7394a1ece57186bb619c6baa9a501fe960f18c59
angie
Mon Jun 17 16:49:44 2013 -0700
Last-minute bugfixes and wording tweaks. refs #6152
diff --git src/hg/hgVai/hgVai.c src/hg/hgVai/hgVai.c
index 7504d90..779a76b 100644
--- src/hg/hgVai/hgVai.c
+++ src/hg/hgVai/hgVai.c
@@ -234,34 +234,36 @@
//#*** ------------------ end verbatim ---------------
printf("
"
"Select Genome Assembly and Region
\n");
/* Print clade, genome and assembly line. */
hgGatewayCladeGenomeDb();
//#*** No longer ending form here...
}
void askUserForVariantCustomTrack()
/* Tell the user that we need a custom track of variants to work on. */
{
puts(" ");
-printf("
Upload Variants as Custom Track
\n");
-printf("Please create a custom track containing your variants of interest, using either "
+printf("
Upload Variants
\n");
+printf("Please provide a set of variant calls to annotate, as either a custom track in "
"pgSnp or "
- "VCF format: \n");
+ "VCF format, "
+ "or a VCF track on your "
+ "track hub: \n");
printCtAndHubButtons();
puts(" ");
}
typedef boolean TdbFilterFunction(struct trackDb *tdb, void *filterData);
/* Return TRUE if tdb passes filter criteria. */
void rFilterTrackList(struct trackDb *trackList, struct slRef **pPassingRefs,
TdbFilterFunction *filterFunc, void *filterData)
/* Recursively apply filterFunc and filterData to all tracks in fullTrackList and
* their subtracks. Add an slRef to pPassingRefs for each track/subtrack that passes.
* Caller should slReverse(pPassingRefs) when recursion is all done. */
{
struct trackDb *tdb;
for (tdb = trackList; tdb != NULL; tdb = tdb->next)
@@ -307,34 +309,34 @@
*retGroupRefList = groupRefList;
}
}
boolean isVariantCustomTrack(struct trackDb *tdb, void *filterData)
/* This is a TdbFilterFunction to get custom or hub tracks with type pgSnp or vcfTabix. */
{
return ((sameString(tdb->grp, "user") || isHubTrack(tdb->track)) &&
(sameString(tdb->type, "pgSnp") || sameString(tdb->type, "vcfTabix")));
}
void selectVariants(struct slRef *varGroupList, struct slRef *varTrackList)
/* Offer selection of user's variant custom tracks. */
{
printf("
Select Variants
\n");
-printf("If you have more than one custom track in "
+printf("If you have more than one custom track or hub track in "
"pgSnp or "
"VCF format, "
- "please select the one you wish to annotate. \n");
+ "please select the one you wish to annotate: \n");
printf("variants: ");
printf(" \n");
printf("maximum number of variants to be processed:\n");
char *curLimit = cartUsualString(cart, "hgva_variantLimit", "10000");
char *limitLabels[] = { "10", "100", "1,000", "10,000", "100,000" };
char *limitValues[] = { "10", "100", "1000", "10000", "100000" };
cgiMakeDropListWithVals("hgva_variantLimit", limitLabels, limitValues, ArraySize(limitLabels),
@@ -657,37 +659,38 @@
printf("exon of non-coding gene \n");
puts(" ");
endCollapsibleSection();
}
void selectFiltersKnownVar()
/* Options to restrict output based on overlap with known variants. */
{
boolean gotCommon = findSnpBed4("Common", NULL, NULL);
boolean gotMult = findSnpBed4("Mult", NULL, NULL);
if (!gotCommon && !gotMult)
return;
startCollapsibleSection("filtersVar", "Known variation", FALSE);
if (gotMult)
{
- cartMakeCheckBox(cart, "hgva_exclude_snpMult", FALSE);
- printf("Exclude variants mapped to multiple genomic locations by dbSNP \n");
+ cartMakeCheckBox(cart, "hgva_include_snpMult", TRUE);
+ printf("Include variants even if they are co-located with variants that have been mapped to "
+ "multiple genomic locations by dbSNP \n");
}
if (gotCommon)
{
- cartMakeCheckBox(cart, "hgva_exclude_snpCommon", FALSE);
- printf("Exclude \"common\" variants "
+ cartMakeCheckBox(cart, "hgva_include_snpCommon", TRUE);
+ printf("Include variants even if they are co-located with \"common\" variants "
"(uniquely mapped variants with global minor allele frequency (MAF) "
"of at least 1%% according to dbSNP) \n");
}
puts(" ");
endCollapsibleSection();
}
void selectFiltersCons()
/* Options to restrict output based on overlap with conserved elements. */
{
struct slRef *elTrackRefList = NULL;
tdbFilterGroupTrack(fullTrackList, fullGroupList, isConsElTrack, NULL, NULL, &elTrackRefList);
if (elTrackRefList == NULL)
return;
startCollapsibleSection("filtersCons", "Conservation", FALSE);
@@ -733,31 +736,31 @@
puts("");
}
void selectOutput()
/* Just VEP text for now... should also have VEP HTML with limited # lines too.
* Next: custom track with same subset of info as we would stuff in VEP */
{
puts(" ");
printf("