Translate BED/GFF to nodes

[Chris7]

This translates GFF/BED entries to be node centric.
Here's how simple.gff gets translated to sample foo (simple.fa + simple.vcf)

m123	HAVANA	gene	1	20	.	-	.	ID=ENSG00000294541.1
m123	HAVANA	transcript	1	20	.	-	.	ID=ENST00000724296.1;Parent=ENSG00000294541.1
m123	HAVANA	exon	4	8	.	-	.	ID=exon:ENST00000724296.1:1;Parent=ENST00000724296.1
m123	HAVANA	exon	10	14	.	-	.	ID=exon:ENST00000724296.1:2;Parent=ENST00000724296.1
m123	HAVANA	exon	16	19	.	-	.	ID=exon:ENST00000724296.1:3;Parent=ENST00000724296.1
m123	ENSEMBL	gene	3	15	.	-	.	ID=ENSG00000277248.1
m123	ENSEMBL	transcript	3	15	.	-	.	ID=ENST00000615943.1;Parent=ENSG00000277248.1
m123	ENSEMBL	exon	3	15	.	-	.	ID=exon:ENST00000615943.1:1;Parent=ENST00000615943.1

3	HAVANA	gene	1	3	.	-	.	ID=ENSG00000294541.1
3	HAVANA	gene	4	5	.	-	.	ID=ENSG00000294541.1
3	HAVANA	gene	6	20	.	-	.	ID=ENSG00000294541.1
3	HAVANA	transcript	1	3	.	-	.	ID=ENST00000724296.1;Parent=ENSG00000294541.1
3	HAVANA	transcript	4	5	.	-	.	ID=ENST00000724296.1;Parent=ENSG00000294541.1
3	HAVANA	transcript	6	20	.	-	.	ID=ENST00000724296.1;Parent=ENSG00000294541.1
3	HAVANA	exon	4	5	.	-	.	ID=exon:ENST00000724296.1:1;Parent=ENST00000724296.1
3	HAVANA	exon	6	8	.	-	.	ID=exon:ENST00000724296.1:1;Parent=ENST00000724296.1
3	HAVANA	exon	10	14	.	-	.	ID=exon:ENST00000724296.1:2;Parent=ENST00000724296.1
3	HAVANA	exon	16	19	.	-	.	ID=exon:ENST00000724296.1:3;Parent=ENST00000724296.1
3	ENSEMBL	gene	4	5	.	-	.	ID=ENSG00000277248.1
3	ENSEMBL	gene	6	15	.	-	.	ID=ENSG00000277248.1
3	ENSEMBL	transcript	4	5	.	-	.	ID=ENST00000615943.1;Parent=ENSG00000277248.1
3	ENSEMBL	transcript	6	15	.	-	.	ID=ENST00000615943.1;Parent=ENSG00000277248.1
3	ENSEMBL	exon	4	5	.	-	.	ID=exon:ENST00000615943.1:1;Parent=ENST00000615943.1
3	ENSEMBL	exon	6	15	.	-	.	ID=exon:ENST00000615943.1:1;Parent=ENST00000615943.1

Notably, repeat IDs are allowed by the spec

ID
    Indicates the ID of the feature. The ID attribute is required for features that have children (e.g. gene and mRNAs), or for those that span multiple lines, but are optional for other features. IDs for each feature must be unique within the scope of the GFF file. In the case of discontinuous features (i.e. a single feature that exists over multiple genomic locations) the same ID may appear on multiple lines. All lines that share an ID must collectively represent a single feature.

[dkhofer]

This is minor, but might be good to add a comment here and in the gff code saying this is a sample from simple.vcf, it took me a couple minutes to work my way through the data flow

[dkhofer]

LGTM!