added setReadsToHighlight() method to AlignmentTrack

[wilsonGen]

added setReadsToHighlight() method to AlignmentTrack
which can take an array of read names, then highlight the reads
for example :
const bamTracks = browser.findTracks('type', 'alignment')
bamTracks[0].alignmentTrack.setReadsToHighlight(["readName1", "readName2"])
bamTracks[0].updateViews()

also added
"highlightedReadsOutlineColor" (optional)
"readsToHighlight" (optional)
in Alignment Track options,
which allow configuration of the color of the highlighted reads,
and the configuration of the reads to highlight
for example:

{
type: "alignment",
format: "bam",
name: "NA12889",
url: "gs://genomics-public-data/platinum-genomes/bam/NA12878_S1.bam",
indexURL: "gs://genomics-public-data/platinum-genomes/bam/NA12878_S1.bam.bai",
sort: {
chr: "chr1",
position: 155155358
option": "BASE",
direction: "ASC"
},
highlightedReadsOutlineColor: "#0000ff",
readsToHighlight: ["readName1", "readName2"]
}

[wilsonGen]

Hi, sorry for bothering, since it has been a month, is there any problem with the changes?
Please let me know if there is any problem with the changes, I am open to discuss and would like to improve it, thank you!

[jrobinso]

Thanks for this, sorry for the delay. I've been swamped with other urgent issues, I'll get to this when I can.

[jrobinso]

OK looks good, but let's shorten the names a bit. Maybe just

highlightedReads
setHighlightedReads()
highlightColor

I am going to independently rename the existing highlighted read variable to "selectedRead" or "clickedRead".

[jrobinso]

I will merge and do the renaming.

[wilsonGen]

OK, thank you!

[jrobinso]

OK I did some minor refactoring, including a subtle change for session saving. The shortened names are as suggested above. Also, I added a setHighlightedReads() function to BAMTrack, to avoid exposing the internal AlignmentTrack in the API. Finally, updateViews() is called from setHighlightedReads().

Updated example

               const bamTracks = browser.findTracks('type', 'alignment')
                bamTracks[0].setHighlightedReads(["SRR099953.99059361", "SRR099953.79101554"])

Modified example config

                    {
                        type: "alignment",
                        url: "https://1000genomes.s3.amazonaws.com/phase3/data/NA19625/exome_alignment/NA19625.mapped.ILLUMINA.bwa.ASW.exome.20120522.bam",
                        indexURL: "https://1000genomes.s3.amazonaws.com/phase3/data/NA19625/exome_alignment/NA19625.mapped.ILLUMINA.bwa.ASW.exome.20120522.bam.bai",
                        name: "NA12878n",
                        highlightColor: "#0000ff",
                        highlightedReads: ["SRR099953.99059361", "SRR099953.79101554"]
                    }

[wilsonGen]

That's great! Thank you so much!