Covbuildmerge

[jhellewell14]

For the build command the user can now specify --min-count auto and the mixture model from the cov command will be fit to the first two fastq files provided by the user. This calculates a minimum kmer cutoff which is subsequently used in the build command.

• The input for min-count is now a struct that can handle a mix of auto and u16 values. There is a parser in cli.rs called valid_min_kmer that goes from the user provided string to the required struct (ValidMinKmer, defined in cli.rs).
• Added some utility functions that count the number of fastq files in a list of files and select the first 2 of those files in io_utils.rs. Also wrote an iterator version of the function any_fastq.
• Fixed some clippy warning elided lifetimes and other warnings.
• If the user provides a value for min-count it is used unless it is <1. If they specify auto an attempt is made to fit the mixture model. If this works the inferred value is used. If there are less than 2 fastq files passed by the user the default value of 5 is used. If no value is provided for min-count the default value of 5 is used. All activity regarding the value used is reported to the user via log::info!.

[johnlees]

Looks good! One question about whether we can use a generic

And I guess we should merge in master which will hopefully fix codecov

[codecov]

Codecov Report

Attention: Patch coverage is 92.42424% with 5 lines in your changes missing coverage. Please review.

Project coverage is 96.07%. Comparing base (d66b021) to head (394edf1).
Report is 18 commits behind head on master.

Files with missing lines	Patch %	Lines
src/io_utils.rs	90.90%	4 Missing ⚠️
src/cli.rs	90.90%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #89      +/-   ##
==========================================
+ Coverage   93.10%   96.07%   +2.96%     
==========================================
  Files          16       16              
  Lines        2263     2803     +540     
==========================================
+ Hits         2107     2693     +586     
+ Misses        156      110      -46     

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[johnlees]

Nice!