Nothing
.aseq.Run <- function(bam.files,aseq.path,genotype.dir,out.dir,mbq,mrq,mdc,model.path,cores,bam.chr.encoding)
{
tryCatch(
{
## Create VCF file
model = snpgdsOpen(model.path,readonly = F)
snp.list = snpgdsSNPList(model)
vcf = cbind(snp.list$chromosome,
pos=snp.list$position,
sapply(strsplit(snp.list$snp.id,':'),'[[',3),
read.gdsn(index.gdsn(model,"snp.ref")),
read.gdsn(index.gdsn(model,"snp.alt")),
".",".",".")
colnames(vcf)= c("#CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO")
if(bam.chr.encoding)
vcf[,1] = paste("chr",vcf[,1],sep="")
write.table(vcf,file.path(out.dir,"ModelPositions.vcf"),sep="\t",quote=F,row.names=F)
snpgdsClose(model)
## Check ASEQ path or download
if(.get.OS()=="linux")
{
aseq.exec = file.path(aseq.path,"ASEQ")
if(!file.exists(aseq.exec))
{
download.file("https://github.com/cibiobcg/EthSEQ_Data/raw/master/ASEQ_binaries/linux64/ASEQ",file.path(aseq.path,"ASEQ"))
#unzip(file.path(aseq.path,"ASEQ.zip"),exdir=aseq.path)
Sys.chmod(aseq.exec, mode = "0755", use_umask = TRUE)
}
for (b in bam.files)
{
.message.Date(paste("Computing pileup of BAM file ",b,sep=""))
command = paste(aseq.exec," vcf=",file.path(out.dir,"ModelPositions.vcf")," bam=",b," mode=GENOTYPE threads=",cores," htperc=0.2 mbq=",mbq,
" mrq=",mrq," mdc=",mdc," out=",genotype.dir,sep="")
system(command,ignore.stderr = T,ignore.stdout = T)
}
}
if(.get.OS()=="osx")
{
aseq.exec = file.path(aseq.path,"ASEQ")
if(!file.exists(aseq.exec))
{
download.file("https://github.com/cibiobcg/EthSEQ_Data/raw/master/ASEQ_binaries/macosx/ASEQ",file.path(aseq.path,"ASEQ"))
Sys.chmod(aseq.exec, mode = "0755", use_umask = TRUE)
}
for (b in bam.files)
{
command = paste(aseq.exec," vcf=",file.path(out.dir,"ModelPositions.vcf")," bam=",b," mode=GENOTYPE threads=",cores," htperc=0.2 mbq=",mbq,
" mrq=",mrq," mdc=",mdc," out=",genotype.dir,sep="")
system(command,ignore.stderr = T,ignore.stdout = T)
}
}
if(.get.OS()=="windows")
{
aseq.exec = file.path(aseq.path,"ASEQ.exe")
if(!file.exists(aseq.exec))
{
download.file("https://github.com/cibiobcg/EthSEQ_Data/raw/master/ASEQ_binaries/win32/ASEQ.exe",file.path(aseq.path,"ASEQ.exe"))
}
for (b in bam.files)
{
command = paste(aseq.exec," vcf=",file.path(out.dir,"ModelPositions.vcf")," bam=",b," mode=GENOTYPE threads=",cores," htperc=0.2 mbq=",mbq,
" mrq=",mrq," mdc=",mdc," out=",genotype.dir,sep="")
system(command,ignore.stderr = T,ignore.stdout = T)
}
}
}, error = function(e) {
.message.Date(e)
return(FALSE)
})
return(TRUE)
}
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