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  • #4

Closed
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Opened Aug 24, 2015 by Peter Cock@p-j-a-cock

oa command does not report the version

The current usage text does not report the tool version:

$ oa -h
usage: oa [-h] [--no-log] [--no-progress]
          {list,index,buildgraph,seeds,compact,fasta,path,cutlow,graphstats,unfoldrdna,unfold,fillgaps}
          ...

optional arguments:
  -h, --help            show this help message and exit
  --no-log              Do not create a logfile for the assembling
  --no-progress         Do not print the progress bar during assembling

subcommands:
  valid subcommands

  {list,index,buildgraph,seeds,compact,fasta,path,cutlow,graphstats,unfoldrdna,unfold,fillgaps}
                        additional help
    list                List information about a read index
    index               Index a set of reads
    buildgraph          Build the initial assembling graph
    seeds               Build the set of seed reads
    compact             Recompact the assembling graph
    fasta               Build a fasta file from the assembling graph
    path                Build a fasta file from a path across the assembling
                        graph
    cutlow              Cut low coverage edge in an assembling graph
    graphstats          Print some statistics about the assembling graph
    unfoldrdna          Assembling graph unfolder for the nuclear rDNA complex
    unfold              Universal assembling graph unfolder
    fillgaps            Fill gaps of a partially assembled graph

Furthermore I would have expected oa -v and/or oa --version to report the version only, and immediately exit. e.g.

$ os -v
ORG.asm version 0.1.0b3
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Reference: org-asm/org-asm#4