Fix ROI deletion feature

[milandomazet]

Hello, this PR fixes a bug related to deletion of (user defined) ROIs. As we've moved roiSet to the menuItems method of ROIMenu we can now directly delete the ROI in question as there was a bug in finding the exact ROI (and its set) a user selected.

As can be seen in the video when a user defines a ROI over a ROI provided through config and then tries to delete it, the ROI provided through config gets deleted instead of the user defined one. In addition the ROI table was not being updated accordingly when a ROI is deleted.

Screen.Recording.2024-09-02.at.20.21.21.mov

[milandomazet]

I believe this line was causing the issue as it was not an exact match for start and end but we don't need this method now.

[milandomazet]

FYI @turner

[turner]

@milandomazet can you clarify what you mean by " when a user defines a ROI over a ROI provided through config "? What do you mean by over here?

[milandomazet]

@turner as you can see in the video basically the user defined region contains the previously provided region. For example region provided through config is chr1:100-150 and user defines a new region manually that is chr1:50-200

[turner]

@milandomazet I did a test with your igvjs code in igv-web app. I pre-configured the app with a single ROI:

{
	"version": "3.0.4",
	"showSampleNames": false,
	"reference": {
		"id": "hg19",
		"name": "Human (GRCh37/hg19)",
		"fastaURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg19/hg19.fasta",
		"indexURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg19/hg19.fasta.fai",
		"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz",
		"aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chromAlias.txt",
		"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit",
		"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes",
		"chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY"
	},
	"locus": "chr1:67,640,673-67,699,067",
	"roi": [
		{
			"name": "ROI set 2",
			"color": "rgba(3,52,249,0.25)",
			"features": [
				{
					"chr": "chr1",
					"start": 67670000,
					"end": 67671080,
					"name": "Set 2 feature 1"
				}
			],
			"isVisible": true
		}
	],
	"tracks": [
		{
			"type": "sequence",
			"order": -9007199254740991
		},
		{
			"name": "Refseq Genes",
			"format": "refgene",
			"id": "hg19_genes",
			"url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ncbiRefSeq.txt.gz",
			"indexed": false,
			"order": 1000000,
			"infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$",
			"type": "annotation",
			"height": 70
		}
	]
}

screenshot:

I then created a user-defined ROI:

I then deleted the user-defined ROI. It is correctly deleted and is nolonger visible in the table or in the browser. When I saved the session The user-generated ROI is present in the session file with an empty feature list:

{
	"version": "3.0.4",
	"showSampleNames": false,
	"reference": {
		"id": "hg19",
		"name": "Human (GRCh37/hg19)",
		"fastaURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg19/hg19.fasta",
		"indexURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg19/hg19.fasta.fai",
		"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz",
		"aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chromAlias.txt",
		"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit",
		"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes",
		"chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY"
	},
	"locus": "chr1:67,666,220-67,673,519",
	"roi": [
		{
			"name": "ROI set 2",
			"color": "rgba(3,52,249,0.25)",
			"features": [
				{
					"chr": "chr1",
					"start": 67670000,
					"end": 67671080,
					"name": "Set 2 feature 1"
				}
			],
			"isVisible": true
		},
		{
			"name": "user defined",
			"color": "rgba(136,135,135,0.125)",
			"features": [],
			"isUserDefined": true,
			"isVisible": true
		}
	],
	"tracks": [
		{
			"type": "sequence",
			"order": -9007199254740991
		},
		{
			"name": "Refseq Genes",
			"format": "refgene",
			"id": "hg19_genes",
			"url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ncbiRefSeq.txt.gz",
			"indexed": false,
			"order": 1000000,
			"infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$",
			"type": "annotation",
			"height": 70
		}
	]
}

[milandomazet]

@turner thanks for the feedback! To be honest I've never used session saving so I was not even checking this. Great point not just for this PR but for any future things I might do on IGV.js :)

Let me know if you see any issues with this approach.