@teselagen/bio-parsers 0.1.18 → 0.1.20

package/index.d.ts

@@ -11,5 +11,6 @@ export { default as jsonToBed } from "./jsonToBed";
 export { default as cleanUpTeselagenJsonForExport } from "./utils/cleanUpTeselagenJsonForExport";
 export { default as parseUracilFeatures } from "./utils/parseUracilFeatures";
 export { default as jsonToJsonString } from "./jsonToJsonString";
+export { default as validateSequenceArray } from "./utils/validateSequenceArray";
 export { default as ab1ToJson, convertBasePosTraceToPerBpTrace } from "./ab1ToJson";
 export { default as searchWholeObjByName, searchWholeObjByNameSimple, searchWholeObjByNameSimpleArray } from "./utils/searchWholeObjByName";

package/index.js

@@ -31051,7 +31051,7 @@ function parseGeneiousJson(geneiousJson) {
     searchWholeObjByNameSimpleArray("annotation", geneiousJsonInner),
     function(feature) {
       if (feature) {
-        const name2 = searchWholeObjByNameSimple("description", feature);
+        const name2 = (searchWholeObjByNameSimple("description", feature) || "").substring(0, 255);
         const intervals = searchWholeObjByNameSimpleArray("interval", feature);
         const type = searchWholeObjByNameSimple("type", feature);
         const firstInterval = intervals[0];
@@ -31662,9 +31662,17 @@ function anyToJson(fileContentStringOrFileObj, options) {
         return snapgeneToJson(fileContentStringOrFileObj, options);
       } else if (/^(geneious)$/.test(ext)) {
         const a = yield getUint8ArrayFromFile(fileContentStringOrFileObj);
-        const b = unzipSync(a);
-        const c = Object.values(b)[0];
-        const d = new TextDecoder().decode(c, { stream: false });
+        let d;
+        try {
+          d = new TextDecoder().decode(a, { stream: false });
+          if (!d.includes("<geneious")) {
+            throw new Error("not geneious");
+          }
+        } catch (e) {
+          const b = unzipSync(a);
+          const c = Object.values(b)[0];
+          d = new TextDecoder().decode(c, { stream: false });
+        }
         return geneiousXmlToJson(d, options);
       } else {
         fileContentString = yield getUtf8StringFromFile(
@@ -33645,3 +33653,4 @@ exports.searchWholeObjByName = searchWholeObjByName;
 exports.searchWholeObjByNameSimple = searchWholeObjByNameSimple;
 exports.searchWholeObjByNameSimpleArray = searchWholeObjByNameSimpleArray;
 exports.snapgeneToJson = snapgeneToJson;
+exports.validateSequenceArray = validateSequenceArray;

package/index.mjs

@@ -31049,7 +31049,7 @@ function parseGeneiousJson(geneiousJson) {
     searchWholeObjByNameSimpleArray("annotation", geneiousJsonInner),
     function(feature) {
       if (feature) {
-        const name2 = searchWholeObjByNameSimple("description", feature);
+        const name2 = (searchWholeObjByNameSimple("description", feature) || "").substring(0, 255);
         const intervals = searchWholeObjByNameSimpleArray("interval", feature);
         const type = searchWholeObjByNameSimple("type", feature);
         const firstInterval = intervals[0];
@@ -31660,9 +31660,17 @@ function anyToJson(fileContentStringOrFileObj, options) {
         return snapgeneToJson(fileContentStringOrFileObj, options);
       } else if (/^(geneious)$/.test(ext)) {
         const a = yield getUint8ArrayFromFile(fileContentStringOrFileObj);
-        const b = unzipSync(a);
-        const c = Object.values(b)[0];
-        const d = new TextDecoder().decode(c, { stream: false });
+        let d;
+        try {
+          d = new TextDecoder().decode(a, { stream: false });
+          if (!d.includes("<geneious")) {
+            throw new Error("not geneious");
+          }
+        } catch (e) {
+          const b = unzipSync(a);
+          const c = Object.values(b)[0];
+          d = new TextDecoder().decode(c, { stream: false });
+        }
         return geneiousXmlToJson(d, options);
       } else {
         fileContentString = yield getUtf8StringFromFile(
@@ -33643,5 +33651,6 @@ export {
   searchWholeObjByName,
   searchWholeObjByNameSimple,
   searchWholeObjByNameSimpleArray,
-  snapgeneToJson
+  snapgeneToJson,
+  validateSequenceArray
 };

package/index.umd.js

@@ -31053,7 +31053,7 @@ ${seq.sequence}
       searchWholeObjByNameSimpleArray("annotation", geneiousJsonInner),
       function(feature) {
         if (feature) {
-          const name3 = searchWholeObjByNameSimple("description", feature);
+          const name3 = (searchWholeObjByNameSimple("description", feature) || "").substring(0, 255);
           const intervals = searchWholeObjByNameSimpleArray("interval", feature);
           const type = searchWholeObjByNameSimple("type", feature);
           const firstInterval = intervals[0];
@@ -31664,9 +31664,17 @@ ${seq.sequence}
           return snapgeneToJson(fileContentStringOrFileObj, options);
         } else if (/^(geneious)$/.test(ext)) {
           const a = yield getUint8ArrayFromFile(fileContentStringOrFileObj);
-          const b = unzipSync(a);
-          const c = Object.values(b)[0];
-          const d = new TextDecoder().decode(c, { stream: false });
+          let d;
+          try {
+            d = new TextDecoder().decode(a, { stream: false });
+            if (!d.includes("<geneious")) {
+              throw new Error("not geneious");
+            }
+          } catch (e) {
+            const b = unzipSync(a);
+            const c = Object.values(b)[0];
+            d = new TextDecoder().decode(c, { stream: false });
+          }
           return geneiousXmlToJson(d, options);
         } else {
           fileContentString = yield getUtf8StringFromFile(
@@ -33647,5 +33655,6 @@ ${seq.sequence}
   exports2.searchWholeObjByNameSimple = searchWholeObjByNameSimple;
   exports2.searchWholeObjByNameSimpleArray = searchWholeObjByNameSimpleArray;
   exports2.snapgeneToJson = snapgeneToJson;
+  exports2.validateSequenceArray = validateSequenceArray;
   Object.defineProperty(exports2, Symbol.toStringTag, { value: "Module" });
 });

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/bio-parsers",
-  "version": "0.1.18",
+  "version": "0.1.20",
   "type": "commonjs",
   "dependencies": {
     "@gmod/gff": "^1.2.1",