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
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