informative/progress messages printed to STDERR instead of STDOUT

[carandraug]

While running, mixcr prints some of the messages about progress to STDERR instead of STDOUT. I can submit a patch to fix this, but this seems to be done on purpose although I can't understand why.

[dbolotin]

Hi, sorry for the late response. Originally this was made to allow different kinds of piping (like piping align output directly to assemble action, or something like this). Unfortunately, piping to assemble action is impossible as assemble action reads original vdjca file twice (one for core clonotypes assembly and one for low quality mapping), but still, it is practically possible for example to pipe align action output to exportAlignments.

Like this (this doesn't work, but can easily be implemented):

mixcr align input_R1.fastq input_R2.fastq | mixcr exportAlignments - -

For me it seems like it can be handy in some cases. It would be great to hear your thoughts on this matter.

[carandraug]

I didn't realize that there were plans to make it work with pipes. Indeed, such usage would be very nice and would suit my case perfectly. I would be able to do:

%-clones.txt: %-R1.fastq %-R2.fastq
    mixcr align $^ | mixcr assemble | mixcr exportClones > $@

instead of:

%-clones.txt: %-R1.fastq %-R2.fastq
    mixcr align $^ $*.vdjca > /dev/null
    mixcr assemble $*.vdjca $*.clns  > /dev/null
    mixcr exportClones $*.clns $@  > /dev/null
    $(RM) $*.vdjca $*.clns

On the other hand, I can see how that would be more work for you and I am unsure of how many people would appreciate being able to use pipes.

Whatever way you go, it would be nice to also have options to control that output, either a --progress option (since --verbose is already taken) or a --quiet option.

Something like this two options:

• Moving on to make mixcr being able to use pipes
  • move all progress printed to STDERR
  • have all progress messages off by default and add new --progress option
• Forget about pipes completely
  • move all progress printed to STDOUT
  • add new --quiet option to silence progress information

[PoslavskySV]

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