07f19e67fafd6351ff6408c07c4e6b546f3cbb16
angie
  Mon Dec 19 11:03:05 2016 -0800
Make hgVai's back-end default for include_intergenic the same as the UI default.  refs #12216 note-23

diff --git src/hg/hgVai/hgVai.c src/hg/hgVai/hgVai.c
index 2f4e388..97b1d58 100644
--- src/hg/hgVai/hgVai.c
+++ src/hg/hgVai/hgVai.c
@@ -1368,31 +1368,31 @@
 }
 
 void textOpen()
 /* Start serving up plain text, possibly via a pipeline to gzip. */
 {
 char *fileName = cartUsualString(cart, "hgva_outFile", "");
 char *compressType = cartUsualString(cart, "hgva_compressType", textOutCompressGzip);
 compressPipeline = textOutInit(fileName, compressType, NULL);
 }
 
 void setGpVarFuncFilter(struct annoGrator *gpVarGrator)
 /* Use cart variables to configure gpVarGrator's filtering by functional category. */
 {
 struct annoGratorGpVarFuncFilter aggvFuncFilter;
 ZeroVar(&aggvFuncFilter);
-aggvFuncFilter.intergenic = cartUsualBoolean(cart, "hgva_include_intergenic", FALSE);
+aggvFuncFilter.intergenic = cartUsualBoolean(cart, "hgva_include_intergenic", TRUE);
 aggvFuncFilter.upDownstream = cartUsualBoolean(cart, "hgva_include_upDownstream", TRUE);
 aggvFuncFilter.nmdTranscript = cartUsualBoolean(cart, "hgva_include_nmdTranscript", TRUE);
 aggvFuncFilter.exonLoss = cartUsualBoolean(cart, "hgva_include_exonLoss", TRUE);
 aggvFuncFilter.utr = cartUsualBoolean(cart, "hgva_include_utr", TRUE);
 aggvFuncFilter.cdsSyn = cartUsualBoolean(cart, "hgva_include_cdsSyn", TRUE);
 aggvFuncFilter.cdsNonSyn = cartUsualBoolean(cart, "hgva_include_cdsNonSyn", TRUE);
 aggvFuncFilter.intron = cartUsualBoolean(cart, "hgva_include_intron", TRUE);
 aggvFuncFilter.splice = cartUsualBoolean(cart, "hgva_include_splice", TRUE);
 aggvFuncFilter.nonCodingExon = cartUsualBoolean(cart, "hgva_include_nonCodingExon", TRUE);
 aggvFuncFilter.noVariation = cartUsualBoolean(cart, "hgva_include_noVariation", TRUE);
 annoGratorGpVarSetFuncFilter(gpVarGrator, &aggvFuncFilter);
 }
 
 struct annoGrator *gratorForSnpBed4(struct hash *gratorsByName, char *suffix,
 				    struct annoAssembly *assembly, char *chrom,