inclusion of xg and gcsa indexes in git repo (lrc_kir)

[ekg]

@adamnovak I just noticed that we've included a few indexes in the repo (test/graphs/refonly-lrc_kir.vg.gcsa for instance). These come to a few mb, which will increase the bulk of the repository. I'm more concerned that they'll need to be updated when we change index formats. When updating binary files, git isn't very smart. It will just add several megabytes to the repo. Is it OK if I remove these?

[adamnovak]

You can try. But they might be in there for the tests; they may need to be
regenerated dynamically when you run the tests, which will add to the test
runtime.

On Thu, Sep 15, 2016 at 10:46 AM, Erik Garrison notifications@github.com
wrote:

@adamnovak https://github.com/adamnovak I just noticed that we've
included a few indexes in the repo (test/graphs/refonly-lrc_kir.vg.gcsa
for instance). These come to a few mb, which will increase the bulk of the
repository. I'm more concerned that they'll need to be updated when we
change index formats. When updating binary files, git isn't very smart. It
will just add several megabytes to the repo. Is it OK if I remove these?

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[ekg]

It adds a handful of secThis is true. It takes about 30 seconds to generate them on my system.

However, we will increase the repo size by 2.5MB every time we update the index formats. What do you think?

[adamnovak]

Maybe we can keep them in Github LFS or something, even though they aren't
large.

We could also just delete them. Or preserve them between test runs.

On Thu, Sep 15, 2016 at 11:36 AM, Erik Garrison notifications@github.com
wrote:

It adds a handful of secThis is true. It takes about 30 seconds to
generate them on my system.

However, we will increase the repo size by 2.5MB every time we update the
index formats. What do you think?

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[ekg]

I've deleted them in the fragment-length branch. I can undo it if you'd
prefer.

I think we will save 30 seconds in other ways when the default mapping
algorithm changes.

On Thu, Sep 15, 2016 at 9:01 PM adamnovak notifications@github.com wrote:

Maybe we can keep them in Github LFS or something, even though they aren't
large.

We could also just delete them. Or preserve them between test runs.

On Thu, Sep 15, 2016 at 11:36 AM, Erik Garrison notifications@github.com
wrote:

It adds a handful of secThis is true. It takes about 30 seconds to
generate them on my system.

However, we will increase the repo size by 2.5MB every time we update the
index formats. What do you think?

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