Add GTEx import resources

[KoalaQin]

This is to add an automated import function for GTEx data to gnomAD resources. Instead of using manually reheadered file, I downloaded the original expression and sample metadata to get the tissue information, while keeping the original GTEx Sample ID.
The only thing is that where we put these original files for importing?

[jkgoodrich]

Suggested change

	path="gs://gnomad-public-requester-pays/resources/grch38/gtex_rsem/gtex_rsem_v7.mt",
	path="gs://gnomad-public-requester-pays/resources/grch37/gtex/gtex_rsem_v7.mt",

[jkgoodrich]

Would it work to just not use row_key="transcript_id" when importing?

[KoalaQin]

When it's key, I can't remove the version number using annotate.

[jkgoodrich]

Yeah, but I think without row_key="transcript_id" in the import it won't already be keyed

[KoalaQin]

You're right, I had row_key in my test code.

[KoalaQin]

I also add a resource for CDS intervals, I was digging into Beryl's "CDS" bed (located here as of now: gs://gnomad-public/papers/2019-tx-annotation/data/other_data/gencode.v19.CDS.Hail.021519.bed) and found it's not accurate for the following reasons:

1. all the start positions were 1bp smaller than the Gencode GTF, it causes confusions when using import_bed by default: left inclusive but right exclusive, while import_gtf is left and right inclusive by default;
2. when merging back to Gencode intervals, they were not only "CDS" but also the other features:
   "CDS" 723784
   "Selenocysteine" 19
   "UTR" 54082
   "exon" 743326
   "gene" 162
   "start_codon" 84144
   "stop_codon" 76196
   "transcript" 171
   Good news is that it included all the CDS intervals minus the 1bp left/right confusion, I think it's better to start directly from the Gencode GTF file.

[jkgoodrich]

Yeah, but I think without row_key="transcript_id" in the import it won't already be keyed

[jkgoodrich]

I just have one comment and then this is good to go. I think I would like to wait on adding the gencode filter function to a PR where it is needed so I can see it used

[jkgoodrich]

LGTM!