Update parsing of several fields

[nakib103]

We need to update how hypsipyle parse VEP annotations for some fields as described -

Phenotype

Current header - "VAR_SYNONYMS"
Updated header - "PHENOTYPES"

pattern - <phenotype>+<source>+<feature affected>
Multiple phenotype is separated by an &

example -

ANGIOTENSINOGEN+MIM_morbid+ENSG00000135744&HYPERTENSION__ESSENTIAL+MIM_morbid+ENSG00000135744&RENAL_TUBULAR_DYSGENESIS+MIM_morbid+ENSG00000135744&NON_RARE_IN_EUROPE:_Essential_hypertension+Orphanet+ENSG00000135744&Renal_tubular_dysgenesis_of_genetic_origin+Orphanet+ENSG00000135744&ClinVar:_phenotype_not_specified+ClinVar+rs699&HYPERTENSION__ESSENTIAL__SUSCEPTIBILITY_TO+ClinVar+rs699&Hypertensive_disorder+ClinVar+rs699&Preeclampsia__susceptibility_to+ClinVar+rs699&RENAL_TUBULAR_DYSGENESIS+ClinVar+rs699&Susceptibility_to_progression_to_renal_failure_in_IgA_nephropathy+ClinVar+rs699&Coronary_Artery_Disease+NHGRI-EBI_GWAS_catalog+rs699&Diastolic_blood_pressure+NHGRI-EBI_GWAS_catalog+rs699&Mean_arterial_pressure+NHGRI-EBI_GWAS_catalog+rs699&Systolic_blood_pressure+NHGRI-EBI_GWAS_catalog+rs699

Alternative names (data not available in 110 because of VEP cache issue)

Current header - none
Updated header - "VAR_SYNONYMS"

pattern - <source>::<name>&<name>..
Multiple synonyms separated by --

ClinVar::RCV000835695&RCV000405686&RCV000242838&RCV000019693&RCV000019692&RCV000019691&VCV000018068--OMIM::106150.0001--PharmGKB::PA166153539--UniProt::VAR_007096--COSMIC::COSM42556

Ancestral allele

Current header - none
Updated header - "AA"

Just allele sequence
There are some exceptional cases: - if there is an insertion or ? if chrom cannot be looked up in FASTA
example -
G

Frequency

Current header - "FREQ" (outside of CSQ - directly under INFO)
Updated header - frequency field under CSQ coming from --custom annotation fror gnomAD and --af_1kg flag for 1000Genomes

full list of fields:

gnoamd_exomes -

gnomAD_exomes|gnomAD_exomes_AF|gnomAD_exomes_AC|gnomAD_exomes_AN|gnomAD_exomes_AF_afr|gnomAD_exomes_AC_afr|gnomAD_exomes_AN_afr|gnomAD_exomes_AF_amr|gnomAD_exomes_AC_amr|gnomAD_exomes_AN_amr|gnomAD_exomes_AF_asj|gnomAD_exomes_AC_asj|gnomAD_exomes_AN_asj|gnomAD_exomes_AF_eas|gnomAD_exomes_AC_eas|gnomAD_exomes_AN_eas|gnomAD_exomes_AF_fin|gnomAD_exomes_AC_fin|gnomAD_exomes_AN_fin|gnomAD_exomes_AF_nfe|gnomAD_exomes_AC_nfe|gnomAD_exomes_AN_nfe|gnomAD_exomes_AF_oth|gnomAD_exomes_AC_oth|gnomAD_exomes_AN_oth|gnomAD_exomes_AF_sas|gnomAD_exomes_AC_sas|gnomAD_exomes_AN_sas

example -

rs699|0.548141|137772|251344|0.845055|13722|16238|0.719601|24891|34590|0.439968|4434|10078|0.838792|15417|18380|0.441035|9544|21640|0.419703|47706|113666|0.500163|3069|6136|0.620231|18989|30616

gnoamd_genomes -
Same as gnomad_exomes except it will have gnomad_genomes prefix.

1000Genoems -

AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF

example -

0.7051|0.9032|0.6354|0.8532|0.4115|0.636

Primary source

Current header - "source" (value taken from VCF file header)
Updated header - "SOURCE" (an INFO field - can be read from the INFO field for each variant)

example -

1	33878	ENSVVVI00100001	T	G	.	.	SOURCE=Ensembl;CSQ=G|missense_variant&splice_region_variant....