Message-ID: <95f7fc3a-eace-8159-5c29-3e1562069318@roswellpark.org>
Date: 2017-10-18T20:40:21Z
From: Martin Morgan
Subject: [Bioc-devel] Updating Rsamtools to support BAMs with >65535 CIGAR operators
In-Reply-To: <A57EB988-1F51-421B-BBD3-F7661484279D@broadinstitute.org>
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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