Parse error (with example) on somatic flag

[lbeltrame]

This record has its somatic flag improperly parsed or a wrong annotation, causing a CHECK violation when loading data:

chr1    1757111 COSM2186304     C       T       104     PASS    CALLERS=vardict;LSEQ=GTTCCCATGGTCTCACGGGG;MSI=2;MSILEN=1;RSEQ=GGTGATGTGGATGGAGGCCC;SAMPLE=115;SHIFT3=0;SOMATIC;SOR=inf;SSF=0.00699;STATUS=LikelySomatic;TYPE=SNV;VD=8;ac_exac_all=67;an_exac_all=14896;ac_adj_exac_afr=0;an_adj_exac_afr=992;ac_adj_exac_amr=2;an_adj_exac_amr=478;ac_adj_exac_eas=0;an_adj_exac_eas=776;ac_adj_exac_fin=5;an_adj_exac_fin=188;ac_adj_exac_nfe=49;an_adj_exac_nfe=5242;ac_adj_exac_oth=2;an_adj_exac_oth=162;ac_adj_exac_sas=9;an_adj_exac_sas=7058;num_exac_Het=67;num_exac_Hom=0;rs_ids=rs199931813;DB;DP=8;AF=1;gnomAD_AF=0.0041326;gnomAD_AC=635;gnomAD_AN=153658;af_exac_all=0.0044979;af_adj_exac_afr=0;af_adj_exac_amr=0.0041841;af_adj_exac_eas=0;af_adj_exac_fin=0.0266;af_adj_exac_nfe=0.0093476;af_adj_exac_oth=0.012346;af_adj_exac_sas=0.0012751;max_aaf_all=0.0266;AN=2;AC=2;CSQ=T|missense_variant|MODERATE|NADK|ENSG00000008130|Transcript|ENST00000378625|protein_coding|6/14||ENST00000378625.5:c.775G>A|ENSP00000367890.1:p.Ala259Thr|980/3653|775/1776|259/591|A/T|Gcc/Acc|rs199931813&COSM2186304||-1||SNV|HGNC|HGNC:29831|YES|1|A2|CCDS55562.1|ENSP00000367890|O95544||UPI000013CBEB||Ensembl|C|C|||tolerated_low_confidence(0.66)|benign(0)|HAMAP:MF_00361||0.0004|0|0|0|0.002|0|0.004133|0.0006937|0.0005605|0.01324|0|0.005884|0.006368|0.002555|0.001275|0.01324|gnomAD_ASJ||0&1|0&1|||||;hg19_chr=1;hg19_pos=1688550;cds_strand=-;refcodon=GCC;codonpos=1;codon_degeneracy=0;Ancestral_allele=C;AltaiNeandertal=./.;Denisova=./.;Ensembl_geneid=ENSG00000008130;Ensembl_transcriptid=ENST00000378625;Ensembl_proteinid=ENSP00000367890;LRT_score=0.591224;LRT_converted_rankscore=0.05588;LRT_pred=U;LRT_Omega=1.404420;MutationTaster_score=1,1,1,1,1;MutationTaster_converted_rankscore=0.08979;MutationTaster_pred=N,N,N,N,N;MutationTaster_model=simple_aae,simple_aae,without_aae,without_aae,without_aae;MutationTaster_AAE=A259T,A259T,.,.,.;MutationAssessor_UniprotID=.;MutationAssessor_variant=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=0.91;FATHMM_converted_rankscore=0.44858;FATHMM_pred=T;PROVEAN_score=-0.04;PROVEAN_converted_rankscore=0.07606;PROVEAN_pred=N;Transcript_id_VEST3=ENST00000378625,NM_001198994.1,ENST00000344463;Transcript_var_VEST3=A259T,A259T,A259T;VEST3_score=0.016,0.016,0.017;VEST3_rankscore=0.00296;MetaSVM_score=-1.0467;MetaSVM_rankscore=0.15317;MetaSVM_pred=T;MetaLR_score=0.0509;MetaLR_rankscore=0.21651;MetaLR_pred=T;Reliability_index=10;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;REVEL_score=0.028;REVEL_rankscore=0.06556;MutPred_score=.;MutPred_rankscore=.;MutPred_protID=.;MutPred_AAchange=.;MutPred_Top5features=.;CADD_raw=-0.340294;CADD_raw_rankscore=0.06553;CADD_phred=0.536;DANN_score=0.66932906727060915;DANN_rankscore=0.07963;fathmm-MKL_coding_score=0.01558;fathmm-MKL_coding_rankscore=0.05045;fathmm-MKL_coding_pred=N;fathmm-MKL_coding_group=AEFBI;Eigen_coding_or_noncoding=c;Eigen-raw=-1.47882079249812;Eigen-phred=0.08786482;Eigen-PC-raw=-1.52959862678593;Eigen-PC-phred=0.09699956;Eigen-PC-raw_rankscore=0.02082;GenoCanyon_score=0.65871501298584;GenoCanyon_score_rankscore=0.22232;integrated_fitCons_score=0.460665;integrated_fitCons_score_rankscore=0.09008;integrated_confidence_value=0;GM12878_fitCons_score=0.577304;GM12878_fitCons_score_rankscore=0.32598;GM12878_confidence_value=0;H1-hESC_fitCons_score=0.575934;H1-hESC_fitCons_score_rankscore=0.26927;H1-hESC_confidence_value=0;HUVEC_fitCons_score=0.491896;HUVEC_fitCons_score_rankscore=0.06948;HUVEC_confidence_value=0;GERP++_NR=2.79;GERP++_RS=-0.673;GERP++_RS_rankscore=0.10751;phyloP100way_vertebrate=-1.278000;phyloP100way_vertebrate_rankscore=0.02896;phyloP20way_mammalian=-0.159000;phyloP20way_mammalian_rankscore=0.10730;phastCons100way_vertebrate=0.000000;phastCons100way_vertebrate_rankscore=0.06329;phastCons20way_mammalian=0.000000;phastCons20way_mammalian_rankscore=0.01567;SiPhy_29way_pi=0.2057:0.4572:0.2015:0.1356;SiPhy_29way_logOdds=1.6517;SiPhy_29way_logOdds_rankscore=0.02582;gnomAD_exomes_AC=605;gnomAD_exomes_AN=147092;gnomAD_exomes_AF=4.113072e-03;gnomAD_genomes_AC=129;gnomAD_genomes_AN=30896;gnomAD_genomes_AF=4.175298e-03;Interpro_domain=Inorganic polyphosphate/ATP-NAD kinase, domain 1;GTEx_V6p_gene=.;GTEx_V6p_tissue=.     GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM      ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. 1/1:8:8:6,2:0,0:0,8:1:0,2:22.6:1:34.9:1:1:0:60:16:1:0:2.8       ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.       ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.       ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.

Somehow the somatic flag in this record is parsed as "0&1". The annotation on this record was made with the latest VEP.

[lbeltrame]

My guess is that it's probably related to #55 (in that case I also get empty strings somatic flags).

[lbeltrame]

I've figured out what happens. VEP has a field called SOMATIC and when building things in gene_info it will overwrite whatever is in the variant record (since we already have a SOMATIC there), causing issues to no end down the road.