How can show soft clipped regions?

Manuel-DominguezCBG commented 7 months ago

First at all, thanks for this powerful combination of tools.

How can I show soft-clipped region in the jupyter.

I need this

but I cannot see this in my notebook

this is my code

import igv_notebook
igv_notebook.init()

b = igv_notebook.Browser(
    {
        "genome": "hg38",
        "locus": "chr22:24,376,166-24,376,456"
    }
)

b.load_track(
    {
        "name": "",
        "path": "/mnt/c/Users/dominm/Desktop/IGV_2.16.2/COSMIC.bam",
        "indexPath": "/mnt/c/Users/dominm/Desktop/IGV_2.16.2/COSMIC.bam.bai",
        "format": "bam",
        "type": "alignment"
    })

b.search('chr17:43094574-43095012')

jrobinso commented 4 months ago

Sorry for missing this. Did you read the documentation? In particular did you try the "showSoftClips" option?

https://github.com/igvteam/igv.js/wiki/Alignment-Track

Manuel-DominguezCBG commented 4 months ago

Yes I found this and I forgot to close this issue. Thank you so much

igvteam / igv-notebook

How can show soft clipped regions? #27