vec <- function(x) {

  v <- rep("",le)
  xx <- unlist(x)
  lx <- length(xx)
  l1 <- lx%/%2
  l2 <- 1:l1
  lg <- 2*l2
  lu <- lg-1
  
  ux <-xx[lu]
  gx <-xx[lg]

  ma <- match(ux,fields)

  v[ma] <- gx

  return(v)
}

ancestorSNPsAA <- read.table(paste("/seppdata/sepp/linkage/release_new/ALL.wgs.phase1_intergrated_calls.20101123.snps_indels_svs.sites.vcf",sep=""),header = FALSE, sep = "\t", quote = "",as.is = TRUE,skip=28)


infoA <- ancestorSNPsAA$V8




fields <- c("LDAF","AVGPOST","RSQ","ERATE","THETA","CIEND","CIPOS","END","HOMLEN","HOMSEQ","SVLEN","SVTYPE","AC","AN","DEL","GT","DS","GL","AA","AF","AMR_AF","ASN_AF","AFR_AF","EUR_AF","VT","SNPSOURCE")

le <- length(fields)



LL <- sapply(strsplit(infoA,";"), function(x) strsplit(x,"="))
LL1 <- sapply(LL,vec)


annotationA <- cbind(ancestorSNPsAA$V1,ancestorSNPsAA$V2,ancestorSNPsAA$V3,ancestorSNPsAA$V4,ancestorSNPsAA$V5,t(LL1))


colN <- c("CHROM","POS","ID","REF","ALT","LDAF","AVGPOST","RSQ","ERATE","THETA","CIEND","CIPOS","END","HOMLEN","HOMSEQ","SVLEN","SVTYPE","AC","AN","DEL","GT","DS","GL","AA","AF","AMR_AF","ASN_AF","AFR_AF","EUR_AF","VT","SNPSOURCE")

colnames(annotationA) <- colN

save(annotationA,file="annotationA.Rda")

annotationAChr1 <- annotationA[which(annotationA[,1]=="1"),] 

save(annotationAChr1,file="annotationAChr1.Rda")