a7c9586b9cdeefd418f099915bf06c51981297f8
angie
  Tue Dec 20 11:53:25 2016 -0800
Added command line options for filtering output by functional category.  refs #12216 note-25

diff --git src/hg/utils/vai.pl src/hg/utils/vai.pl
index e5cd4cd..4b5c4d0 100755
--- src/hg/utils/vai.pl
+++ src/hg/utils/vai.pl
@@ -24,30 +24,52 @@
 
 # GetOpt option configuration for options that don't directly map to hgva_... CGI params,
 # and references to the corresponding global variables or handlers:
 my %optionConfig = ('hgVai=s' => \$hgVai,
                     'position=s' => \$position,
                     'rsId' => \$rsId,
                     'udcCache' => \$udcCache,
                     'dry-run|n|debug' => \$debug,
                     'help|h' => sub { usage(0) },
                    );
 
 # Command line options that map directly to hgva_... CGI params, with their default values
 # and descriptions
 my %paramOptions = ( geneTrack => ['refGene', '=track',
                                    'Genome Browser track with transcript predictions'],
+                     include_intergenic => ['on', '=on|off',
+                                            'Include intergenic variants in output'],
+                     include_upDownstream => ['on', '=on|off',
+                                              'Include upstream and downstream variants in output'],
+                     include_nmdTranscript => ['on', '=on|off',
+                                               'Include variants in NMD transcripts in output'],
+                     include_exonLoss => ['on', '=on|off',
+                                          'Include exon loss variants in output'],
+                     include_utr => ['on', '=on|off',
+                                     'Include 3\' and 5\' UTR variants in output'],
+                     include_cdsSyn => ['on', '=on|off',
+                                        'Include CDS synonymous variants in output'],
+                     include_cdsNonSyn => ['on', '=on|off',
+                                           'Include CDS non-synonymous variants in output'],
+                     include_intron => ['on', '=on|off',
+                                        'Include intron variants in output'],
+                     include_splice => ['on', '=on|off',
+                                        'Include splice site and splice region variants in output'],
+                     include_nonCodingExon => ['on', '=on|off',
+                                               'Include non-coding exon variants in output'],
+                     include_noVariation => ['on', '=on|off',
+                                             'Include "variants" with no observed variation in output'],
                      variantLimit => [10000, '=N',
                                       'Maximum number of variants to process'],
                    );
 
 
 # CGI params and values to be passed to hgVai are collected here:
 my %hgVaiParams = ( $doQueryParam => 'go',
                   );
 
 sub usage($) {
   # Show usage and exit with the given status.
   my ($status) = @_;
 
   print STDERR <<EOF