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CFSAN-Biostatistics / snp-pipeline

SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
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samtools version check #19

Closed rlpires closed 4 years ago

rlpires commented 4 years ago

The minimal version requirement for samtools fails if for example the user deploys samtools version 1.10. This is because as a number 1.10 is smaller than the minimal version, 1.4. A fix is straightforward. What is the protocol, should I submit a pull request?

Greets, -- RP

stevendavis commented 4 years ago

Sure, you may submit a pull request. You may also add yourself to AUTHORS.rst if you would like to do so. You will be our first external contributor.

rlpires commented 4 years ago

Sure, you may submit a pull request. You may also add yourself to AUTHORS.rst if you would like to do so. You will be our first external contributor.

OK, I shall start a pull request. According to your flow, to which branch should it go? Adding myself to the AUTHORS file with such a minimal change will give me an impostor syndrome feeling!

stevendavis commented 4 years ago

Please make the change in the 2.2-branch. I will propagate the changes to master and release the next version. There are samtools versions checks in run.py and map_reads.py.

stevendavis commented 4 years ago

Fixed in version 2.2.1. I had to fix something else and just went ahead and fixed this also.