On 28 Apr 2016, at 15:03, Tagliamonte,Massimiliano S <[email protected]>
wrote:
> ... I'm ashamed to ask... what is the dash ( "-" )before redirecting the
> output?
> i.e.: flagstat - > myfile.stats. If I don't use the dash, it gives me a
> broken pipe error. I did some googling, still not sure of its meaning.
It's a filename argument that many Unix commands interpret specially to mean
standard input (or standard output, depending on context):
http://unix.stackexchange.com/questions/41828/what-does-dash-at-the-end-of-a-command-mean
Many samtools commands take an optional input filename argument or 0-or-more
input filename arguments, and read from standard input if you give zero input
filenames. This is the standard convention for Unix filter commands. So e.g.
"blah | samtools view -" and "blah | samtools view" are equivalent.
However a few samtools commands still require exactly one input filename
command. So "samtools flagstat" just shows the usage instructions, and you
need to say "samtools flagstat -" to get it to read from standard input. (In
our copious spare time, we'll probably eventually get all the samtools commands
to default to standard input if there are no input filenames given: I think
there's only a few left.)
John
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