{"action":"created","issue":{"url":"https://api.github.com/repos/atks/vt/issues/21","labels_url":"https://api.github.com/repos/atks/vt/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/atks/vt/issues/21/comments","events_url":"https://api.github.com/repos/atks/vt/issues/21/events","html_url":"https://github.com/atks/vt/issues/21","id":74126389,"number":21,"title":"running uniq causes loss of data in INFO field. ","user":{"login":"deannachurch","id":4339273,"avatar_url":"https://avatars.githubusercontent.com/u/4339273?v=3","gravatar_id":"","url":"https://api.github.com/users/deannachurch","html_url":"https://github.com/deannachurch","followers_url":"https://api.github.com/users/deannachurch/followers","following_url":"https://api.github.com/users/deannachurch/following{/other_user}","gists_url":"https://api.github.com/users/deannachurch/gists{/gist_id}","starred_url":"https://api.github.com/users/deannachurch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deannachurch/subscriptions","organizations_url":"https://api.github.com/users/deannachurch/orgs","repos_url":"https://api.github.com/users/deannachurch/repos","events_url":"https://api.github.com/users/deannachurch/events{/privacy}","received_events_url":"https://api.github.com/users/deannachurch/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-05-07T21:00:11Z","updated_at":"2015-05-07T22:31:04Z","closed_at":null,"body":"I've just take a VCF file and ran normalize on it to get the following results:\r\n\r\n````\r\n1       1886346 rs35830547      G       GGCC    .       PASS    DBSNP=dbSNP_126;EA_AC=1377,3247;AA_AC=1189,1297;TAC=2566,4544;MAF=29.7794,47.8278,36.09;GTS=A1A1,A1R,RR;EA_GTC=306,765,1241;AA_GTC=406,377,460;GTC=712,1142,1701;DP=90;GL=KIAA1751;CP=0;CG=0.6;AA=.;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_001080484.1:utr-3;HGVS_CDNA_VAR=NM_001080484.1:c.*669_*670insCGG;HGVS_PROTEIN_VAR=.;CDS_SIZES=NM_001080484.1:2289;GS=.;PH=.;EA_AGE=.;AA_AGE=.;GRCh38_POSITION=1:1954908;OLD_VARIANT=1:1886347:G/GCCG\r\n1       1886346 ~rs35830547     G       GGCC    .       PASS    DBSNP=dbSNP_126;EA_AC=1375,3249;AA_AC=1194,1296;TAC=2569,4545;MAF=29.7362,47.9518,36.1119;GTS=A1A1,A1R,RR;EA_GTC=305,765,1242;AA_GTC=408,378,459;GTC=713,1143,1701;DP=90;GL=KIAA1751;CP=0;CG=0.2;AA=.;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_001080484.1:utr-3;HGVS_CDNA_VAR=NM_001080484.1:c.*668_*669insGCG;HGVS_PROTEIN_VAR=.;CDS_SIZES=NM_001080484.1:2289;GS=.;PH=.;EA_AGE=.;AA_AGE=.;GRCh38_POSITION=1:1954909;OLD_VARIANT=1:1886348:C/CCGC\r\n1       1886346 ~rs35830547     G       GGCC    .       PASS    DBSNP=dbSNP_126;EA_AC=1374,3246;AA_AC=1190,1296;TAC=2564,4542;MAF=29.7403,47.8681,36.0822;GTS=A1A1,A1R,RR;EA_GTC=305,764,1241;AA_GTC=406,378,459;GTC=711,1142,1700;DP=88;GL=KIAA1751;CP=0;CG=-0.3;AA=.;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_001080484.1:utr-3;HGVS_CDNA_VAR=NM_001080484.1:c.*667_*668insGGC;HGVS_PROTEIN_VAR=.;CDS_SIZES=NM_001080484.1:2289;GS=.;PH=.;EA_AGE=.;AA_AGE=.;GRCh38_POSITION=1:1954910;OLD_VARIANT=1:1886349:C/CGCC\r\n````\r\n\r\nbut then when I run uniq, only one of the 'OLD_VARIANT' tags is added\r\n````\r\n1       1886346 ~rs35830547     G       GGCC    .       PASS    DBSNP=dbSNP_126;EA_AC=1374,3246;AA_AC=1190,1296;TAC=2564,4542;MAF=29.7403,47.8681,36.0822;GTS=A1A1,A1R,RR;EA_GTC=305,764,1241;AA_GTC=406,378,459;GTC=711,1142,1700;DP=88;GL=KIAA1751;CP=0;CG=-0.3;AA=.;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_001080484.1:utr-3;HGVS_CDNA_VAR=NM_001080484.1:c.*667_*668insGGC;HGVS_PROTEIN_VAR=.;CDS_SIZES=NM_001080484.1:2289;GS=.;PH=.;EA_AGE=.;AA_AGE=.;GRCh38_POSITION=1:1954910;OLD_VARIANT=1:1886349:C/CGCC\r\n````\r\n\r\nIt would be good to carrier the INFO field for all of them."},"comment":{"url":"https://api.github.com/repos/atks/vt/issues/comments/100038500","html_url":"https://github.com/atks/vt/issues/21#issuecomment-100038500","issue_url":"https://api.github.com/repos/atks/vt/issues/21","id":100038500,"user":{"login":"atks","id":3708476,"avatar_url":"https://avatars.githubusercontent.com/u/3708476?v=3","gravatar_id":"","url":"https://api.github.com/users/atks","html_url":"https://github.com/atks","followers_url":"https://api.github.com/users/atks/followers","following_url":"https://api.github.com/users/atks/following{/other_user}","gists_url":"https://api.github.com/users/atks/gists{/gist_id}","starred_url":"https://api.github.com/users/atks/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/atks/subscriptions","organizations_url":"https://api.github.com/users/atks/orgs","repos_url":"https://api.github.com/users/atks/repos","events_url":"https://api.github.com/users/atks/events{/privacy}","received_events_url":"https://api.github.com/users/atks/received_events","type":"User","site_admin":false},"created_at":"2015-05-07T22:31:04Z","updated_at":"2015-05-07T22:31:04Z","body":"The merging of the INFO fields will be tricky here.  \r\n\r\nI can make a special case of the OLD_VARIANT tag and merge the values found there.  The other INFO tags I am not willing to merge because of ambiguity encountered if the INFO tag has an expectation of the number of values that is recorded.\r\n\r\nIs this ok?\r\n"}}