Feature request: check return codes of LAST, validate input in bash script

[wdecoster]

Hi,

Sorry, it's me again. Test driving Picky on a relatively small dataset before I'll do any big comparisons.

Before I realized I had to manually modify the LongRead.sh script which was written by Picky.pl script, I executed the script, which just ran without printing obvious error messages. I had to check a log file to figure out what was wrong. In this case, I did not set my lastdb and did not change the lastal executable.

I would suggest you:

• check if the input specified in the bash script is valid (e.g. file or executable exists) and raise errors early and explicitly state the problem.

• check the return codes of LAST and other commands in the bash script and act accordingly. Now the script just continues. Partially, this could be addressed using the solution provided here: https://stackoverflow.com/a/2871034/6631639

• provide options/flags to set the lastdb/lastal executable in the picky.pl script script. Manually editing the bash script is annoying.

Users are dumb and unfortunately, need a lot of help to figure out issues which are probably obvious to the developers. I'm waiting for a reply from my supervisor and have some time left today, but if I was in a hurry I would probably already have given up on Picky :-(

Cheers,
Wouter