updating getSequenceDataBetweenRange to properly handle annotations t…

…hat overlap themselves
TeselaGen · Aug 16, 2021 · d846f2d · d846f2d
1 parent ebaeb43
commit d846f2d
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Showing 2 changed files with 34 additions and 2 deletions.
diff --git a/src/getSequenceDataBetweenRange.js b/src/getSequenceDataBetweenRange.js
@@ -1,4 +1,4 @@
-const { flatMap, extend } = require("lodash");
+const { flatMap, extend, forEach } = require("lodash");
 const { getRangeLength } = require("ve-range-utils");
 const convertDnaCaretPositionOrRangeToAa = require("./convertDnaCaretPositionOrRangeToAA");
 const insertSequenceDataAtPosition = require("./insertSequenceDataAtPosition");
@@ -53,14 +53,30 @@ module.exports = function getSequenceDataBetweenRange(
       seqDataToUse,
       range.start
     );
-    return getSequenceDataBetweenRange(
+
+    const toRet = getSequenceDataBetweenRange(
       extendedSeqData,
       {
         start: range.end + 1,
         end: range.end
       },
       options
     );
+    annotationTypes.forEach(type => {
+      //we need to go through and adjust any anns where overlapsSelf=true to no longer overlap themselves if they match the range completely
+      forEach(toRet[type], ann => {
+        if (
+          ann.overlapsSelf &&
+          ann.start === 0 &&
+          getRangeLength(ann, seqDataToUse.sequence.length) ===
+            getRangeLength(range, seqDataToUse.sequence.length)
+        ) {
+          ann.overlapsSelf = false;
+          ann.end = toRet.sequence.length - 1;
+        }
+      });
+    });
+    return tidyUpSequenceData(toRet);
   }
   return tidyUpSequenceData(seqDataToReturn);
 };

diff --git a/src/getSequenceDataBetweenRange.test.js b/src/getSequenceDataBetweenRange.test.js
@@ -17,6 +17,14 @@ describe("getSequenceDataBetweenRange", function() {
         //         ffffffff gg
         sequence: "tttggggaaaccc",
         //          ttg
+        parts: [
+          {
+            start: 1,
+            end: 3,
+            name: "iOverlapMyself",
+            overlapsSelf: true
+          }
+        ],
         features: [
           {
             start: 0,
@@ -36,8 +44,16 @@ describe("getSequenceDataBetweenRange", function() {
         overlapsSelf: true
       }
     );
+    res.parts[0].overlapsSelf.should.equal(false); //if the range perfectly overlaps the selfOverlapped annotation, the annotation should no longer be wrapping
     res.should.containSubset({
       sequence: "ttggggaaaccctttg",
+      parts: [
+        {
+          start: 0,
+          end: 15,
+          name: "iOverlapMyself"
+        }
+      ],
       features: [
         {
           start: 0,