"Download GFF3" omits Parent and resets score and source

[dariober]

As of commit 22db7bd, the exporting (downloading) of features to gff file has the following issues:

• the source and score fields are reset to missing value and those values become attributes.
• The Parent attribute is omitted

For example, the test file packages/apollo-cli/test_data/tiny.fasta.gff3 is:

ctgA	example	contig	1	50	1234567	.	.	Name=ctgA;multivalue=val1,val2,val3;aKey=Q;aNumber=987
ctgA	example	BAC	10	20	.	.	.	ID=b101.2;Name=b101.2;Note=Fingerprinted BAC with end reads
ctgA	example	SNP	10	30	0.987	.	.	ID=FakeSNP1;Name=FakeSNP;Note=This is a fake SNP that should appear at 1000 with length 1
ctgA	example	gene	100	200	.	+	.	ID=EDEN;Name=EDEN;Note=protein kinase
ctgA	example	mRNA	100	200	.	+	.	ID=EDEN.1;Parent=EDEN;Name=EDEN.1;Note=Eden splice form 1;Index=1
ctgB	someExample	contig	1	50	.	.	.	Name=SomeContig
ctgC	example	gene	100	200	.	+	.	ID=MyGene
ctgC	example	mRNA	100	200	.	+	.	ID=MyGene.1;Parent=MyGene
ctgC	example	CDS	100	170	.	+	.	ID=MyExon.1;Parent=MyGene.1
ctgC	example	gene	150	250	.	+	.	ID=AnotherGene
ctgC	example	mRNA	150	250	.	+	.	ID=mRNA.1;Parent=AnotherGene
ctgC	example	CDS	150	201	.	+	.	ID=CDS.1;Parent=mRNA.1

when exported it becomes:

ctgA	.	contig	1	50	.	.	.	gff_score=1234567;gff_source=example;multivalue=val1,val2,val3;aKey=Q;aNumber=987;Name=ctgA
ctgB	.	contig	1	50	.	.	.	gff_source=someExample;Name=SomeContig
ctgA	.	BAC	10	20	.	.	.	gff_source=example;gff_id=b101.2;Name=b101.2;Note=Fingerprinted BAC with end reads
ctgA	.	SNP	10	30	.	.	.	gff_score=0.987;gff_source=example;gff_id=FakeSNP1;Name=FakeSNP;Note=This is a fake SNP that should appear at 1000 with length 1
ctgA	.	gene	100	200	.	+	.	gff_source=example;gff_id=EDEN;Name=EDEN;Note=protein kinase
ctgA	.	mRNA	100	200	.	+	.	gff_source=example;gff_id=EDEN.1;Index=1;Name=EDEN.1;Note=Eden splice form 1
ctgC	.	gene	100	200	.	+	.	gff_source=example;gff_id=MyGene
ctgC	.	mRNA	100	200	.	+	.	gff_source=example;gff_id=MyGene.1
ctgC	.	CDS	100	170	.	+	.	gff_source=example;gff_id=MyExon.1
ctgC	.	gene	150	250	.	+	.	gff_source=example;gff_id=AnotherGene
ctgC	.	mRNA	150	250	.	+	.	gff_source=example;gff_id=mRNA.1
ctgC	.	CDS	150	201	.	+	.	gff_source=example;gff_id=CDS.1

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See also #203.