Enable `create` to take input from stdin
jdidion opened this issue · comments
John Didion commented
It looks like create
relies on the file extension to determine the type of input, which precludes using /dev/stdin
as the input file. Since create
doesn't have many filtering options, it is often necessary to use samtools view
to filter the file (e.g. remove duplicate reads) upstream of create
.
You could be fancy and try to sniff the file type using the magic bytes, or you could just add an option for the user to specify the file type.
Aaron Quinlan commented
We will look into this, but will likely be a while before this could be implemented.