Fix check_accuracy.r script

[gregorgorjanc]

This should be made easy to run. I now get this:

❯ ./check_accuracy.r
Error in file(file, "rt") : cannot open the connection
Calls: assessPeeling -> as.matrix -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'outputs/multilocus.dosage.txt': No such file or directory
Execution halted

In AlphaImpute2 I get:

❯ ./check_accuracy.r

Accuracy results for full imputation algorithm:
[1] "outputs/ai2.genotypes"
     generation yield yieldMissing       acc
[1,]          0     1            1 0.9594271
[2,]          1     1            1 0.9919062
[3,]          2     1            1 0.9982353
[4,]          3     1            1 0.9977857
...

[XingerTang]

We are no longer using tests/accuracy_tests/checkResults.r or example/checkAccuracy.r to check the accuracy of the output results. They are discarded. For the accuracy tests, we are using assess_peeling in the tests/accuracy_tests/run_accu_test.py to check the accuracy.

[gregorgorjanc]

I agree that our accuracy test suite is more comprehensive, but it would be good to show users some accuracy of imputation in the examples. Either using a simple script in the example or the more comprehensive from accuracy tests. The latter would be better.