Re: lofreq in Debian
Would you then advise that we wait for your next release before
proceeding with the packaging? We can wait a bit if the change is more
involved.
If, on the other hand, you see that you still do require functionality
from samtools libbam that is not in htslib, let us know and we can try
to work something out on that end.
Many thanks for your support
Afif
--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
على الثلاثاء 5 كانون الثاني 2016 23:21، كتب Andreas WILM:
> Hi Afif,
>
> I did not know that all functionality is now exposed through htslib.
> There are definitely some convenience functions or clones of samtools in
> LoFreq (e.g. for lofreq index etc.) but I'm not sure if there's more
> specific to samtools that's not already part of htslib. I'm happy to
> remove any unnecessary dependency but it seems this requires some
> rewriting since data structure names changed (e.g. the change from bam.h
> to sam.h esp. in lofreq_alnqual).
>
> Andreas
>
>
> Andreas WILM, PhD
> Research Associate
> Computational and Systems Biology
> Genome Institute of Singapore
> http://www.gis.a-star.edu.sg
>
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