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? Thanks in advance, Heng _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
