars: true
   });
   newData = tidyUpSequenceData(newData, {
     annotationsAsObjects: true,
-    noTranslationData: true
+    noTranslationData: true,
+    doNotRemoveInvalidChars: true
   });
   [oldData, newData].forEach((d) => {
     [
@@ -12711,7 +12713,10 @@ const patchSeqWithDiff = /* @__PURE__ */ __name((oldData, diff, { ignoreKeys = [
     delete diff[k];
   });
   return jsondiffpatch_umdExports.patch(
-    tidyUpSequenceData(lodashExports.cloneDeep(oldData), { annotationsAsObjects: true }),
+    tidyUpSequenceData(lodashExports.cloneDeep(oldData), {
+      annotationsAsObjects: true,
+      doNotRemoveInvalidChars: true
+    }),
     diff
   );
 }, "patchSeqWithDiff");
@@ -13284,7 +13289,9 @@ function arrayRotate(arr, count) {
 }
 __name(arrayRotate, "arrayRotate");
 function rotateSequenceDataToPosition(sequenceData, caretPosition, options) {
-  const newSequenceData = tidyUpSequenceData(sequenceData, options);
+  const newSequenceData = tidyUpSequenceData(sequenceData, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
   newSequenceData.sequence = rotateBpsToPosition(
     newSequenceData.sequence,
     caretPosition
@@ -13321,7 +13328,7 @@ function adjustAnnotationsToInsert(annotationsToBeAdjusted, insertStart, insertL
 __name(adjustAnnotationsToInsert, "adjustAnnotationsToInsert");
 function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSequenceData, caretPositionOrRange, options = {}) {
   const { maintainOriginSplit } = options;
-  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, options);
+  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
   const sequenceDataToInsert = tidyUpSequenceData(
     _sequenceDataToInsert,
     options
@@ -13339,6 +13346,7 @@ function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSeq
         return acc[type] = [];
       }, {})), {
         sequence: "",
+        doNotRemoveInvalidChars: true,
         proteinSequence: "",
         chromatogramData: void 0
       }),
@@ -21533,7 +21541,7 @@ function getSequenceDataBetweenRange(seqData, range, options = {}) {
   if (!range)
     return seqData;
   const { exclude = {}, excludePartial = {} } = options;
-  const seqDataToUse = tidyUpSequenceData(seqData, options);
+  const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
   annotationTypes.forEach((type) => {
     delete seqDataToUse[`filtered${lodashExports.startCase(type)}`];
   });
@@ -21584,9 +21592,9 @@ function getSequenceDataBetweenRange(seqData, range, options = {}) {
         }
       });
     });
-    return tidyUpSequenceData(toRet, options);
+    return tidyUpSequenceData(toRet, __spreadValues({ doNotRemoveInvalidChars: true }, options));
   }
-  return tidyUpSequenceData(seqDataToReturn, options);
+  return tidyUpSequenceData(seqDataToReturn, __spreadValues({ doNotRemoveInvalidChars: true }, options));
 }
 __name(getSequenceDataBetweenRange, "getSequenceDataBetweenRange");
 function getAnnotationsBetweenRange(annotationsToBeAdjusted, range, maxLength, shouldExcludePartial) {
@@ -21633,7 +21641,7 @@ function getComplementSequenceAndAnnotations(pSeqObj, options = {}) {
   const newSeqObj = Object.assign({}, seqObj, {
     sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
   });
-  return tidyUpSequenceData(newSeqObj, options);
+  return tidyUpSequenceData(newSeqObj, __spreadValues({ doNotRemoveInvalidChars: true }, options));
 }
 __name(getComplementSequenceAndAnnotations, "getComplementSequenceAndAnnotations");
 function getCutsiteType(restrictionEnzyme) {
@@ -21839,7 +21847,7 @@ __name(getReverseComplementAnnotation, "getReverseComplementAnnotation");
 function getReverseComplementSequenceAndAnnoations(pSeqObj, options = {}) {
   const seqObj = tidyUpSequenceData(
     getSequenceDataBetweenRange(pSeqObj, options.range),
-    options
+    __spreadValues({ doNotRemoveInvalidChars: true }, options)
   );
   const newSeqObj = Object.assign(
     {},
@@ -21859,7 +21867,9 @@ function getReverseComplementSequenceAndAnnoations(pSeqObj, options = {}) {
       return acc;
     }, {})
   );
-  return tidyUpSequenceData(newSeqObj, options);
+  return tidyUpSequenceData(newSeqObj, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
 }
 __name(getReverseComplementSequenceAndAnnoations, "getReverseComplementSequenceAndAnnoations");
 function getReverseSequenceString(sequence) {

package/index.mjs

@@ -12673,11 +12673,13 @@ __name(tidyUpSequenceData, "tidyUpSequenceData");
 const getDiffFromSeqs = /* @__PURE__ */ __name((oldData, newData, { ignoreKeys = [] } = {}) => {
   oldData = tidyUpSequenceData(oldData, {
     annotationsAsObjects: true,
-    noTranslationData: true
+    noTranslationData: true,
+    doNotRemoveInvalidChars: true
   });
   newData = tidyUpSequenceData(newData, {
     annotationsAsObjects: true,
-    noTranslationData: true
+    noTranslationData: true,
+    doNotRemoveInvalidChars: true
   });
   [oldData, newData].forEach((d) => {
     [
@@ -12709,7 +12711,10 @@ const patchSeqWithDiff = /* @__PURE__ */ __name((oldData, diff, { ignoreKeys = [
     delete diff[k];
   });
   return jsondiffpatch_umdExports.patch(
-    tidyUpSequenceData(lodashExports.cloneDeep(oldData), { annotationsAsObjects: true }),
+    tidyUpSequenceData(lodashExports.cloneDeep(oldData), {
+      annotationsAsObjects: true,
+      doNotRemoveInvalidChars: true
+    }),
     diff
   );
 }, "patchSeqWithDiff");
@@ -13282,7 +13287,9 @@ function arrayRotate(arr, count) {
 }
 __name(arrayRotate, "arrayRotate");
 function rotateSequenceDataToPosition(sequenceData, caretPosition, options) {
-  const newSequenceData = tidyUpSequenceData(sequenceData, options);
+  const newSequenceData = tidyUpSequenceData(sequenceData, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
   newSequenceData.sequence = rotateBpsToPosition(
     newSequenceData.sequence,
     caretPosition
@@ -13319,7 +13326,7 @@ function adjustAnnotationsToInsert(annotationsToBeAdjusted, insertStart, insertL
 __name(adjustAnnotationsToInsert, "adjustAnnotationsToInsert");
 function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSequenceData, caretPositionOrRange, options = {}) {
   const { maintainOriginSplit } = options;
-  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, options);
+  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
   const sequenceDataToInsert = tidyUpSequenceData(
     _sequenceDataToInsert,
     options
@@ -13337,6 +13344,7 @@ function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSeq
         return acc[type] = [];
       }, {})), {
         sequence: "",
+        doNotRemoveInvalidChars: true,
         proteinSequence: "",
         chromatogramData: void 0
       }),
@@ -21531,7 +21539,7 @@ function getSequenceDataBetweenRange(seqData, range, options = {}) {
   if (!range)
     return seqData;
   const { exclude = {}, excludePartial = {} } = options;
-  const seqDataToUse = tidyUpSequenceData(seqData, options);
+  const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
   annotationTypes.forEach((type) => {
     delete seqDataToUse[`filtered${lodashExports.startCase(type)}`];
   });
@@ -21582,9 +21590,9 @@ function getSequenceDataBetweenRange(seqData, range, options = {}) {
         }
       });
     });
-    return tidyUpSequenceData(toRet, options);
+    return tidyUpSequenceData(toRet, __spreadValues({ doNotRemoveInvalidChars: true }, options));
   }
-  return tidyUpSequenceData(seqDataToReturn, options);
+  return tidyUpSequenceData(seqDataToReturn, __spreadValues({ doNotRemoveInvalidChars: true }, options));
 }
 __name(getSequenceDataBetweenRange, "getSequenceDataBetweenRange");
 function getAnnotationsBetweenRange(annotationsToBeAdjusted, range, maxLength, shouldExcludePartial) {
@@ -21631,7 +21639,7 @@ function getComplementSequenceAndAnnotations(pSeqObj, options = {}) {
   const newSeqObj = Object.assign({}, seqObj, {
     sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
   });
-  return tidyUpSequenceData(newSeqObj, options);
+  return tidyUpSequenceData(newSeqObj, __spreadValues({ doNotRemoveInvalidChars: true }, options));
 }
 __name(getComplementSequenceAndAnnotations, "getComplementSequenceAndAnnotations");
 function getCutsiteType(restrictionEnzyme) {
@@ -21837,7 +21845,7 @@ __name(getReverseComplementAnnotation, "getReverseComplementAnnotation");
 function getReverseComplementSequenceAndAnnoations(pSeqObj, options = {}) {
   const seqObj = tidyUpSequenceData(
     getSequenceDataBetweenRange(pSeqObj, options.range),
-    options
+    __spreadValues({ doNotRemoveInvalidChars: true }, options)
   );
   const newSeqObj = Object.assign(
     {},
@@ -21857,7 +21865,9 @@ function getReverseComplementSequenceAndAnnoations(pSeqObj, options = {}) {
       return acc;
     }, {})
   );
-  return tidyUpSequenceData(newSeqObj, options);
+  return tidyUpSequenceData(newSeqObj, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
 }
 __name(getReverseComplementSequenceAndAnnoations, "getReverseComplementSequenceAndAnnoations");
 function getReverseSequenceString(sequence) {

package/index.umd.js

@@ -12677,11 +12677,13 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   const getDiffFromSeqs = /* @__PURE__ */ __name((oldData, newData, { ignoreKeys = [] } = {}) => {
     oldData = tidyUpSequenceData(oldData, {
       annotationsAsObjects: true,
-      noTranslationData: true
+      noTranslationData: true,
+      doNotRemoveInvalidChars: true
     });
     newData = tidyUpSequenceData(newData, {
       annotationsAsObjects: true,
-      noTranslationData: true
+      noTranslationData: true,
+      doNotRemoveInvalidChars: true
     });
     [oldData, newData].forEach((d) => {
       [
@@ -12713,7 +12715,10 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       delete diff[k];
     });
     return jsondiffpatch_umdExports.patch(
-      tidyUpSequenceData(lodashExports.cloneDeep(oldData), { annotationsAsObjects: true }),
+      tidyUpSequenceData(lodashExports.cloneDeep(oldData), {
+        annotationsAsObjects: true,
+        doNotRemoveInvalidChars: true
+      }),
       diff
     );
   }, "patchSeqWithDiff");
@@ -13286,7 +13291,9 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   }
   __name(arrayRotate, "arrayRotate");
   function rotateSequenceDataToPosition(sequenceData, caretPosition, options) {
-    const newSequenceData = tidyUpSequenceData(sequenceData, options);
+    const newSequenceData = tidyUpSequenceData(sequenceData, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
     newSequenceData.sequence = rotateBpsToPosition(
       newSequenceData.sequence,
       caretPosition
@@ -13323,7 +13330,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   __name(adjustAnnotationsToInsert, "adjustAnnotationsToInsert");
   function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSequenceData, caretPositionOrRange, options = {}) {
     const { maintainOriginSplit } = options;
-    let existingSequenceData = tidyUpSequenceData(_existingSequenceData, options);
+    let existingSequenceData = tidyUpSequenceData(_existingSequenceData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
     const sequenceDataToInsert = tidyUpSequenceData(
       _sequenceDataToInsert,
       options
@@ -13341,6 +13348,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
           return acc[type] = [];
         }, {})), {
           sequence: "",
+          doNotRemoveInvalidChars: true,
           proteinSequence: "",
           chromatogramData: void 0
         }),
@@ -21535,7 +21543,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     if (!range)
       return seqData;
     const { exclude = {}, excludePartial = {} } = options;
-    const seqDataToUse = tidyUpSequenceData(seqData, options);
+    const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
     annotationTypes.forEach((type) => {
       delete seqDataToUse[`filtered${lodashExports.startCase(type)}`];
     });
@@ -21586,9 +21594,9 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
           }
         });
       });
-      return tidyUpSequenceData(toRet, options);
+      return tidyUpSequenceData(toRet, __spreadValues({ doNotRemoveInvalidChars: true }, options));
     }
-    return tidyUpSequenceData(seqDataToReturn, options);
+    return tidyUpSequenceData(seqDataToReturn, __spreadValues({ doNotRemoveInvalidChars: true }, options));
   }
   __name(getSequenceDataBetweenRange, "getSequenceDataBetweenRange");
   function getAnnotationsBetweenRange(annotationsToBeAdjusted, range, maxLength, shouldExcludePartial) {
@@ -21635,7 +21643,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     const newSeqObj = Object.assign({}, seqObj, {
       sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
     });
-    return tidyUpSequenceData(newSeqObj, options);
+    return tidyUpSequenceData(newSeqObj, __spreadValues({ doNotRemoveInvalidChars: true }, options));
   }
   __name(getComplementSequenceAndAnnotations, "getComplementSequenceAndAnnotations");
   function getCutsiteType(restrictionEnzyme) {
@@ -21841,7 +21849,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   function getReverseComplementSequenceAndAnnoations(pSeqObj, options = {}) {
     const seqObj = tidyUpSequenceData(
       getSequenceDataBetweenRange(pSeqObj, options.range),
-      options
+      __spreadValues({ doNotRemoveInvalidChars: true }, options)
     );
     const newSeqObj = Object.assign(
       {},
@@ -21861,7 +21869,9 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
         return acc;
       }, {})
     );
-    return tidyUpSequenceData(newSeqObj, options);
+    return tidyUpSequenceData(newSeqObj, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
   }
   __name(getReverseComplementSequenceAndAnnoations, "getReverseComplementSequenceAndAnnoations");
   function getReverseSequenceString(sequence) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.11",
+  "version": "0.3.12",
   "dependencies": {
     "@teselagen/range-utils": "0.3.7",
     "bson-objectid": "^2.0.4",

package/src/diffUtils.js

@@ -6,11 +6,13 @@ import tidyUpSequenceData from "./tidyUpSequenceData";
 const getDiffFromSeqs = (oldData, newData, { ignoreKeys = [] } = {}) => {
   oldData = tidyUpSequenceData(oldData, {
     annotationsAsObjects: true,
-    noTranslationData: true
+    noTranslationData: true,
+    doNotRemoveInvalidChars: true
   });
   newData = tidyUpSequenceData(newData, {
     annotationsAsObjects: true,
-    noTranslationData: true
+    noTranslationData: true,
+    doNotRemoveInvalidChars: true
   });
 
   [oldData, newData].forEach(d => {
@@ -47,7 +49,10 @@ const patchSeqWithDiff = (oldData, diff, { ignoreKeys = [] } = {}) => {
     delete diff[k];
   });
   return patch(
-    tidyUpSequenceData(cloneDeep(oldData), { annotationsAsObjects: true }),
+    tidyUpSequenceData(cloneDeep(oldData), {
+      annotationsAsObjects: true,
+      doNotRemoveInvalidChars: true
+    }),
     diff
   );
 };

package/src/getComplementSequenceAndAnnotations.js

@@ -15,5 +15,5 @@ export default function getComplementSequenceAndAnnotations(
   const newSeqObj = Object.assign({}, seqObj, {
     sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
   });
-  return tidyUpSequenceData(newSeqObj, options);
+  return tidyUpSequenceData(newSeqObj, {doNotRemoveInvalidChars: true,...options});
 }

package/src/getReverseComplementSequenceAndAnnotations.js

@@ -13,7 +13,7 @@ export default function getReverseComplementSequenceAndAnnoations(
 ) {
   const seqObj = tidyUpSequenceData(
     getSequenceDataBetweenRange(pSeqObj, options.range),
-    options
+    { doNotRemoveInvalidChars: true, ...options }
   );
   const newSeqObj = Object.assign(
     {},
@@ -33,5 +33,8 @@ export default function getReverseComplementSequenceAndAnnoations(
       return acc;
     }, {})
   );
-  return tidyUpSequenceData(newSeqObj, options);
+  return tidyUpSequenceData(newSeqObj, {
+    doNotRemoveInvalidChars: true,
+    ...options
+  });
 }

package/src/getSequenceDataBetweenRange.js

@@ -16,7 +16,7 @@ export default function getSequenceDataBetweenRange(
 ) {
   if (!range) return seqData;
   const { exclude = {}, excludePartial = {} } = options;
-  const seqDataToUse = tidyUpSequenceData(seqData, options);
+  const seqDataToUse = tidyUpSequenceData(seqData, {doNotRemoveInvalidChars: true,...options});
   annotationTypes.forEach(type => {
     delete seqDataToUse[`filtered${startCase(type)}`];
   });
@@ -78,10 +78,10 @@ export default function getSequenceDataBetweenRange(
         }
       });
     });
-    return tidyUpSequenceData(toRet, options);
+    return tidyUpSequenceData(toRet, {doNotRemoveInvalidChars: true,...options});
   }
 
-  return tidyUpSequenceData(seqDataToReturn, options);
+  return tidyUpSequenceData(seqDataToReturn, {doNotRemoveInvalidChars: true,...options});
 }
 
 function getAnnotationsBetweenRange(

package/src/insertSequenceDataAtPositionOrRange.js

@@ -18,7 +18,7 @@ export default function insertSequenceDataAtPositionOrRange(
   //when inserting new seq, n bps of the new seq should go in before the origin and the rest should be
   //inserted at the sequence start
   const { maintainOriginSplit } = options;
-  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, options);
+  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, {doNotRemoveInvalidChars: true,...options});
   const sequenceDataToInsert = tidyUpSequenceData(
     _sequenceDataToInsert,
     options
@@ -48,6 +48,7 @@ export default function insertSequenceDataAtPositionOrRange(
           return (acc[type] = []);
         }, {}),
         sequence: "",
+        doNotRemoveInvalidChars: true,
         proteinSequence: "",
         chromatogramData: undefined
       },

package/src/rotateSequenceDataToPosition.js

@@ -9,7 +9,10 @@ export default function rotateSequenceDataToPosition(
   caretPosition,
   options
 ) {
-  const newSequenceData = tidyUpSequenceData(sequenceData, options);
+  const newSequenceData = tidyUpSequenceData(sequenceData, {
+    doNotRemoveInvalidChars: true,
+    ...options
+  });
 
   //update the sequence
   newSequenceData.sequence = rotateBpsToPosition(