Support NCBI microbe GTF/GFF with no transcripts (CDS only)

[nuno-agostinho]

Fixes #1620

Support NCBI GTF/GFF annotation files that only contain CDS lines: these CDS lines are children from gene IDs (instead of transcript IDs, as usual in Ensembl annotation files) and don't have exons as children.

If a CDS is a child from a gene and has no exons of its own, parse the feature as a single-exon transcript with the same strand, start and end as the CDS.

TODO

• Support NCBI microbe GTF/GFF annotation
• Only activate when using option --cds_as_transcript_gxf
• Fix unit tests
• Document --cds_as_transcript_gxf in public docs

Testing

Example files for avian paramyxovirus 1

• GCF_004786615.1_ASM478661v1_genomic.fna.gz
• GCF_004786615.1_ASM478661v1_genomic.gff.gz
• GCF_004786615.1_ASM478661v1_genomic.gtf.gz

Example VCF

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT iso1
NC_075404.1 980 . T C 12078.64 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.924;DP=624;ExcessHet=0.0000;FS=1.120;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=19.87;ReadPosRankSum=0.149;SOR=0.728 GT:AD:DP:GQ:PL 0/1:236,372:608:99:12086,0,6929
NC_075404.1 3666 . C T 15573.64 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.079;DP=770;ExcessHet=0.0000;FS=7.765;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=20.88;ReadPosRankSum=0.795;SOR=0.362 GT:AD:DP:GQ:PL 0/1:235,511:746:99:15581,0,5829
NC_075404.1 3812 . A G 534.64 ReadPosRankSum-8 AC=1;AF=0.500;AN=2;BaseQRankSum=1.096;DP=826;ExcessHet=0.0000;FS=15.515;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=0.66;ReadPosRankSum=-12.298;SOR=2.487 GT:AD:DP:GQ:PL 0/1:722,85:807:99:542,0,23105
NC_075404.1 4631 . T C 1817.64 ReadPosRankSum-8 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.725;DP=846;ExcessHet=0.0000;FS=22.208;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=2.24;ReadPosRankSum=-13.945;SOR=1.685 GT:AD:DP:GQ:PL 0/1:680,133:813:99:1825,0,21905
NC_075404.1 289 . G A 924.64 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.811;DP=720;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=0.000;QD=1.50;ReadPosRankSum=-5.861;SOR=0.631 GT:AD:DP:GQ:PL 0/1:531,87:618:99:932,0,16256

Example command

./vep --i sample.vcf \
      --gtf GCF_004786615.1_ASM478661v1_genomic.gtf.gz \
      --fasta GCF_004786615.1_ASM478661v1_genomic.fna.gz

Test conditions

• Command without --cds_as_transcript_gxf should return a warning if there are CDS in the annotation whose parent is a gene record
• Command with --cds_as_transcript_gxf should successfully use the CDS in the annotation as single-exon transcripts