`gotcloud test` fails on Ubuntu 16.10

[pjvandehaar]

indel

HWE_LPVAL and HWE_LLR often differ by up to 1% in:

test/indel/expected/indel/final/all.genotypes.vcf.gz
test/indel/expected/indel/final/merge/all.genotypes.20.bcf

beagle & thunder

Fails because I'm missing the perl module LWP/UserAgent.pm. perl -MCPAN -e 'install Bundle::LWP' can install it, fixing the issue.

nan was replaced by NaN in:

test/umake/expected/beagletest/beagle/chr20/chr20.filtered.PASS.beagled.vcf.gz
test/umake/expected/beagletest/beagle/chr20/split/bgl.1.chr20.PASS.1.vcf.gz
test/umake/expected/beagletest/thunder/chr20/ALL/split/chr20.filtered.PASS.beagled.ALL.split.1.vcf.gz
test/umake/expected/thundertest/thunder/chr20/ALL/thunder/chr20.filtered.PASS.beagled.ALL.thunder.1.vcf.gz
test/umake/expected/thundertest/thunder/chr20/ALL/thunder/chr20.filtered.PASS.beagled.ALL.thunder.vcf.gz

Lots of .conf files got re-ordered, but the ones I checked were all identical when sorted.

[pjvandehaar]

TODO:

• [ ] Allow HWE_LPVAL and HWE_LLR to drift by 1% in test/indel/expected/indel/final/all.genotypes.vcf.gz and test/indel/expected/indel/final/merge/all.genotypes.20.bcf.

  • screenshot in https://github.com/statgen/gotcloud/commit/c546acd1c23933e24db4c62c0c6e56bd87cf228a#commitcomment-21688567
  • Make sure that people think this change is acceptable.
  • then modify the line https://github.com/statgen/gotcloud/blob/master/scripts/diff_results_indel.sh#L45 to skip these files (and their .tbis), and we'll check them in a new line below.
  • it'd be easy to just ignore them, but given that they changed between GCC versions, it seems like we NEED to test them.

• [ ] Resolve the LWP/UserAgent.pm problem. Either:

  • remember how gotcloud/Makefile works
  • just drop LWP/UserAgent.pm somewhere in the repo
  • use something fancy like Carton
  • ask somebody who is better at perl

• [ ] Permit [nN]a[Nn] in output.

  • seems like people think this isn't a problem, so we should just ignore it in the tests.