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Old 03-07-2014, 12:44 PM   #12
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
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As for help, the major problem is the formatting on screens with 80 columns. Wrapping is hard to read plus there is too much information for a quick reference. I suggest trying to limit the help messages to 80 columns and then direct the user to a longer formatted README or extended help. I know that the current help says to look at the README.

Also parsing '-h' on the command line would be nice. While displaying help when no commands are given is good it is also useful to be able to use '-h'.

As an example of the first paragraph, at the moment the help includes:

Code:
maxsites=5          Maximum number of total alignments to print per read.  Only relevant when secondary=t.
quickmatch=f        Generate cigar strings more quickly.  Must be true to generate secondary site cigar strings.
keepnames=f         Keep original names of paired reads, rather than ensuring both reads have the same name.
All useful information to be sure but these could shortened and the extended information put into a formatted README. E.g.

Code:
maxsites=5          Max. number of total alignments to print
quickmatch=f        Generate cigar strings more quickly.
keepnames=f         Keep original names of paired reads
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