Provide some options to reduce output files

iqbal-lab-org / make_prg

Code to create a PRG from a Multiple Sequence Alignment file

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Provide some options to reduce output files #26

Closed mbhall88 closed 3 years ago

mbhall88 commented 3 years ago

Added

-S, --seqid option to name the PRG sequence, which by default uses the file name.
-N shortcut for max nesting
-L shortcut for min match length
--log to enable specifying log file should go to path. Default behaviour is now that log goes to stderr by default
--summary option to specify that user wants a summary file, rather than the default behaviour where they get no choice
-O, --output-type option to specify what output files are required. Defaults to all

Changed

Summary file not written by default

mbhall88 commented 3 years ago

Lovely code, I learned from the OutputType class, and nice tests on the class.

Yeah, I recently implemented something similar in rasusa for allowing the user to specify the compression format. I basically stole the idea from bcftools -O option

mbhall88 commented 3 years ago

I guess merging this will require us to bump the version to 0.2.0. Is this going to cause problems with your prototype @leoisl?

leoisl commented 3 years ago

Yeah, this is a bit annoying, I am sorry. We can either: bump to version 0.1.2; or just bump to 0.2.0, and treat my fork and this fork totally separate (I don't really like this option).

The issue is that we are still not sure that we will keep the dynamic updates or change to another method to update the PanRG. However, as it is on the paper, I do think we should at least push the dynamic updates to the main repo. I think I will drop all my current priorities, and make the dynamic-update make_prg stable, finishing its interfacing with gramtools, adding unit tests, etc. Then we can merge it to this repo, and therefore have a single main branch of development. The later I push this, the harder will also be to solve the conflicts when merging. What do you think? @iqbal-lab Ok to do that, or would you prefer to leave this merge for later?

iqbal-lab commented 3 years ago

Fine with me, I thought it was already merged

mbhall88 commented 3 years ago

Well it sounds like the best option is to not make a release for the stuff in this PR and instead wait until you merge your fork into this main fork. Then we can release it all as v0.2.0 - a mega release!