76b1ff207748ca1da3d929e5286ccb72bd0528ef
angie
  Wed Jun 12 13:29:36 2013 -0700
Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42.  refs #6152
diff --git src/hg/hgVai/hgVai.c src/hg/hgVai/hgVai.c
index 75ef188..e85b7f9 100644
--- src/hg/hgVai/hgVai.c
+++ src/hg/hgVai/hgVai.c
@@ -455,31 +455,31 @@
     else
 	safef(cartVar, sizeof(cartVar), "hgva_track_%s_%s", database, table);
     boolean defaultChecked = (sameString("dbNsfpSift", table) ||
 			      sameString("dbNsfpPolyPhen2", table));
     cartMakeCheckBox(cart, cartVar, defaultChecked);
     printf("%s<BR>\n", description);
     }
 }
 
 void selectDbNsfp(struct slName *dbNsfpTables)
 /* Let user select scores/predicitions from various tools collected by dbNSFP. */
 {
 if (dbNsfpTables == NULL)
     return;
 startCollapsibleSection("dbNsfp", "Database of Non-synonymous Functional Predictions (dbNSFP)",
-			FALSE);
+			TRUE);
 printf("<A HREF='https://sites.google.com/site/jpopgen/dbNSFP' TARGET=_BLANK>dbNSFP</A> "
        "(<A HREF='http://onlinelibrary.wiley.com/doi/10.1002/humu.21517/abstract' "
        "TARGET=_BLANK>Liu <em>et al.</em> 2011</A>) "
        "release 2.0 "
        "provides pre-computed scores and predictions of functional significance "
        "from a variety of tools.  Every possible coding change to transcripts in "
  //#*** hardcoded version info... sigh, we need trackDb... or metaDb??
        "Gencode release 9 (Ensembl 64, Dec. 2011) gene predictions "
        "has been evaluated.  "
        "<em>Note: This may not encompass all transcripts in your "
        "selected gene set.</em><BR>\n");
 //#*** Another cheap hack: reverse alph order happens to be what we want,
 //#*** but priorities would be cleaner:
 slReverse(&dbNsfpTables);
 struct slName *table;
@@ -538,31 +538,31 @@
 struct trackDb *tdb = tdbForTrack(database, table->name, &fullTrackList);
 if (tdb != NULL)
     {
     if (retTdb != NULL)
 	*retTdb = tdb;
     return TRUE;
     }
 return foundIt;
 }
 
 void selectDbSnp(boolean gotSnp)
 /* Offer to include rsID (and other fields, or leave that for advanced output??) if available */
 {
 if (!gotSnp)
     return;
-startCollapsibleSection("dbSnp", "Known variation", FALSE);
+startCollapsibleSection("dbSnp", "Known variation", TRUE);
 cartMakeCheckBox(cart, "hgva_rsId", TRUE);
 printf("Include <A HREF='http://www.ncbi.nlm.nih.gov/projects/SNP/' TARGET=_BLANK>dbSNP</A> "
        "rs# ID if one exists<BR>\n");
 puts("<BR>");
 endCollapsibleSection();
 }
 
 boolean isConsElTrack(struct trackDb *tdb, void *filterData)
 /* This is a TdbFilterFunction to get "phastConsNwayElements" tracks. */
 {
 return (startsWith("phastCons", tdb->table) && stringIn("Elements", tdb->table));
 }
 
 boolean isConsScoreTrack(struct trackDb *tdb, void *filterData)
 /* This is a TdbFilterFunction to get tracks that start with "phastCons" (no Elements)
@@ -627,31 +627,31 @@
 puts("<BR>");
 printf("<div class='sectionLiteHeader'>Select More Annotations (optional)</div>\n");
 // Make wrapper table for collapsible sections:
 puts("<TABLE border=0 cellspacing=5 cellpadding=0 style='padding-left: 10px;'>");
 selectDbNsfp(dbNsfpTables);
 selectDbSnp(gotSnp);
 selectCons(elTrackRefList, scoreTrackRefList);
 puts("</TABLE>");
 }
 
 void selectFiltersFunc()
 /* Options to restrict variants based on gene region/soTerm from gpFx */
 {
 startCollapsibleSection("filtersFunc", "Functional role", FALSE);
 printf("Include variants annotated as<BR>\n");
-cartMakeCheckBox(cart, "hgva_include_intergenic", FALSE);
+cartMakeCheckBox(cart, "hgva_include_intergenic", TRUE);
 printf("intergenic<BR>\n");
 cartMakeCheckBox(cart, "hgva_include_upDownstream", TRUE);
 printf("upstream/downstream of gene<BR>\n");
 cartMakeCheckBox(cart, "hgva_include_utr", TRUE);
 printf("5' or 3' UTR<BR>\n");
 cartMakeCheckBox(cart, "hgva_include_cdsSyn", TRUE);
 printf("CDS - synonymous coding change<BR>\n");
 cartMakeCheckBox(cart, "hgva_include_cdsNonSyn", TRUE);
 printf("CDS - non-synonymous (missense, stop gain/loss, frameshift etc)<BR>\n");
 cartMakeCheckBox(cart, "hgva_include_intron", TRUE);
 printf("intron<BR>\n");
 cartMakeCheckBox(cart, "hgva_include_splice", TRUE);
 printf("splice site or splice region<BR>\n");
 cartMakeCheckBox(cart, "hgva_include_nonCodingExon", TRUE);
 printf("exon of non-coding gene<BR>\n");