9c97053863a72bc89330747d32a1c36d0bdfb706
angie
  Fri Oct 20 15:12:53 2017 -0700
Adding HGVS options to vai.pl (HGVS terms are included by default if RefSeq transcripts are chosen).

diff --git src/hg/utils/vai.pl src/hg/utils/vai.pl
index ba31029..abfb991 100755
--- src/hg/utils/vai.pl
+++ src/hg/utils/vai.pl
@@ -24,30 +24,35 @@
 
 # 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=s' => \$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'],
+                     hgvsG => ['on', '=on|off', 'Include HGVS g. (genomic) terms in output (RefSeq transcripts only)'],
+                     hgvsCN => ['on', '=on|off', 'Include HGVS c./n. (coding/noncoding) terms in output (RefSeq transcripts only)'],
+                     hgvsP => ['on', '=on|off', 'Include HGVS p. (protein) terms in output (RefSeq transcripts only)'],
+                     hgvsPAddParens => ['off', '=on|off', 'Add parentheses around HGVS p. predicted changes'],
+                     hgvsBreakDelIns => ['off', '=on|off', 'HGVS delins: show "delAGinsTT" instead of "delinsTT"'],
                      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',