[Bioc-devel] Updating Rsamtools to support BAMs with >65535 CIGAR operators

Martin Morgan martin.morgan at roswellpark.org
Wed Oct 18 22:40:21 CEST 2017

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


or as a simple diff to me (martin.morgan @ roswellpark.org)


> Thanks in advance,
> Heng

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