From 38b2acfc0be6b26be3d66a26cd5e7d900ec64aa2 Mon Sep 17 00:00:00 2001
From: wilsonGen <103169735+wilsonGen@users.noreply.github.com>
Date: Tue, 4 Jul 2023 13:13:06 +0800
Subject: [PATCH] can sort as pairs when view as pairs, sort as single reads
 otherwise (#1659)

---
 js/bam/alignmentContainer.js |  2 +-
 js/bam/bamAlignmentRow.js    | 12 ++++++------
 js/bam/bamTrack.js           |  3 ++-
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/js/bam/alignmentContainer.js b/js/bam/alignmentContainer.js
index d15bdd6a4..b45f1a2a9 100644
--- a/js/bam/alignmentContainer.js
+++ b/js/bam/alignmentContainer.js
@@ -160,7 +160,7 @@ class AlignmentContainer {
         const newRows = []
         const undefinedRow = []
         for (let row of this.packedAlignmentRows) {
-            const alignment = row.findAlignment(options.position)
+            const alignment = row.findAlignment(options.position, options.sortAsPairs)
             if (undefined !== alignment) {
                 newRows.push(row)
             } else {
diff --git a/js/bam/bamAlignmentRow.js b/js/bam/bamAlignmentRow.js
index c06801d2a..868664353 100644
--- a/js/bam/bamAlignmentRow.js
+++ b/js/bam/bamAlignmentRow.js
@@ -23,7 +23,7 @@
  * THE SOFTWARE.
  */
 
-import {StringUtils} from "../../node_modules/igv-utils/src/index.js"
+import { StringUtils } from "../../node_modules/igv-utils/src/index.js"
 
 const isString = StringUtils.isString
 const hashCode = StringUtils.hashCode
@@ -36,17 +36,17 @@ class BamAlignmentRow {
         this.score = undefined
     }
 
-    findAlignment(genomicLocation) {
+    findAlignment(genomicLocation, sortAsPairs = false) {
 
         const alignmentContains = (a, genomicLocation) => {
-            return genomicLocation >= a.start && genomicLocation < a.start + a.lengthOnRef
+            return genomicLocation >= a.start && genomicLocation < a.start + (sortAsPairs ? a.fragmentLength : a.lengthOnRef)
         }
 
         // find single alignment that overlaps sort location
         let centerAlignment
         for (let i = 0; i < this.alignments.length; i++) {
             const a = this.alignments[i]
-            if (genomicLocation >= a.start && genomicLocation < a.start + a.lengthOnRef) {
+            if (genomicLocation >= a.start && genomicLocation < a.start + (sortAsPairs ? a.fragmentLength : a.lengthOnRef)) {
                 if (a.paired) {
                     if (a.firstAlignment && alignmentContains(a.firstAlignment, genomicLocation)) {
                         centerAlignment = a.firstAlignment
@@ -64,11 +64,11 @@ class BamAlignmentRow {
 
     }
 
-    getSortValue({position, option, tag}, alignmentContainer) {
+    getSortValue({ position, option, tag, sortAsPairs }, alignmentContainer) {
 
         if (!option) option = "BASE"
 
-        const alignment = this.findAlignment(position)
+        const alignment = this.findAlignment(position, sortAsPairs)
         if (undefined === alignment) {  // This condition should never occur
             return Number.MAX_VALUE
         }
diff --git a/js/bam/bamTrack.js b/js/bam/bamTrack.js
index 06cabaa90..a5397bab0 100644
--- a/js/bam/bamTrack.js
+++ b/js/bam/bamTrack.js
@@ -1240,7 +1240,8 @@ class AlignmentTrack {
                 chr: viewport.referenceFrame.chr,
                 position: Math.floor(clickState.genomicLocation),
                 option: option,
-                direction: direction
+                direction: direction,
+                sortAsPairs: viewport.trackView.track.viewAsPairs
             }
             this.parent.sortObject = newSortObject
             viewport.cachedFeatures.sortRows(newSortObject)