Commit 32ace308 authored by Holger Brandl's avatar Holger Brandl
Browse files

added workaround for MT chromosome

parent de486ecb
......@@ -159,13 +159,14 @@ chromInfo <- read_tsv(chromInfoFile, col_names=F) %>% set_names("chromosome", "c
read_tsv(chromInfoFile, col_names=F) %>%
set_names("chromosome", "chr_length") %>%
mutate(chromosome=str_replace(chromosome, "chrM", "MT") %>% str_replace("chr", "")) %>%
mutate(chromosome=str_replace(chromosome, "M", "MT") %>% str_replace("chr", "")) %>%
mutate(chromosome=str_replace(chromosome, "chrM", "M") %>% str_replace("chr", "")) %>%
mutate(chromosome=factor(as.character(chromosome), levels=chrOrderBam)) %>% arrange(chromosome) %>%
filter(!is.na(chromosome)) %>%
write.delim(stdout(), header=F, quote=F)
' | Rscript --vanilla - $1 $2 2> /dev/null
}
cs_sync_order_bam2bed
export -f cs_sync_order_chrominfo2bam
cs_sync_order_bam2bed(){
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment