Parse mobile element insertion/deletion

[nuno-agostinho]

ENSVAR-832

Changelog

1. Support insertion/deletion of mobile elements in VCF (added unit tests to check for this):

Symbolic alternative allele	SO term
<INS:ME>	mobile_element_insertion
<DEL:ME>	mobile_element_deletion
<INS:ME:ALU>	Alu_insertion
<DEL:ME:ALU>	Alu_deletion
<INS:ME:HERV>	HERV_insertion
<DEL:ME:HERV>	HERV_deletion
<INS:ME:LINE1> or <INS:ME:L1>	LINE1_insertion
<DEL:ME:LINE1> or <DEL:ME:L1>	LINE1_deletion
<INS:ME:SVA>	SVA_insertion
<DEL:ME:SVA>	SVA_deletion

2. Decrease reliance on SVTYPE (deprecated in VCF 4.4)

   • Only use SVTYPE if ALT is undefined or . (tested in unit tests)
   • Fix CNV unit tests based on SVTYPE instead of ALT

3. Fix bug: CNV would be considered duplication instead of copy_number_variation in cases of multiple symbolic alleles, such as <CN0>,<CN2>,<CN3> (added unit tests to check for this)

Testing

Test VEP with mobile elements such as:

1 170626220 alu_ins T <INS:ME:ALU> . . TSD=TAAATTTCAGTTTT;SVTYPE=ALU;MEINFO=AluYa5,1,281,-;SVLEN=280;CS=ALU_umary;AC=12;AF=0.00239617;NS=2504;AN=5008;EAS_AF=0;EUR_AF=0;AFR_AF=0.0091;AMR_AF=0;SAS_AF=0;SITEPOST=1 GT 0|0
2 14477084  mobile_element_del C <DEL:ME>  12  PASS  IMPRECISE;SVTYPE=DEL;END=14477381;SVLEN=-297;MEINFO=AluYa5,5,307,+;CIPOS=-22,18;CIEND=-12,32  GT:GQ 0/1:12
2 14477084  alu_del C <DEL:ME:ALU>  12  PASS  IMPRECISE;SVTYPE=DEL;END=14477381;SVLEN=-297;MEINFO=AluYa5,5,307,+;CIPOS=-22,18;CIEND=-12,32  GT:GQ 0/1:12
3 9425916   l1_ins C <INS:ME:L1> 23  PASS  IMPRECISE;SVTYPE=INS;END=9425916;SVLEN=6027;CIPOS=-16,22;MIINFO=L1HS,1,6025,- GT:GQ 1/1:15

[olaaustine]

LGTM! Thank you for the changes @nuno-agostinho