Htsget Bam support broken since v2.9.0 about igv.js HOT 7 CLOSED

from igv.js.

Unfortunately we can no longer support htsget as there are no reference test servers available, and the project itself does not seem to be active. For example this ticket has been open for more almost 3 years, in fact there are no project updates in three years: ga4gh/htsget-refserver#33.

That said, your change should not affect any other code negatively so I would accept is as a PR. I'm in general hesitant to accept PRs that I cannot personally test, but will make an exception in this special case.

from igv.js.

Thanks @jrobinso, happy to raise a PR for this. I'm ready to push my branch - can you add me as a collaborator to the repo please?

from igv.js.

@jmgenomics You don't need to be a collaborator to submit a PR.

from igv.js.

BTW the chr alias table is important and should not be removed. Without it files aligned to a reference with UCSC naming conventions ("chr1", etc) cannot be read if the loaded reference uses the other convention ("1", etc).

This is also the reason the header is read first. It allows the chr alias table to be built. Without this the query for alignments will fail if there is a mismatch in the chr naming convention.

I don't understand why the code as-is fails unless the server has not implemented the "class=header" query, in which case the server is non-conforming. What is your server returning for the "readHeader" method, implementation below.

    async readHeaderData() {
        const url = `${getUrl(this.config)}?class=header&format=${this.format}`
        const ticket = await igvxhr.loadJson(url, buildOptions(this.config))
        return await this.loadUrls(ticket.htsget.urls)
    }

For these reasons I could not accept this change as a PR. Sorry I just gave it a cursory glance earlier, I should have looked in more detail.

from igv.js.

Our Htsget server does support header queries and the data returned appears to be ok.

I think the issue with header.chrAliasTable being undefined may be due to bamUtil.js::decodeBamHeader(). It declares chrAliasTable but never assigns to it after that?

from igv.js.

I looked back into the code history and found statements from the last working version that had been removed wrt population of chrAliasTable.

I have raised a PR for your consideration.

from igv.js.