updating primer mapping to split primers above and below the sequence…

… instead of mapping them all to be above
TeselaGen · Jan 13, 2022 · ccab5ef · ccab5ef
1 parent 4255073
commit ccab5ef
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Showing 4 changed files with 36 additions and 12 deletions.
diff --git a/src/mapAnnotationsToRows.js b/src/mapAnnotationsToRows.js
@@ -7,12 +7,12 @@ const {
 module.exports = function mapAnnotationsToRows(
   annotations,
   sequenceLength,
-  bpsPerRow
+  bpsPerRow,
+  { splitForwardReverse } = {}
 ) {
   const annotationsToRowsMap = {};
   const yOffsetLevelMap = {};
   const wrappedAnnotations = {};
-
   each(annotations, function(annotation) {
     const containsLocations = !!(
       annotation.locations && annotation.locations.length
@@ -31,7 +31,8 @@ module.exports = function mapAnnotationsToRows(
           bpsPerRow,
           annotationsToRowsMap,
           yOffsetLevelMap,
-          containsLocations
+          containsLocations,
+          splitForwardReverse
         });
         wrappedAnnotations[annotation.id] = true;
         // annotation.yOffset = wrappedAnnotations[annotation.id];
@@ -45,7 +46,8 @@ module.exports = function mapAnnotationsToRows(
       bpsPerRow,
       annotationsToRowsMap,
       yOffsetLevelMap,
-      containsLocations
+      containsLocations,
+      splitForwardReverse
     });
     if (containsLocations) {
       annotation.locations.forEach(location => {
@@ -56,7 +58,8 @@ module.exports = function mapAnnotationsToRows(
           bpsPerRow,
           annotationsToRowsMap,
           yOffsetLevelMap,
-          location
+          location,
+          splitForwardReverse
         });
       });
     }
@@ -78,7 +81,8 @@ function mapAnnotationToRows({
   annotationsToRowsMap,
   yOffsetLevelMap,
   location,
-  containsLocations
+  containsLocations,
+  splitForwardReverse
 }) {
   const ranges = splitRangeIntoTwoPartsIfItIsCircular(
     location || annotation,
@@ -93,13 +97,19 @@ function mapAnnotationToRows({
       if (!annotationsToRowsMap[rowNumber]) {
         annotationsToRowsMap[rowNumber] = [];
       }
+      const key = splitForwardReverse
+        ? annotation.forward
+          ? rowNumber + "_forward"
+          : rowNumber + "_reverse"
+        : rowNumber;
+
       const annotationsForRow = annotationsToRowsMap[rowNumber];
-      if (!yOffsetLevelMap[rowNumber]) {
-        yOffsetLevelMap[rowNumber] = [];
+      if (!yOffsetLevelMap[key]) {
+        yOffsetLevelMap[key] = [];
       }
 
       let yOffset;
-      const yOffsetsForRow = yOffsetLevelMap[rowNumber];
+      const yOffsetsForRow = yOffsetLevelMap[key];
       const start =
         rowNumber === startingRow ? range.start : rowNumber * bpsPerRow;
       const end =

diff --git a/src/prepareRowData.js b/src/prepareRowData.js
@@ -12,7 +12,8 @@ module.exports = function prepareRowData(sequenceData, bpsPerRow) {
     rowMap[type] = mapAnnotationsToRows(
       sequenceData[type],
       sequenceLength,
-      bpsPerRow
+      bpsPerRow,
+      { splitForwardReverse: type === "primers" }
     );
   });
 

diff --git a/src/prepareRowData.test.js b/src/prepareRowData.test.js
@@ -24,7 +24,7 @@ describe("prepareRowData", function() {
       parts: { a: annotation1 },
       cutsites: { b: annotation2 },
       orfs: [annotation2],
-      primers: [annotation2],
+      primers: [annotation2, { id: "asdfa", start: 1, end: 3, forward: true }], //reverse primers shouldn't offset forward primers
       warnings: [annotation2],
       assemblyPieces: [annotation2],
       lineageAnnotations: [annotation2]

diff --git a/src/prepareRowData_output1.json b/src/prepareRowData_output1.json
@@ -127,6 +127,19 @@
                 "end": 4,
                 "yOffset": 0,
                 "enclosingRangeType": "end"
+            },
+            {
+                "id": "asdfa",
+                "annotation": {
+                    "id": "asdfa",
+                    "start": 1,
+                    "end": 3,
+                    "forward": true
+                },
+                "start": 1,
+                "end": 3,
+                "yOffset": 0,
+                "enclosingRangeType": "beginningAndEnd"
             }
         ],
         "guides": [],
@@ -375,4 +388,4 @@
         "guides": [],
         "sequence": "a"
     }
-]
+]