Use stderr for all logging messages

[kdm9]

Hi Nik,

We have been using sickle in a UNIX pipeline, and in some cases sickle prints logging or summary information to stdout, which ends up in with the fastq records. This PR simply changes all logging or debugging statements outside of --help and --version to use stderr, not stdout.

[najoshi]

Hi Kevin,

I purposely put summary information on stdout, because stderr should only
be used for diagnostic and error messages. You can use the --quiet option
to suppress the summary output, which should allow it to work in your
pipeline.

• Nik.

On Mon, Jul 13, 2015 at 9:48 PM, Kevin Murray notifications@github.com
wrote:

Hi Nik,

We have been using sickle in a UNIX pipeline, and in some cases sickle
prints logging or summary information to stdout, which ends up in with the
fastq records. This PR simply changes all logging or debugging statements

outside of --help and --version to use stderr, not stdout.

You can view, comment on, or merge this pull request online at:

#43
Commit Summary

• Use stderr for all logging messages

File Changes

• M src/sliding.c
  https://github.com/najoshi/sickle/pull/43/files#diff-0 (10)
• M src/trim_paired.c
  https://github.com/najoshi/sickle/pull/43/files#diff-1 (22)
• M src/trim_single.c
  https://github.com/najoshi/sickle/pull/43/files#diff-2 (4)

Patch Links:

• https://github.com/najoshi/sickle/pull/43.patch
• https://github.com/najoshi/sickle/pull/43.diff

—
Reply to this email directly or view it on GitHub
#43.

Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)

[kdm9]

OK Nik, fair enough. The reason for using stderr is that we would like the information which sickle provides. Would you be interested in a CLI flag which activates stderr logging? Or even logic which automatically redirects all logging to stderr if the output filename(s) are -?