| "
"Haplotype sorting order: using ");
char *centerChrom = cartOptionalStringClosestToHome(cart, tdb, parentLevel,
"centerVariantChrom");
if (isEmpty(centerChrom))
{
// Unspecified in cart -- describe the default action
printf(VCF_HAPLOSORT_DEFAULT_DESC " as anchor. |
\n");
if (isNotEmpty(thisChrom))
{
// but we do have a candidate, so offer to make it the center:
puts("| ");
vcfCfgHaplotypeCenterHiddens(track, thisName, thisChrom, thisPos);
char label[256];
safef(label, sizeof(label), "Use %s", nameOrDefault(thisName, "this variant"));
cgiMakeButton("submit", label);
printf(" as anchor |
\n");
}
else
printf("| To anchor the sorting to a particular variant, "
"click on the variant in the genome browser, "
"and then click on the 'Use this variant' button on the next page."
" |
\n");
}
else
{
// Describe the one specified in cart.
int centerPos = cartUsualIntClosestToHome(cart, tdb, parentLevel, "centerVariantPos",
-1);
char *centerName = cartStringClosestToHome(cart, tdb, parentLevel, "centerVariantName");
if (isNotEmpty(thisChrom))
{
// These form inputs are for either "use me" or clear:
vcfCfgHaplotypeCenterHiddens(track, thisName, thisChrom, thisPos);
// Is this variant the same as the center variant specified in cart?
if (sameString(thisChrom, centerChrom) && sameString(thisName, centerName) &&
thisPos == centerPos)
printf("this variant as anchor.\n");
else
{
// make a "use me" button
printf("%s at %s:%d as anchor.\n| \n",
nameOrDefault(centerName, "variant"), centerChrom, centerPos+1);
char label[256];
safef(label, sizeof(label), "Use %s", nameOrDefault(thisName, "this variant"));
cgiMakeButton("submit", label);
printf(" as anchor |
\n");
}
}
else
{
// Form inputs (in case the clear button is clicked)
vcfCfgHaplotypeCenterHiddens(track, centerName, centerChrom, centerPos);
printf("%s at %s:%d as anchor.\n",
nameOrDefault(centerName, "variant"), centerChrom, centerPos+1);
}
// Make a clear button that modifies the hiddens using onClick
puts("| ");
struct dyString *onClick = dyStringNew(0);
dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantChrom', ''); ",
formName, track);
dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantName', ''); ",
formName, track);
dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantPos', 0);",
formName, track);
dyStringPrintf(onClick, "document.%s.submit(); return false;", formName);
cgiMakeButtonWithOnClick("submit", "Clear selection", NULL, onClick->string);
printf(" (use " VCF_HAPLOSORT_DEFAULT_DESC ") |
\n");
}
puts("
");
}
}
//TODO: share this code w/hgTracks, hgc in hg/lib/vcfFile.c
static struct vcfFile *vcfHopefullyOpenHeader(struct cart *cart, struct trackDb *tdb)
/* Defend against network errors and return the vcfFile object with header data, or NULL. */
{
#if (defined USE_TABIX && defined KNETFILE_HOOKS)
knetUdcInstall();
if (udcCacheTimeout() < 300)
udcSetCacheTimeout(300);
#endif//def USE_TABIX && KNETFILE_HOOKS
char *db = cartString(cart, "db");
struct sqlConnection *conn = hAllocConnTrack(db, tdb);
-char *fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, tdb->table, hDefaultChrom(db));
+char *fileOrUrl = NULL;
+char *chrom = cartOptionalString(cart, "c");
+if (chrom != NULL)
+ fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, tdb->table, chrom);
+if (fileOrUrl == NULL)
+ fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, tdb->table, hDefaultChrom(db));
hFreeConn(&conn);
+if (fileOrUrl == NULL)
+ return NULL;
int vcfMaxErr = 100;
struct vcfFile *vcff = NULL;
/* protect against temporary network error */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
vcff = vcfTabixFileMayOpen(fileOrUrl, NULL, 0, 0, vcfMaxErr, -1);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
if (isNotEmpty(errCatch->message->string))
warn("unable to open %s: %s", fileOrUrl, errCatch->message->string);
}
errCatchFree(&errCatch);
return vcff;
}
static void vcfCfgHapClusterEnable(struct cart *cart, struct trackDb *tdb, char *name,
boolean parentLevel)
/* Let the user enable/disable haplotype sorting display. */
{
boolean hapClustEnabled = cartUsualBooleanClosestToHome(cart, tdb, parentLevel,
VCF_HAP_ENABLED_VAR, TRUE);
char cartVar[1024];
safef(cartVar, sizeof(cartVar), "%s." VCF_HAP_ENABLED_VAR, name);
cgiMakeCheckBox(cartVar, hapClustEnabled);
printf("", boxed ? " width='100%'" : "");
struct vcfFile *vcff = vcfHopefullyOpenHeader(cart, tdb);
if (vcff != NULL)
{
boolean parentLevel = isNameAtParentLevel(tdb, name);
if (vcff->genotypeCount > 1)
{
puts("Haplotype sorting display");
puts("When this display mode is enabled and genotypes are phased or homozygous, "
"each genotype is split into two independent haplotypes. "
"These local haplotypes are clustered by similarity around a central variant. "
"Haplotypes are reordered for display using the clustering tree, which is "
"drawn in the left label area. "
"Local haplotype blocks can often be identified using this display. ");
vcfCfgHapCluster(cart, tdb, vcff, name, parentLevel);
}
puts("Filters");
vcfCfgMinQual(cart, tdb, vcff, name, parentLevel);
vcfCfgFilterColumn(cart, tdb, vcff, name, parentLevel);
vcfCfgMinAlleleFreq(cart, tdb, vcff, name, parentLevel);
}
else
{
printf("Sorry, couldn't access VCF file.
\n");
}
puts(" | ");
if (boxed && fileExists(hHelpFile("hgVcfTrackHelp")))
printf("VCF configuration help | ");
printf("
");
if (!boxed && fileExists(hHelpFile("hgVcfTrackHelp")))
printf("VCF "
"configuration help
");
cfgEndBox(boxed);
}