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maize-genetics / phg_v2

Practical Haplotype Graph (PHG) version 2
https://phg.maizegenetics.net/
Apache License 2.0
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[BUG]: map-kmers does not fully strip file extension that includes .gz suffix #205

Closed matthewwiese closed 3 months ago

matthewwiese commented 3 months ago

Description

Hi folks. Minor UX bug. phg map-kmers does not fully strip a .fastq.gz extension as per what is written in the documentation here (scroll down to the "Note" below example directory listing). My mapping keyfile entries look like this:

SRR11038088 data/fastq/PRJNA605407/SRR11038088_1.fastq.gz   data/fastq/PRJNA605407/SRR11038088_2.fastq.gz

The resulting read mapping file looks like SRR11038088_1.fastq_readMapping.txt. Seems like a little bit of additional logic to determine if a file is gzipped is all that's needed.

Not sure if this is addressed in the branch Zack linked me last week - if so, sorry for the unnecessary issue!

I'm loving using v2 so far, the whole experience has been smooth. Also, props on the documentation, it is a dream!

Expected behavior

I expected the full file extension to be removed as is written in the documentation.

PHG version

2.3.16.153

zrm22 commented 3 months ago

Hi Matt,

No this is new, I will update after I merge in the other branch. The other branch will bring PHGv2 up to version 2.4 and we can go from there with new updates. I will keep you posted when this is brought in.

Thanks for bringing it to our attention!

Zack

zrm22 commented 3 months ago

In PR now: here

zrm22 commented 3 months ago

This has been updated with the most recent version of PHGv2.4