Re: lofreq in Debian
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
On 6/1/16 14:59, Afif Elghraoui wrote:
Thanks for your quick response. I am definitely linking dynamically to
htslib and have managed all the other dependencies. However, samtools
(as intended to be installed by its developers) is not supposed to
provide any library, as the externally useful functionality was supposed
to be made available through htslib.
I am simply wondering if you are using the samtools static library and
headers only for the convenience samtools functions you are making
available through lofreq. If this is the case, I am then asking if you
mind whether we remove those convenience functions from lofreq in the
Debian package.
Many thanks and regards
Afif
--
Andreas WILM, PhD
Research Associate
Computational and Systems Biology
Genome Institute of Singapore
http://www.gis.a-star.edu.sg
-------------------------------
This e-mail and any attachments are only for the use of the intended recipient and may be confidential and/or privileged. If you are not the recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person as it may be an offence under the Official Secrets Act.
-------------------------------
Reply to: