> Sounds great; please make a pull request against > > https://github.com/Bioconductor/Rsamtools
I will send a pull request tomorrow. I will probably have some technical questions on testing and may ask you there on github. Thanks for the quick response. Heng > On Oct 18, 2017, at 16:40, Martin Morgan <martin.mor...@roswellpark.org> > wrote: > > On 10/18/2017 04:32 PM, Heng Li wrote: >> Hi, >> I am not sure whether I should send the request to this mailing list in this >> case, but I am not sure what is the best place to ask. >> Anyway, an alignment with >65535 operators can't be encoded in the current >> BAM format. Unfortunately, a tiny fraction of ultra-long nanopore reads will >> be aligned with >65535 ops, which means none of the existing BAM readers >> works with ultra-long reads. To address this issue, we can move long CIGAR >> to a tag in the file and move it back in memory when the file is read. >> I can update Rsamtools to support long-cigar BAMs with the approach above. >> The update will keep API the same but will slightly alter ABI – struct >> bam1_core_t in samtools/bam.c needs to be enlarged. If you think it is ok, I >> can generate a patch file against the git.bioconductor.org HEAD. >> What do you (or the current maintainer) think? What is the best way to send >> this patch? > > Sounds great; please make a pull request against > > https://github.com/Bioconductor/Rsamtools > > or as a simple diff to me (martin.morgan @ roswellpark.org) > > Martin > >> Thanks in advance, >> Heng > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
