opened
adamnovak
username_0
Surject is currently completely broken. This fixes it to actually include mappings in the surjected alignments, and to work on both strands.
Restore surject
issue
created
ekg
username_1
I had started to hack at surject but hadn't really gotten far. The code
needs to be moved into the Mapper. Then it needs to be extended to the new
indexes.
comment
created
ekg
username_1
Thanks for catching the non functionality though. What are you using it for
now?

On Mon, Apr 4, 2016, 23:49 Erik Garrison <erik.garrison@gmail.com> wrote:

> I had started to hack at surject but hadn't really gotten far. The code
> needs to be moved into the Mapper. Then it needs to be extended to the new
> indexes.
>
>
comment
created
adamnovak
username_0
We're surjecting reads so we can look at the BAMs on the genome browser and
see if the alignments we are getting out of VG make sense. It's easier than
messing about with GraphViz and jq to subset a GAM.

On Mon, Apr 4, 2016 at 2:49 PM, Erik Garrison <notifications@github.com>
wrote:

> Thanks for catching the non functionality though. What are you using it for
> now?
>
>
> On Mon, Apr 4, 2016, 23:49 Erik Garrison <erik.garrison@gmail.com> wrote:
>
> > I had started to hack at surject but hadn't really gotten far. The code
> > needs to be moved into the Mapper. Then it needs to be extended to the
> new
> > indexes.
> >
> >
comment
created
ekg
username_1
(As you know) the problem is that the surjection isn't the same as the
original alignment. But we don't have the mechanism to efficiently extract
the alignments to a region yet...

On Tue, Apr 5, 2016, 00:00 username_0 <notifications@github.com> wrote:

> We're surjecting reads so we can look at the BAMs on the genome browser and
> see if the alignments we are getting out of VG make sense. It's easier than
> messing about with GraphViz and jq to subset a GAM.
>
> On Mon, Apr 4, 2016 at 2:49 PM, Erik Garrison <notifications@github.com>
> wrote:
>
> > Thanks for catching the non functionality though. What are you using it
> for
> > now?
> >
> >
> > On Mon, Apr 4, 2016, 23:49 Erik Garrison <erik.garrison@gmail.com>
> wrote:
> >
> > > I had started to hack at surject but hadn't really gotten far. The code
> > > needs to be moved into the Mapper. Then it needs to be extended to the
> > new
> > > indexes.
> > >
> > >
comment