Different adapters for BAMs and FASTQs

[Stikus]

Hello, looks like problem described here #64 was not fully fixed.

In FASTQ reports we're getting PolyA/PolyG adapters:

fastqc_report.html

But in BAM reports we're still getting SOLID:

fastqc_report.html

Looks like this is the source of adapter: https://github.com/smithlabcode/falco/blob/master/src/FalcoConfig.cpp#L224

Is this intended behavior?

[serge2016]

The last change in https://github.com/s-andrews/FastQC/releases/tag/v0.12.0 is:

The default adapters removed the SOLID adapter, but added polyA
and polyG since these can both provide useful information and are
often trimmed from sequences in a similar manner to adapters.

[andrewdavidsmith]

Thanks @serge2016 and @Stikus I'll take care of this. BTW I rewrote the engine and a new major version will be significantly faster, and on top of that can use threads well.

[serge2016]

Thank you, @andrewdavidsmith, sounds great! We are ready to test!

[Stikus]

@andrewdavidsmith Thanks for announcement, but is there any ETA for this? We are planning to add Falco as FastQC replacement in production and we want to use faster version of code (in our case FastQC takes 2+ hours, current Falco - 1+, speed up will be much appreciated).

[andrewdavidsmith]

I'll respond on the adapters first: the adapters were updated in the config file, but if the config file wasn't found, then it would default back to hard-coded adapters, and those didn't get updated. I'm doing that now.

[andrewdavidsmith]

This should be fixed in the master branch with f6ab200