LDPred2: Effective sample size, cores used, hyperparameters

[deepchocolate]

Fixes #149 and #175

Changes proposed in this pull request:

• snp_ldsc uses multiple cores
• Effective sample size can be provided as nr cases (--n-cases) and nr controls ( --n-controls)
• Maximum of hyper parameter p can be provided (--hyper-p-max) to snp_ldpred2_auto
• Diagnostic plots named after --name-score if given

Before submitting

• I've read and followed all steps in the Making a pull request
  section of the CONTRIBUTING docs.
• I've updated or added any relevant docstrings following the syntax described in the
  Writing docstrings section of the CONTRIBUTING docs.
• If this PR fixes a bug, I've added a test that will fail without my fix.
• If this PR adds a new feature, I've added tests that sufficiently cover my new functionality.

[deepchocolate]

@espenhgn @ofrei I discovered a problem with using --out-merge in that the diagnostic plots will replace each other. Will fix #175 in this PR aswell. I suggest using the --name-score argument for that purpose.

[espenhgn]

@espenhgn @ofrei I discovered a problem with using --out-merge in that the diagnostic plots will replace each other. Will fix #175 in this PR aswell. I suggest using the --name-score argument for that purpose.

Ok. I looked through the rest of this PR as is, and looks good to me. Just waiting for the test script to finish.

[espenhgn]

Don't know if this PR introduced this test crash with the LDpred2 test script:

...
Test appending score to output file
Runing unittests on output
-- Failure (???): Appended score output ----------------------------------------
hasAllColumns(tmp, cnamesExp) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
Execution halted

Do you also see this?

[deepchocolate]

Don't know if this PR introduced this test crash with the LDpred2 test script:

...
Test appending score to output file
Runing unittests on output
-- Failure (???): Appended score output ----------------------------------------
hasAllColumns(tmp, cnamesExp) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
Execution halted

Do you also see this?

Ah, yes! It's because I removed running both the auto and inf mode in that part of the tests.
I didn't see it because I only ran the extended.sh tests the last time which I thought was sufficient.
Will fix!

[deepchocolate]

@espenhgn Turned out to be the memory issue again as termination due to memory is not captured as an error.. My impression from watching the process is that memory usage peaks at about 8GB.

[espenhgn]

Ok. If you think memory is the issue, maybe then there is not so much I can do to run all tests reliably on this VM I'm using. The usual situation is that there are only 3-4GB of RAM available for actual use, when background processes are running:

But maybe I'm also causing more issues by using VSCode to connect/edit directly as many small processes are created.

[espenhgn]

Looks good. The test crash I encountered appears to be memory related

[deepchocolate]

@espenhgn Added the fix for #175 if you wish to inspect

[espenhgn]

@espenhgn Added the fix for #175 if you wish to inspect

I trust you to merge this :)