copied from another thread:

On Thu, Sep 8, 2011 at 7:30 AM, Anton Nekrutenko <an...@bx.psu.edu> wrote:

> What we are thinking of lately is switching to unaligned BAM for
> everyting. One of the benefits here is the ability to add readgroups from
> day 1 simplifying multisample analyses down the road.
>

this seems to be the simplest solution; i like it a lot.  really, only the
reads need to be compressed, most other outfiles are tiny by comparison, so
a more general solution may be overkill.  and if compression of everything
is desired, zfs works well -- another of our sites (LANL) uses this and
recommended it to me too.  i just haven't been able to convince my own IT
people to go this route for technical reason beyond my attention span.

On Tue, Sep 6, 2011 at 9:05 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Tue, Sep 6, 2011 at 5:00 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> > Peter Cock wrote:
> >> On Tue, Sep 6, 2011 at 3:24 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> >> > Ideally, there'd just be a column on the dataset table indicating
> >> > whether the dataset is compressed or not, and then tools get a new
> >> > way to indicate whether they can directly read compressed inputs, or
> >> > whether the input needs to be decompressed first.
> >> >
> >> > --nate
> >>
> >> Yes, that's what I was envisioning Nate.
> >>
> >> Are there any schemes other than gzip which would make sense?
> >> Perhaps rather than a boolean column (compressed or not), it
> >> should specify the kind of compression if any (e.g. gzip).
> >
> > Makes sense.
> >
> >> We need something which balances compression efficiency (size)
> >> with decompression speed, while also being widely supported in
> >> libraries for maximum tool uptake.
> >
> > Yes, and there's a side effect of allowing this: you may decrease
> > efficiency if the tools used downstream all require decompression,
> > and you waste a bunch of time decompressing the dataset multiple
> > times.
>
> While decompression wastes CPU time and makes things slower,
> there is less data IO from disk (which may be network mounted)
> which makes things faster. So overall, depending on the setup
> and the task at hand, it could be faster.
>
> Is it time to file an issue on bitbucket to track this potential
> enhancement?
>
> Peter
>
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