Thanks John, I made two pull requests to add the feature back in, although
there were some slight modifications:
* '-x' was taken for outputting HEX, so I used '-Y'.
* there was no character in the flag string for supplementary alignments,
so I used 'S'.
htslib: https://github.com/samtools/htslib/pull/134/files
samtools: https://github.com/samtools/samtools/pull/301
Thank-you for considering my request,
N
On Thu, Sep 25, 2014 at 6:59 PM, John Marshall <[email protected]> wrote:
> On 25 Sep 2014, at 16:29, Nils Homer <[email protected]> wrote:
> > I see that the "samtools view -X" option is missing. This option is
> incredibly useful for debugging SAM/BAM (and now CRAM) records. It seems
> that this option was lost in the newest release. Would it be possible to
> add that back in?
>
> The hex/symbolic flags functionality wasn't offered by htslib's
> sam_write1(), so this functionality disappeared with the move to htslib.
> Yes, we're planning to bring it back as time permits.
>
> John
>
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