Feature/compara datachecks

[CristiGuijarro]

Addition of new critical compara DCs converted from HCs:

• AlignmentCoordinates
• CheckComparaStableIDs
• CheckConservationScore
• CheckCAFETable
• CheckConstrainedElementsTable
• CheckDuplicatedTaxaNames
• CheckFlatProteinTrees
• CheckGeneGainLossData
• CheckFirstLastRelease - (split into CheckReleaseNulls & CheckReleaseConsistency)
• CheckGenomicAlignGenomeDBs
• HighConfidence - (from EGHighConfidence)
• CheckEmptyLeavesTrees
• CheckSpeciesSetTable
• CheckSpeciesTreeNodeAttr
• CheckSynteny
• MultipleGenomicAlignBlockIds
• CheckHomology
• MemberProductionCounts

Addition of new method:

• is_one_to_many

[coveralls]

Pull Request Test Coverage Report for Build 870

• 16 of 16 (100.0%) changed or added relevant lines in 2 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.01%) to 98.59%

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Totals
Change from base Build 868:	0.01%
Covered Lines:	1818
Relevant Lines:	1844

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💛 - Coveralls

[muffato]

Overall, good job :) Many DCs are ready to go straight in !

You may have noticed that the coverage has dropped by almost 1%. This is because you don't have unit-tests for the new methods you have added. All the utility functions should be thoroughly. Can you please add some in t/TestDataCheck.t ?

[muffato]

Forgot to mention it but 🥇 for documenting the new methods

[CristiGuijarro]

• Add is_one_to_many to t/TestDataCheck.t

• Going to include at least one more DC in this PR (MemberProductionCounts)

[muffato]

Something I just spotted because I looked at the changes from the terminal. You have many lines that end with some trailing whitespace. Although we don't enforce it in Perl (we will in Python, though) it is considered better to clean that up. I don't know what @james-monkeyshines' policy is. In this instance, I would suggest to leave the PR but fix it on the lines you need to change to address the comments. On the next PRs though, make sure the trailing whitespace is removed

[CristiGuijarro]

I am still having arguments with Atom. I hate the trailing white space, but I can't seem to get Atom to understand without then removing trailing white space when it shouldn't.

[muffato]

(haven't finished checking MemberProductionCounts yet)

[muffato]

(I haven't finished MemberProductionCounts and CheckFlatProteinTrees

[muffato]

Almost done :) 😌

[CristiGuijarro]

🙏

[muffato]

🎉

[james-monkeyshines]

Comments on a few minor issues, the only one that needs to be fixed before merging is the name of the module in HighConfidence.