| " "Haplotype sorting order: using "); - char *centerChrom = cartOptionalStringClosestToHome(cart, tdb, compositeLevel, + char *centerChrom = cartOptionalStringClosestToHome(cart, tdb, parentLevel, "centerVariantChrom"); if (isEmpty(centerChrom)) { // Unspecified in cart -- describe the default action printf(VCF_HAPLOSORT_DEFAULT_DESC " as anchor. | ||
| "); vcfCfgHaplotypeCenterHiddens(track, thisName, thisChrom, thisPos); char label[256]; safef(label, sizeof(label), "Use %s", nameOrDefault(thisName, "this variant")); cgiMakeButton("submit", label); printf(" as anchor | ||
| 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",
nameOrDefault(centerName, "variant"), centerChrom, centerPos+1);
char label[256];
safef(label, sizeof(label), "Use %s", nameOrDefault(thisName, "this variant"));
@@ -140,123 +140,123 @@
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 compositeLevel)
+ boolean parentLevel)
/* Let the user enable/disable haplotype sorting display. */
{
-boolean hapClustEnabled = cartUsualBooleanClosestToHome(cart, tdb, compositeLevel,
+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("Enable Haplotype sorting display \n"); } static void vcfCfgHapClusterColor(struct cart *cart, struct trackDb *tdb, char *name, - boolean compositeLevel) + boolean parentLevel) /* Let the user choose how to color the sorted haplotypes. */ { printf("Haplotype coloring scheme: \n"); -char *colorBy = cartUsualStringClosestToHome(cart, tdb, compositeLevel, +char *colorBy = cartUsualStringClosestToHome(cart, tdb, parentLevel, VCF_HAP_COLORBY_VAR, VCF_DEFAULT_HAP_COLORBY); char varName[1024]; safef(varName, sizeof(varName), "%s." VCF_HAP_COLORBY_VAR, name); cgiMakeRadioButton(varName, VCF_HAP_COLORBY_ALTONLY, sameString(colorBy, VCF_HAP_COLORBY_ALTONLY)); printf("reference alleles invisible, alternate alleles in black \n"); cgiMakeRadioButton(varName, VCF_HAP_COLORBY_REFALT, sameString(colorBy, VCF_HAP_COLORBY_REFALT)); printf("reference alleles in blue, alternate alleles in red \n"); cgiMakeRadioButton(varName, VCF_HAP_COLORBY_BASE, sameString(colorBy, VCF_HAP_COLORBY_BASE)); printf("first base of allele (A = red, C = blue, G = green, T = magenta) \n"); } static void vcfCfgHapClusterTreeAngle(struct cart *cart, struct trackDb *tdb, char *name, - boolean compositeLevel) + boolean parentLevel) /* Let the user choose branch shape. */ { printf("Haplotype clustering tree leaf shape: \n"); -char *treeAngle = cartUsualStringClosestToHome(cart, tdb, compositeLevel, +char *treeAngle = cartUsualStringClosestToHome(cart, tdb, parentLevel, VCF_HAP_TREEANGLE_VAR, VCF_DEFAULT_HAP_TREEANGLE); char varName[1024]; safef(varName, sizeof(varName), "%s." VCF_HAP_TREEANGLE_VAR, name); cgiMakeRadioButton(varName, VCF_HAP_TREEANGLE_TRIANGLE, sameString(treeAngle, VCF_HAP_TREEANGLE_TRIANGLE)); printf("draw leaf clusters as < \n"); cgiMakeRadioButton(varName, VCF_HAP_TREEANGLE_RECTANGLE, sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE)); printf("draw leaf clusters as [ \n"); } static void vcfCfgHapClusterHeight(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, - char *name, boolean compositeLevel) + char *name, boolean parentLevel) /* Let the user specify a height for the track. */ { if (vcff != NULL && vcff->genotypeCount > 1) { printf("Haplotype sorting display height: \n"); - int cartHeight = cartUsualIntClosestToHome(cart, tdb, compositeLevel, + int cartHeight = cartUsualIntClosestToHome(cart, tdb, parentLevel, VCF_HAP_HEIGHT_VAR, VCF_DEFAULT_HAP_HEIGHT); char varName[1024]; safef(varName, sizeof(varName), "%s." VCF_HAP_HEIGHT_VAR, name); cgiMakeIntVarInRange(varName, cartHeight, "Height (in pixels) of track", 5, "4", "2500"); puts(" "); } } static void vcfCfgHapCluster(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, - char *name, boolean compositeLevel) + char *name, boolean parentLevel) /* Show controls for haplotype-sorting display, which only makes sense to do when * the VCF file describes multiple genotypes. */ { -vcfCfgHapClusterEnable(cart, tdb, name, compositeLevel); -vcfCfgHaplotypeCenter(cart, tdb, name, compositeLevel, vcff, NULL, NULL, 0, "mainForm"); -vcfCfgHapClusterColor(cart, tdb, name, compositeLevel); -vcfCfgHapClusterTreeAngle(cart, tdb, name, compositeLevel); -vcfCfgHapClusterHeight(cart, tdb, vcff, name, compositeLevel); +vcfCfgHapClusterEnable(cart, tdb, name, parentLevel); +vcfCfgHaplotypeCenter(cart, tdb, name, parentLevel, vcff, NULL, NULL, 0, "mainForm"); +vcfCfgHapClusterColor(cart, tdb, name, parentLevel); +vcfCfgHapClusterTreeAngle(cart, tdb, name, parentLevel); +vcfCfgHapClusterHeight(cart, tdb, vcff, name, parentLevel); puts(" "); } static void vcfCfgMinQual(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, - char *name, boolean compositeLevel) + char *name, boolean parentLevel) /* If checkbox is checked, apply minimum value filter to QUAL column. */ { char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s." VCF_APPLY_MIN_QUAL_VAR, name); -boolean applyFilter = cartUsualBooleanClosestToHome(cart, tdb, compositeLevel, +boolean applyFilter = cartUsualBooleanClosestToHome(cart, tdb, parentLevel, VCF_APPLY_MIN_QUAL_VAR, VCF_DEFAULT_APPLY_MIN_QUAL); cgiMakeCheckBox(cartVar, applyFilter); printf("Exclude variants with Quality/confidence score (QUAL) score less than\n"); -double minQual = cartUsualDoubleClosestToHome(cart, tdb, compositeLevel, VCF_MIN_QUAL_VAR, +double minQual = cartUsualDoubleClosestToHome(cart, tdb, parentLevel, VCF_MIN_QUAL_VAR, VCF_DEFAULT_MIN_QUAL); safef(cartVar, sizeof(cartVar), "%s." VCF_MIN_QUAL_VAR, name); cgiMakeDoubleVar(cartVar, minQual, 10); printf(" \n"); } static void vcfCfgFilterColumn(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, - char *name, boolean compositeLevel) + char *name, boolean parentLevel) /* Show controls for filtering by value of VCF's FILTER column, which uses values defined * in the header. */ { int filterCount = slCount(vcff->filterDefs); if (filterCount < 1) return; printf("Exclude variants with these FILTER values: \n"); char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s."VCF_EXCLUDE_FILTER_VAR, name); jsMakeCheckboxGroupSetClearButton(cartVar, TRUE); puts(" "); jsMakeCheckboxGroupSetClearButton(cartVar, FALSE); char *values[filterCount]; char *labels[filterCount]; int i; @@ -265,67 +265,67 @@ { values[i] = filt->key; struct dyString *dy = dyStringNew(0); dyStringAppend(dy, filt->key); if (isNotEmpty(filt->description)) dyStringPrintf(dy, " (%s)", filt->description); labels[i] = dyStringCannibalize(&dy); } struct slName *selectedValues = NULL; if (cartListVarExistsAnyLevel(cart, tdb, FALSE, VCF_EXCLUDE_FILTER_VAR)) selectedValues = cartOptionalSlNameListClosestToHome(cart, tdb, FALSE, VCF_EXCLUDE_FILTER_VAR); cgiMakeCheckboxGroupWithVals(cartVar, labels, values, filterCount, selectedValues, 1); } static void vcfCfgMinAlleleFreq(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, - char *name, boolean compositeLevel) + char *name, boolean parentLevel) /* Show input for minimum allele frequency, if we can extract it from the VCF INFO column. */ { printf("Minimum minor allele frequency (if INFO column includes AF or AC+AN):\n"); -double cartMinFreq = cartUsualDoubleClosestToHome(cart, tdb, compositeLevel, +double cartMinFreq = cartUsualDoubleClosestToHome(cart, tdb, parentLevel, VCF_MIN_ALLELE_FREQ_VAR, VCF_DEFAULT_MIN_ALLELE_FREQ); char varName[1024]; safef(varName, sizeof(varName), "%s." VCF_MIN_ALLELE_FREQ_VAR, name); cgiMakeDoubleVarInRange(varName, cartMinFreq, "minor allele frequency between 0.0 and 0.5", 5, "0.0", "0.5"); puts(" "); } void vcfCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* VCF: Variant Call Format. redmine #3710 */ { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); printf(" ", boxed ? " width='100%'" : "");
struct vcfFile *vcff = vcfHopefullyOpenHeader(cart, tdb);
if (vcff != NULL)
{
- boolean compositeLevel = isNameAtCompositeLevel(tdb, name);
+ boolean parentLevel = isNameAtParentLevel(tdb, name);
if (vcff->genotypeCount > 1)
{
puts(" | ");
if (boxed && fileExists(hHelpFile("hgVcfTrackHelp")))
printf("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, compositeLevel); + vcfCfgHapCluster(cart, tdb, vcff, name, parentLevel); } puts("Filters"); - vcfCfgMinQual(cart, tdb, vcff, name, compositeLevel); - vcfCfgFilterColumn(cart, tdb, vcff, name, compositeLevel); - vcfCfgMinAlleleFreq(cart, tdb, vcff, name, compositeLevel); + 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(" VCF configuration help | ");
printf(" |