LDpred2: Removed counting of missing genotypes

[deepchocolate]

Fixes #181

Changes proposed in this pull request:

• Removed countMissingGenotypes as it takes a significant amount of time of total execution time (~60%)
• Clarified exception when there are missing genotypes

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]

Noted that bigstatsr::big_prodVec has an ncores argument, so I added parallelization here aswell

[espenhgn]

Thanks @deepchocolate;
Just a preliminary report; some test(s) is failing (ran git clean -fd . in the tests directory beforehand):

$ cd tests && git clean -fd . && cd test_LDpred2
$ bash run.sh
...
Test appending score to output file
Runing unittests on output
-- Failure (???): Appended score output ----------------------------------------
hasAllColumns(tmp, cnamesExp) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Expected columns FID,IID,score,newScore but FID,IID,score were found in /nrec/space/espenh/containers/tests/test_LDpred2/output/public-data.score.inf

-- Failure (???): Appended score output ----------------------------------------
file.exists(filePlot) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Diagnostic plot was not found: /nrec/space/espenh/containers/tests/test_LDpred2/output/newScore.png

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

Can you reproduce it on your end?

I've updated the version and stuff for the next release.

[deepchocolate]

Thanks @deepchocolate; Just a preliminary report; some test(s) is failing (ran git clean -fd . in the tests directory beforehand):

$ cd tests && git clean -fd . && cd test_LDpred2
$ bash run.sh
...
Test appending score to output file
Runing unittests on output
-- Failure (???): Appended score output ----------------------------------------
hasAllColumns(tmp, cnamesExp) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Expected columns FID,IID,score,newScore but FID,IID,score were found in /nrec/space/espenh/containers/tests/test_LDpred2/output/public-data.score.inf

-- Failure (???): Appended score output ----------------------------------------
file.exists(filePlot) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Diagnostic plot was not found: /nrec/space/espenh/containers/tests/test_LDpred2/output/newScore.png

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

Can you reproduce it on your end?

I've updated the version and stuff for the next release.

Are you sure this is not a memory issue again? Because when I ran it, it stopped at the change in scripts/extended.sh, it should stop there if it doesn't receive an error. Don't know why I changed that.

When I fixed that and removed all output files all test passed

[espenhgn]

Yes, I think it is due to lack of memory (during Loading LD reference from /ldpred2_ref/ldref_hm3_plus/LD_with_blocks_chr@.rds LD_with_blocks_chr1.rds : loading LD for 3495 out of 117534 SNPs, but the reason is not captured).
Will check with @ofrei what we can do to upgrade the specs to 16GB of RAM for this VM we're using.
I'm fine with merging as is until that is resolved.

[deepchocolate]

Yes, I think it is due to lack of memory (during Loading LD reference from /ldpred2_ref/ldref_hm3_plus/LD_with_blocks_chr@.rds LD_with_blocks_chr1.rds : loading LD for 3495 out of 117534 SNPs, but the reason is not captured). Will check with @ofrei what we can do to upgrade the specs to 16GB of RAM for this VM we're using. I'm fine with merging as is until that is resolved.

I'm guessing the system terminates the execution somehow so that there's no error returned
Just going to switch back the exit code in extended.sh and then I'll merge