Problem with Refesq Tracks in igv-webapp

[Dirk Haase]

Hi,

we use a self-hosted igv-webapp for viewing session xml-files from a third-party data provider. These session files contain RefSeq-Tracks like this one:

 

<Track name="Refseq HGMD" attributeKey="ncbiRefSeqHgmd.txt.gz" clazz="org.broad.igv.track.FeatureTrack" id=”https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeqHgmd.txt.gz” url=”https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeqHgmd.txt.gz” visible="true" format="refgene" height="35" type="annotation" infoURL=”https://www.ncbi.nlm.nih.gov/gene/?term=$$ “ />

This used to work fine in igv-webapp.2.0.4 and it still works in igv desktop (version 2.19.4). However, in newer versions of igv-webapp (I tried 2.3.0, 2.4.3 and 3.5.2) we run into an error “Unrecognized track”. It looks like the zip file is unzipped immediately and that is what the app tries to render as a track.

Is this a bug in the webapp or is this kind of track no longer supported?

Thanks in advance,

dirk

[Haase, Dr. Dirk]

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ ​​​​ Dr.   Dirk   Haase Dr. Team Software Solutions     MEDIT Service GmbH Teltowkanalstraße 1b ​Lieferanschrift: Siemensstraße 27 12247 Berlin Deutschland   Tel.: +49 89 45246670 dirk....@medit-service.de   Registergericht: Amtsgericht Charlottenburg Handelsregister: HRB 75702 B  Geschäftsführer: Dimitri Malinov, Staffan Ternström   Die Information in dieser E‑Mail ist vertraulich und kann einer Verschwiegenheitserklärung unterliegen. Sie ist nur für den Empfänger bestimmt.  ​Sofern Sie nicht der für diese E‑Mail bestimmte Adressat sind, benachrichtigen Sie bitte den Absender. Sie dürfen diese Nachricht oder Teile dieser  ​Nachricht weder vervielfältigen, veröffentlichen noch in anderer Weise verbreiten oder verwerten.   Denken Sie an die Umwelt und prüfen Sie, ob diese Mail wirklich ausgedruckt werden muss.

[igv-help]

Could you attach an entire XML file, or paste in its contents?

[Dirk Haase]

Unfortunately I can't upload a real file as it would contain sensitive data. But I made up a sample file with identical structure which behaves exactly like an original session.xml.

[igv-help]

OK, thanks for the test.  I found the problem and will deploy a fix soon.  To be honest I don't know how this worked in any version of igv.js / igv-web.   The "format" property of the Track element was ignored.  In many cases the format can be derived from the file extension,  but that does not work for "refgene" files.   It was loading and gunzipping the entire contents to try to determine format.

The "type" field on Resource is not standard, BTW,  I don't know where that comes from.   It's harmless but you might pass along the suggestion to change that property to "format",  unless it's used for some non-IGV purpose.

[igv-help]

This is fixed, igv-webapp version 2.4.5. 

[Dirk Haase]

I deployed the update and now the RefSeq tracks are displayed correctly.

Thank you very much!