Associate EnsemblRelease with each Variant object

[iskandr]

• every Variant must be constructed with an explicit EnsemblRelease (this is mildly annoying/inelegant but simplifies a lot of other code)
• moved a lot of the transcript effect inference from core_logic onto Variant
• renamed VariantEffect to Annotation
• added a Variant.annotate() method, which replaces the need for VariantAnnotator
• got rid of the generic load_variants function, now call load_vcf or load_maf explicitly
• since each Variant carries its own EnsemblRelease, it's now possible for variants from multiple references to be in the same VariantCollection. I've seen a TCGA-derived MAF which mixes NCBI builds, so this might be desirable (it also gives meaning to taking the union of two variant collections aligned to different references). However, the potential for confusion here is suspicious.

[timodonnell]

I'd suggest renaming this default_ensembl

[iskandr]

Can you say more about why that's a better name?
On Feb 20, 2015 11:35 AM, "timodonnell" notifications@github.com wrote:

In test/test_cosmic_mutations.py
#20 (comment):

@@ -9,11 +10,11 @@
FrameShiftTruncation,
)

-annot = VariantAnnotator(75)
+ensembl = EnsemblRelease(75)

I'd suggest renaming this default_ensembl

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https://github.com/hammerlab/varcode/pull/20/files#r25082212.

[timodonnell]

It's used only as a default parameter, right? Otherwise it looks to me like we're declaring that this module uses a particular ensembl release

[timodonnell]

ah wait sorry, nvm. somehow didn't realize this was in a test method.

[iskandr]

👍

[timodonnell]

Well hope you don't mind the pile of comments, but besides all that, LGTM