7e6fe97d6d581f789137df6a01edb603954608c2
angie
  Fri Oct 14 10:18:19 2016 -0700
hgVai's UI default for whether to match up input variants with dbSNP is true but the execution part's default was false -- making it consistent with UI default.

diff --git src/hg/hgVai/hgVai.c src/hg/hgVai/hgVai.c
index d7949ca..a96bad4 100644
--- src/hg/hgVai/hgVai.c
+++ src/hg/hgVai/hgVai.c
@@ -2620,31 +2620,31 @@
 
 enum annoGratorOverlap geneOverlapRule = agoMustOverlap;
 struct joinerDtf *txStatusExtras = getTxStatusExtras(database, geneTrack);
 struct jsonElement *gpConfig = configForStreamer(database, geneTdb, txStatusExtras);
 struct annoGrator *gpVarGrator = hAnnoGratorFromTrackDb(assembly, geneTdb->table, geneTdb, chrom,
                                                         ANNO_NO_LIMIT, primary->asObj,
                                                         geneOverlapRule, gpConfig);
 setGpVarFuncFilter(gpVarGrator);
 
 // Some grators may be used as both filters and output values. To avoid making
 // multiple grators for the same source, hash them by trackName:
 struct hash *gratorsByName = hashNew(8);
 
 struct annoGrator *snpGrator = NULL;
 char *snpDesc = NULL;
-if (cartUsualBoolean(cart, "hgva_rsId", FALSE))
+if (cartUsualBoolean(cart, "hgva_rsId", TRUE))
     snpGrator = gratorForSnpBed4(gratorsByName, "", assembly, chrom, agoNoConstraint, &snpDesc);
 
 // Now construct gratorList in the order in which annoFormatVep wants to see them,
 // i.e. first the gpVar, then the snpNNN, then whatever else:
 struct annoGrator *gratorList = NULL;
 slAddHead(&gratorList, gpVarGrator);
 if (snpGrator != NULL)
     slAddHead(&gratorList, snpGrator);
 
 // Text or HTML output?
 char *outFormat = cartUsualString(cart, "hgva_outFormat", "vepTab");
 boolean doHtml = sameString(outFormat, "vepHtml");
 
 // Initialize VEP formatter:
 struct annoFormatter *vepOut = annoFormatVepNew("stdout", doHtml,