STDIN not working

[hudja]

Hello,

It seems that --stdin is not working, at least on 0.4.1, 0.4.0 and 0.2.2 versions.

(tst) [hudja@ares18 workflow]$ cat tst.fq | fastplong --stdin
Adapter auto-detection is disabled for STDIN mode
ERROR: read input should be specified by --in, or enable --stdin if you want to read STDIN
(tst) [hudja@ares18 workflow]$ cat tst.fq | ./fastplong.0.4.0 --stdin
Adapter auto-detection is disabled for STDIN mode
ERROR: read input should be specified by --in, or enable --stdin if you want to read STDIN
(tst) [hudja@ares18 workflow]$ cat tst.fq | ./fastplong.0.2.2 --stdin
Adapter auto-detection is disabled for STDIN mode
ERROR: read input should be specified by --in, or enable --stdin if you want to read STDIN

fastplong --in tst.fq works fine though.

Thank you!

[CloXD]

Hi! I had the same issue, peeking in the code I found out that to work you need to specify as well the --in as /dev/stdin
to be on the safe side, I'm running as:

cat tst.fq | fastplong --stdin --in /dev/stdin --stdout --out /dev/stdout

and it works