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broadinstitute / barclay

Command line argument parser and online documentation generation utilities for java command line programs.
BSD 3-Clause "New" or "Revised" License
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Fix command line data type display to not use an embedded colon. #172

Closed cmnbroad closed 4 years ago

cmnbroad commented 4 years ago

The command line help for the Barclay parser uses a hybrid display format left over from the legacy parser (--input:GATKPath), which is confusing when Barclay parser syntax is being used. This changes the display syntax for the Barclay parser to use --input <GATKPath>, i.e.:

Required Arguments:

--input,-I <GATKPath>         BAM/SAM/CRAM file containing reads  This argument must be specified at least once.
                              Required. 

--output,-O <GATKPath>        Write output to this file  Required. 
...

See GATK https://github.com/broadinstitute/gatk/issues/6775.

codecov[bot] commented 4 years ago

Codecov Report

Merging #172 into master will not change coverage. The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff            @@
##             master     #172   +/-   ##
=========================================
  Coverage     76.64%   76.64%           
  Complexity      743      743           
=========================================
  Files            32       32           
  Lines          2578     2578           
  Branches        498      498           
=========================================
  Hits           1976     1976           
  Misses          406      406           
  Partials        196      196
Impacted Files Coverage Δ Complexity Δ
...ute/barclay/argparser/NamedArgumentDefinition.java 78.59% <100.00%> (ø) 122.00 <0.00> (ø)

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