Mercurial > repos > simon-gladman > snippy
comparison snippy_core_wrapper.pl @ 22:577b1b17a0ff draft default tip
Added snippy-core tool
| author | simon-gladman |
|---|---|
| date | Thu, 09 Jun 2016 09:44:50 -0400 |
| parents | bcb74072d3a6 |
| children |
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| 21:ebd7a957ff4b | 22:577b1b17a0ff |
|---|---|
| 53 sub setOptions { | 53 sub setOptions { |
| 54 use Getopt::Long; | 54 use Getopt::Long; |
| 55 | 55 |
| 56 @Options = ( | 56 @Options = ( |
| 57 {OPT=>"help", VAR=>\&usage, DESC=>"This help"}, | 57 {OPT=>"help", VAR=>\&usage, DESC=>"This help"}, |
| 58 {OPT=>"mincov=f", VAR=>\$mincov, DEFAULT=>'10.0', DESC=>"The minimum coverage to consider."}, | 58 {OPT=>"mincov=i", VAR=>\$mincov, DEFAULT=>'10.0', DESC=>"The minimum coverage to consider."}, |
| 59 {OPT=>"noref!", VAR=>\$noref, DEFAULT=>0, DESC=>"Don't include the reference in the alignment."}, | 59 {OPT=>"noref!", VAR=>\$noref, DEFAULT=>0, DESC=>"Don't include the reference in the alignment."}, |
| 60 {OPT=>"indirs=s", VAR=>\$indirs, DEFAULT=>"", DESC=>"A whitespace delimited list of the snippy output zipped dirs."}, | 60 {OPT=>"indirs=s", VAR=>\$indirs, DEFAULT=>"", DESC=>"A whitespace delimited list of the snippy output zipped dirs."}, |
| 61 ); | 61 ); |
| 62 | 62 |
| 63 &GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) || usage(); | 63 &GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) || usage(); |