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
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