hepcat72 / htseq2multx Goto Github PK

#1 (comment)

Which would change the goal stated in the requirements on line 5:

https://github.com/PrincetonUniversity/htseq/pull/88/files#diff-3c65b2d41a08a66bc1dbaf00ebf795a7R5

I don't think that the check on the tab character is necessary anymore, but in the absence of documentation explaining why it was put there, there's no way to know for sure.

In fact, with the new accurate monitoring of the exit code of the fastq-multx executable via IO::Pipe::Producer v2.02, using STDERR content to make errors fatal may be unnecessary as well.

Try removing the tab check and see if things work. If they don't, but it back and document why it's there.

Original comment

Yeah, I also struggled over the tab and decided to err on the side of keeping the behavior consistent. I think it's entirely possible that I'd added the tab requirement to mitigate cases where $CHILD_ERROR was non-zero in the original code yet the output was complete. I wish I'd documented why I put that tab-case there.

I suspect that I had mis-remembered how IO::Pipe::Producer exits and that the child could have been exiting non-zero for a legitimate reason despite it looking successful, but I feel like I remember finding code in fastq-multx source where it was exiting non-0 for an inane reason.

It could be that I have fixed things such that it won't inappropriately exit non-0, in which case the tab check is unnecessary. Unfortunately, the only way to find out would be in the wild. So what do you think? Should I remove the tab check and risk a job failing so that I can improve this code or err on the side of consistency?

Originally posted by @hepcat72 in #9 (comment)

It would be nice to have the tests automated in some continuous integration system, GitHub actions, Travis, CircleCI, etc.

• GitHub actions - Setup a Perl environment
• Travis - Building a Perl Project
• CircleCI - Perl is supported, but no demo just yet

Line 536 seems to be generating an error on my system.

sh: 1: Syntax error: Bad fd number

The following extra and modified options apply specifically to the htseq2multx.pl wrapper (as opposed to barcode_splitter).

optional arguments:
  -h, --help            Supply twice to show this message and exit.
  --version             Supply once to get the barcode_splitter version that
                        this wrapper emulates.  Supply twice to get a more
                        verbose version of the barcode_splitter version that
                        this wrapper emulates and the version of this wrapper.

configuration arguments:
  --fastq-multx PATH    Path to the fastq-multx installation.  Default is to use
                        the PATH in the user's environment.
  --debug               Supply this flag to output the fastq-multx command on
                        standard error and not delete the temporary barcode
                        file.
ERROR: The fastq-multx executable appears to not be fastq-multx according to the first 2 lines of its usage.  Use the --fastq-multx option described above to supply fastq-multx.