missing input read files do not throw errors and arguably should

[malcook]

STAR would benefit from catching and raising an error if reading from the input read filesitself raises an error.

At least in one case it does not, namely when --readFilesCommand zcat -f and the --readFilesIn f1,f2,f3 do not exist.

The Log shows it as follows:

ls: cannot access f1: No such file or directory
ls: cannot access f2: No such file or directory
ls: cannot access f3: No such file or directory

Certainly the system call to ls raising an error.

If STAR would itself throw an error in such cases, it would improve the user experience in using it.

[alexdobin]

Good suggestion - thanks, Malcolm!

[alexdobin]

Hi Malcolm

I have pushed a patch into master that fixes this problem, please check it out. There will be an official 2.7.3b release in the next few days.

Cheers
Alex

[malcook]

Finally testing now with version 2.7.9a, I still find that STAR does not raise an error when a file named in readFilesIn does not exist, and does not (at least in combination with --readFilesCommand zcat -f).

;(

[alexdobin]

Hi Malcolm,

thanks for bumping it, will implement this check in the next release.

Cheers
Alex