-V version not in help

[dariober]

Hi- Small bug, unless I'm missing something... Using version 0.5 it appears the -V option to print version works but is not listed by the help printout:

./Genrich/Genrich -V
Genrich, version 0.5
Copyright (C) 2018 John M. Gaspar (jsh58@wildcats.unh.edu)

./Genrich/Genrich -h 
Usage: ./Genrich  -t <file>  -o <file>  [optional arguments]
Required arguments:
  -t  <file>       Input SAM/BAM file(s) for experimental sample(s)
  -o  <file>       Output peak file (in ENCODE narrowPeak format)
Optional I/O arguments:
  -c  <file>       Input SAM/BAM file(s) for control sample(s)
  -f  <file>       Output bedgraph-ish file for p/q values
  -k  <file>       Output bedgraph-ish file for pileups and p-values
  -b  <file>       Output BED file for reads/fragments/intervals
  -R  <file>       Output file for PCR duplicates (only with -r)
Filtering options:
  -r               Remove PCR duplicates
  -e  <arg>        Comma-separated list of chromosomes to exclude
  -E  <file>       Input BED file(s) of genomic regions to exclude
  -m  <int>        Minimum MAPQ to keep an alignment (def. 0)
  -s  <float>      Keep sec alns with AS >= bestAS - <float> (def. 0)
  -y               Keep unpaired alignments (def. false)
  -w  <int>        Keep unpaired alns, lengths changed to <int>
  -x               Keep unpaired alns, lengths changed to paired avg
Options for ATAC-seq:
  -j               Use ATAC-seq mode (def. false)
  -d  <int>        Expand cut sites to <int> bp (def. 100)
Options for peak-calling:
  -q  <float>      Maximum q-value (FDR-adjusted p-value; def. 0.05)
  -p  <float>      Maximum p-value (overrides -q if set)
  -a  <float>      Minimum AUC for a peak (def. 20.0)
  -l  <int>        Minimum length of a peak (def. 0)
  -g  <int>        Maximum distance between signif. sites (def. 100)
Other options:
  -X               Skip peak-calling
  -P               Call peaks directly from a log file (-f)
  -z               Option to gzip-compress output(s)
  -v               Option to print status updates/counts to stderr

[jsh58]

True, there's no description of -V/--version nor -h/--help in the usage message. My preference is to keep the usage message as brief as possible. Those are pretty standard arguments anyway.

[ginolhac]

I like your software, very efficient and clear documentation but I have to admit that @dariober has a point. The classic options for version are -v and --version and here -v is not printing the version. Since the case of v does matter, I think version could be listed in the help.

[jsh58]

I appreciate the interest. However, -v/--verbose are also standard options. Full descriptions of all the command-line options of Genrich are in the README.