Resolve conflicts from upstream merge

igvteam · Feb 4, 2025 · 28eb90a · 28eb90a
2 parents 8f6ffdb + 555b1fb
commit 28eb90a
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Showing 65 changed files with 8,994 additions and 9,786 deletions.
diff --git a/css/_igv-generic-container.scss b/css/_igv-generic-container.scss
@@ -1,9 +1,11 @@
 
 .igv-generic-container {
 
-  position: absolute;
-  top: 0;
-  left:0;
+  position: fixed;
+
+  top: 20%;
+  left: 75%;
+  transform: translateX(-50%);
 
   z-index: 2048;
 

diff --git a/css/_igv-generic-dialog-container.scss b/css/_igv-generic-dialog-container.scss
@@ -32,9 +32,12 @@ $igv-button-width: 75px;
 // generic dialog
 .igv-generic-dialog-container {
 
-  position: absolute;
-  top: 0;
-  left:0;
+  position: fixed;
+
+  top: 20%;
+  left: 75%;
+  transform: translateX(-50%);
+
   width:300px;
   height:200px;
 

diff --git a/css/_igv-ui-alert-dialog.scss b/css/_igv-ui-alert-dialog.scss
@@ -11,12 +11,15 @@ $igv-alert-dialog-body-copy-margin: 16px;
 
 .igv-ui-alert-dialog-container {
 
-  box-sizing: content-box;
+  position: fixed;
+
+  top: 20%;
+  left: 50%;
+  transform: translateX(-50%);
 
-  position: absolute;
   z-index: 2048;
-  top:50%;
-  left:50%;
+
+  box-sizing: content-box;
 
   width:$igv-alert-dialog-width;
   height:$igv-alert-dialog-height;

diff --git a/css/_igv-ui-colorpicker.scss b/css/_igv-ui-colorpicker.scss
@@ -4,9 +4,11 @@ $igv-color-swatch-border-width: 2px;
 
 .igv-ui-generic-container {
 
-  left: 50%;
-  top: 75%;
-  transform: translate(-50%, -25%);
+  position: fixed;
+
+  top: 20%;
+  left: 75%;
+  transform: translateX(-50%);
 
   flex-direction: column;
   flex-wrap: nowrap;

diff --git a/css/_igv-ui-generic-container.scss b/css/_igv-ui-generic-container.scss
@@ -1,15 +1,20 @@
 
 .igv-ui-generic-container {
 
-  box-sizing: content-box;
+  position: fixed;
+
+  top: 20%;
+  left: 75%;
+  transform: translateX(-50%);
 
-  position: absolute;
   z-index: 2048;
 
   background-color: white;
 
   cursor: pointer;
 
+  box-sizing: content-box;
+
   display: flex;
   flex-direction: row;
   flex-wrap: wrap;

diff --git a/css/_igv-ui-generic-dialog-container.scss b/css/_igv-ui-generic-dialog-container.scss
@@ -5,8 +5,17 @@
   box-sizing: content-box;
 
   position: fixed;
-  top: 0;
-  left:0;
+
+  top: 20%;
+  left: 75%;
+  transform: translateX(-50%);
+
+  z-index: 2048;
+
+  background-color: white;
+
+  cursor: pointer;
+
   width:300px;
   height:fit-content;
   padding-bottom: 16px;
@@ -20,10 +29,6 @@
   font-size: medium;
   font-weight: 400;
 
-  z-index: 2048;
-
-  background-color: white;
-
   display: flex;
   flex-flow: column;
   flex-wrap: nowrap;

diff --git a/css/igv.css b/css/igv.css
diff --git a/dev/alignment/alignment-jquery-cleans.html b/dev/alignment/alignment-jquery-cleans.html
@@ -0,0 +1,53 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <title>dev - alignment - jquery cleanse</title>
+</head>
+
+<body>
+
+<div id="igv-container" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div>
+
+<script type="module">
+
+    import igv from "../../js/index.js"
+
+    const config =
+        {
+            "genome": "hg19",
+            "locus": "chr1:155155389",
+            "tracks":
+                [
+                    {
+                        "type": "alignment",
+                        "url": "gs://genomics-public-data/platinum-genomes/bam/NA12878_S1.bam",
+                        "indexURL": "gs://genomics-public-data/platinum-genomes/bam/NA12878_S1.bam.bai",
+                        "name": "NA12878",
+                        "format": "bam",
+                        "sort":
+                            {
+                                "chr": "chr1",
+                                "position": 155155389,
+                                "option": "BASE",
+                                "direction": "ASC"
+                            },
+                        groupBy: "strand",
+                        height: 256,
+                        filter:
+                            {
+                                mq: 30
+                            }
+                    }
+                ]
+        }
+
+    igv.createBrowser(document.getElementById('igv-container'), config).then(browser => {
+        console.log(`browser ${ browser.guid } is good to go`)
+    })
+
+
+</script>
+
+</body>
+
+</html>