de6d2d4e5d0106a57d1ada79e9e36005676c260e chmalee Fri Sep 25 12:39:18 2026 -0700 Add trackDb defined filters, coloring, and mouseovers for vcf tracks, using INFO fields or sub INFO fields, like vep.Consequence, refs #37617, #37618 diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c index 7ba16bd1580..21f29b1995c 100644 --- src/hg/lib/vcfUi.c +++ src/hg/lib/vcfUi.c @@ -1,757 +1,1377 @@ /* vcfUi - Variant Call Format user interface controls that are shared * between more than one CGI. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ +#include <regex.h> #include "common.h" #include "cheapcgi.h" #include "errCatch.h" #include "hCommon.h" #include "hui.h" #include "jsHelper.h" +#include "regexHelper.h" #include "vcf.h" #include "vcfUi.h" #include "knetUdc.h" #include "udc.h" +#include "obscure.h" +#include "bigBedFilter.h" +#include "htmlColor.h" +#include "basicBed.h" +#include "web.h" + +// helper functions for each type of of vcfInfoFilter +static struct vcfInfoDef *vcfInfoDefForFilter(struct vcfFile *vcff, struct trackDb *tdb, + char *field, boolean wantNumber, boolean isList) +/* Return the vcfInfoDef for a filter on INFO field. Warn and return NULL when the field + * is not in the VCF header, has the wrong Number, or has the wrong type. The field must be + * Number=1, or Number=1 or Number=. for a list filter. A numeric filter needs an Integer or + * Float field, and a text or value filter needs a String field. */ +{ +struct vcfInfoDef *infoDef = vcfInfoDefForKey(vcff, field); +if (infoDef == NULL) + warn("track %s: can't filter on INFO field %s: it is not in the VCF header", + tdb->track, field); +else if (isList && infoDef->fieldCount != 1 && infoDef->fieldCount != -1) + warn("track %s: can't filter on INFO field %s: a list filter needs a Number=1 or " + "Number=. field", tdb->track, field); +else if (!isList && infoDef->fieldCount != 1) + warn("track %s: can't filter on INFO field %s: only Number=1 fields can be filtered", + tdb->track, field); +else if (wantNumber && infoDef->type != vcfInfoInteger && infoDef->type != vcfInfoFloat) + warn("track %s: can't filter on INFO field %s: a numeric filter needs an Integer or " + "Float field", tdb->track, field); +else if (!wantNumber && infoDef->type != vcfInfoString) + warn("track %s: can't filter on INFO field %s: a text or value filter needs a String field", + tdb->track, field); +else + return infoDef; +return NULL; +} + +static struct vcfInfoFilter *vcfInfoFilterMakeNumberFilter(struct cart *cart, struct vcfFile *vcff, struct trackDb *tdb, char *filterName, char *defaultLimits, char *fieldName, boolean isHighlight) +{ +struct vcfInfoFilter *filter = NULL; +char *setting = trackDbSettingClosestToHome(tdb, filterName); +struct vcfInfoDef *infoDef = vcfInfoDefForFilter(vcff, tdb, fieldName, TRUE, FALSE); +if (infoDef == NULL) + return NULL; + +if (setting) + { + boolean invalid = FALSE; + double minValueTdb = 0,maxValueTdb = NO_VALUE; + double minLimit=NO_VALUE,maxLimit=NO_VALUE,min = minValueTdb,max = maxValueTdb; + colonPairToDoubles(setting,&minValueTdb,&maxValueTdb); + colonPairToDoubles(defaultLimits,&minLimit,&maxLimit); + getScoreFloatRangeFromCart(cart,tdb,FALSE,filterName,&minLimit,&maxLimit,&min,&max); + if ((int)minLimit != NO_VALUE || (int)maxLimit != NO_VALUE) + { + // assume tdb default values within range! + // (don't give user errors that have no consequence) + if ((min != minValueTdb && (((int)minLimit != NO_VALUE && min < minLimit) + || ((int)maxLimit != NO_VALUE && min > maxLimit))) + || (max != maxValueTdb && (((int)minLimit != NO_VALUE && max < minLimit) + || ((int)maxLimit != NO_VALUE && max > maxLimit)))) + { + invalid = TRUE; + char value[64]; + if ((int)max == NO_VALUE) // min only is allowed, but max only is not + safef(value, sizeof(value), "entered minimum (%g)", min); + else + safef(value, sizeof(value), "entered range (min:%g and max:%g)", min, max); + char limits[64]; + if ((int)minLimit != NO_VALUE && (int)maxLimit != NO_VALUE) + safef(limits, sizeof(limits), "violates limits (%g to %g)", minLimit, maxLimit); + else if ((int)minLimit != NO_VALUE) + safef(limits, sizeof(limits), "violates lower limit (%g)", minLimit); + else //if ((int)maxLimit != NO_VALUE) + safef(limits, sizeof(limits), "violates uppper limit (%g)", maxLimit); + warn("invalid filter by %s: %s %s for track %s", fieldName, value, limits, tdb->track); + } + } + if (invalid) + { + char filterLimitName[64]; + safef(filterLimitName, sizeof(filterLimitName), "%s%s", filterName, _MIN); + cartRemoveVariableClosestToHome(cart,tdb,FALSE,filterLimitName); + safef(filterLimitName, sizeof(filterLimitName), "%s%s", filterName, _MAX); + cartRemoveVariableClosestToHome(cart,tdb,FALSE,filterLimitName); + } + else if (((int)min != NO_VALUE && ((int)minLimit == NO_VALUE || minLimit != min)) + || ((int)max != NO_VALUE && ((int)maxLimit == NO_VALUE || maxLimit != max))) + // Assumes min==NO_VALUE or min==minLimit is no filter + // Assumes max==NO_VALUE or max==maxLimit is no filter! + { + AllocVar(filter); + filter->infoDef = infoDef; + if ((int)max == NO_VALUE || ((int)maxLimit != NO_VALUE && maxLimit == max)) + { + filter->comparisonType = COMPARE_MORE; + filter->value1 = min; + } + else if ((int)min == NO_VALUE || ((int)minLimit != NO_VALUE && minLimit == min)) + { + filter->comparisonType = COMPARE_LESS; + filter->value1 = max; + } + else + { + filter->comparisonType = COMPARE_BETWEEN; + filter->value1 = min; + filter->value2 = max; + } + if (isHighlight) + filter->isHighlight = TRUE; + } + } +return filter; +} + +static struct vcfInfoFilter *vcfInfoFilterMakeFilterText(struct cart *cart, struct vcfFile *vcff, struct trackDb *tdb, char *filterName, char *fieldName, boolean isHighlight) +{ +struct vcfInfoFilter *filter; +char *setting = trackDbSettingClosestToHome(tdb, filterName); +char *value = cartUsualStringClosestToHome(cart, tdb, FALSE, filterName, setting); +if (isEmpty(value)) + return NULL; +char *typeValue = getFilterType(cart, tdb, fieldName, FILTERTEXT_WILDCARD); +struct vcfInfoDef *infoDef = vcfInfoDefForFilter(vcff, tdb, fieldName, FALSE, FALSE); +if (infoDef == NULL) + return NULL; + +AllocVar(filter); +filter->infoDef = infoDef; +if (sameString(typeValue, FILTERTEXT_REGEXP)) + { + filter->comparisonType = COMPARE_REGEXP; + regcomp(&filter->regEx, value, REG_NOSUB); + } +else + { + filter->comparisonType = COMPARE_WILDCARD; + filter->wildCardString = cloneString(value); + } + +filter->isHighlight = isHighlight; +return filter; +} + +int vcfInfoDefSubFieldIndex(const struct vcfInfoDef *def, const char *subFieldName) +/* Parse the "Format: A|B|C|..." clause out of def->description (the same syntax + * looksTabular() in lib/vcf.c keys off of) and return the 0-based index of subFieldName, + * or -1 if the description has no Format clause or the name is absent. */ +{ +if (def == NULL || isEmpty(def->description) || isEmpty(subFieldName)) + return -1; +regmatch_t substrs[8]; +if (!regexMatchSubstr(def->description, COL_DESC_REGEX, substrs, ArraySize(substrs))) + return -1; +int matchSize = substrs[0].rm_eo - substrs[0].rm_so; +char copy[matchSize + 1]; +safencpy(copy, sizeof(copy), def->description + substrs[0].rm_so, matchSize); +char *words[256]; +int nWords = chopByChar(copy, '|', words, ArraySize(words)); +int i; +for (i = 0; i < nWords; i++) + if (sameString(words[i], subFieldName)) + return i; +return -1; +} + +static struct vcfInfoFilter *vcfInfoFilterMakeFilterBy(struct cart *cart, struct vcfFile *vcff, struct trackDb *tdb, char *field, struct slName *choices, boolean isHighlight) +/* Add a vcfInfoFilter using trackDb filterBy statement. + * field may be a plain INFO key, or a dotted key.subField referring to a named + * sub-field of a pipe-separated INFO annotation (e.g. vep.Consequence). */ +{ +struct vcfInfoFilter *filter; +char *setting = NULL; +if (isHighlight) + setting = getHighlightType(cart, tdb, field, HIGHLIGHTBY_DEFAULT); +else + setting = getFilterType(cart, tdb, field, FILTERBY_DEFAULT); + +enum bigBedFilterType comparisonType = COMPARE_HASH; +if (setting) + { + if (sameString(setting, FILTERBY_SINGLE_LIST) + || sameString(setting, FILTERBY_MULTIPLE_LIST_OR) + || sameString(setting, FILTERBY_MULTIPLE_LIST_ONLY_OR) + || sameString(setting, HIGHLIGHTBY_SINGLE_LIST) + || sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_OR) + || sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_ONLY_OR)) + comparisonType = COMPARE_HASH_LIST_OR; + else if (sameString(setting, FILTERBY_MULTIPLE_LIST_AND) + || sameString(setting, FILTERBY_MULTIPLE_LIST_ONLY_AND) + || sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_AND) + || sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_ONLY_AND)) + comparisonType = COMPARE_HASH_LIST_AND; + } +boolean isList = (comparisonType != COMPARE_HASH); + +char *dotPos = strchr(field, '.'); +struct vcfInfoDef *infoDef; +char *baseKey; +char *subFieldName = NULL; +int subFieldIndex = -1; +if (dotPos != NULL) + { + baseKey = cloneStringZ(field, dotPos - field); + subFieldName = cloneString(dotPos + 1); + // Sub-field filters allow any Number, since fields like vep are Number=. + infoDef = vcfInfoDefForKey(vcff, baseKey); + if (infoDef == NULL || infoDef->type != vcfInfoString) + { + warn("track %s: can't filter on %s: %s is not a String INFO field in the VCF header", + tdb->track, field, baseKey); + freeMem(baseKey); + freeMem(subFieldName); + return NULL; + } + subFieldIndex = vcfInfoDefSubFieldIndex(infoDef, subFieldName); + if (subFieldIndex < 0) + { + warn("track %s: filterValues.%s: sub-field '%s' not found in %s INFO Format clause", + tdb->track, field, subFieldName, baseKey); + freeMem(baseKey); + freeMem(subFieldName); + return NULL; + } + freeMem(baseKey); + } +else + { + infoDef = vcfInfoDefForFilter(vcff, tdb, field, FALSE, isList); + if (infoDef == NULL) + return NULL; + } + +AllocVar(filter); +filter->infoDef = infoDef; +filter->subFieldIndex = subFieldIndex; +filter->subFieldName = subFieldName; +filter->comparisonType = comparisonType; +filter->valueHash = newHash(5); +filter->numValuesInHash = slCount(choices); + +for(; choices; choices = choices->next) + hashStore(filter->valueHash, choices->name); + +filter->isHighlight = isHighlight; +return filter; +} + +struct vcfColorByInfo *vcfColorByInfoFromTdb(struct trackDb *tdb, struct vcfFile *vcff) +/* Parse colorByInfo / colorByInfo.<FIELD> settings; returns NULL when + * the feature is not configured on this track. The vcff header is used to check + * that the field is a String INFO field and to resolve the named sub-field of a + * pipe-separated INFO annotation (e.g. vep.Consequence). Warns and returns NULL + * when the field can't be used. */ +{ +char *fieldKey = trackDbSetting(tdb, VCF_COLOR_BY_INFO); +if (isEmpty(fieldKey)) + return NULL; +char settingKey[256]; +safef(settingKey, sizeof(settingKey), "%s.%s", VCF_COLOR_BY_INFO, fieldKey); +char *mapStr = trackDbSetting(tdb, settingKey); +if (isEmpty(mapStr)) + return NULL; + +// If fieldKey is dotted (e.g. vep.Consequence), resolve the named sub-field's +// index within the INFO def's Format clause; the stored fieldKey drops the +// suffix so vcfRecordFindInfo finds the parent INFO element at lookup time. +char *baseKey = fieldKey; +char *subFieldName = NULL; +int subFieldIndex = -1; +char *dotPos = strchr(fieldKey, '.'); +char baseKeyBuf[256]; +if (dotPos == NULL) + { + struct vcfInfoDef *def = vcfInfoDefForKey(vcff, fieldKey); + if (def == NULL || def->type != vcfInfoString) + { + warn("track %s: can't color by %s: it is not a String INFO field in the VCF header", + tdb->track, fieldKey); + return NULL; + } + } +else + { + int baseLen = dotPos - fieldKey; + safencpy(baseKeyBuf, sizeof(baseKeyBuf), fieldKey, baseLen); + baseKey = baseKeyBuf; + subFieldName = dotPos + 1; + struct vcfInfoDef *def = vcfInfoDefForKey(vcff, baseKey); + if (def == NULL || def->type != vcfInfoString) + { + warn("track %s: can't color by %s: %s is not a String INFO field in the VCF header", + tdb->track, fieldKey, baseKey); + return NULL; + } + subFieldIndex = vcfInfoDefSubFieldIndex(def, subFieldName); + if (subFieldIndex < 0) + { + warn("track %s: colorByInfo %s: sub-field '%s' not in %s INFO Format clause", + tdb->track, fieldKey, subFieldName, baseKey); + return NULL; + } + } + +struct vcfColorByInfo *cbi; +AllocVar(cbi); +cbi->fieldKey = cloneString(baseKey); +cbi->valueToRgb = newHash(5); +cbi->orderedColors = NULL; +cbi->subFieldIndex = subFieldIndex; +cbi->subFieldName = (subFieldName != NULL) ? cloneString(subFieldName) : NULL; + +// Comma-separated key=colorSpec pairs. Only #rrggbb hex codes and HTML +// color names are accepted; the r,g,b triple form would collide with +// the pair separator. Build a hash for fast top-level lookup AND an +// ordered slPair list so the sub-field path can iterate in declaration +// order (first declared key with any match across annotations wins). +char *clone = cloneString(mapStr); +char *pairs[64]; +int nPairs = chopByChar(clone, ',', pairs, ArraySize(pairs)); +int i; +for (i = 0; i < nPairs; i++) + { + char *eq = strchr(pairs[i], '='); + if (eq == NULL) + continue; + *eq++ = 0; + char *key = trimSpaces(pairs[i]); + char *colorSpec = trimSpaces(eq); + if (isEmpty(key) || isEmpty(colorSpec)) + continue; + unsigned rgb; + if (!htmlColorForCode(colorSpec, &rgb) && !htmlColorForName(colorSpec, &rgb)) + continue; + struct rgbColor *c; + AllocVar(c); + *c = bedColorToRgb(rgb); + hashAdd(cbi->valueToRgb, key, c); + slPairAdd(&cbi->orderedColors, key, c); + } +slReverse(&cbi->orderedColors); +freeMem(clone); +return cbi; +} + +boolean vcfColorByInfoLookup(struct vcfColorByInfo *cbi, + const struct vcfRecord *rec, + struct rgbColor *out) +/* Look up rec's value for cbi->fieldKey and copy its RGB into *out. + * Returns FALSE when no mapping applies (caller should use a fallback). */ +{ +if (cbi == NULL || rec == NULL) + return FALSE; +const struct vcfInfoElement *ele = vcfRecordFindInfo((struct vcfRecord *)rec, cbi->fieldKey); +if (ele == NULL || ele->count < 1 || ele->missingData[0]) + return FALSE; + +if (cbi->subFieldIndex < 0) + { + // Top-level lookup: single value per record, direct hash hit. + char *valStr = ele->values[0].datString; + if (isEmpty(valStr)) + return FALSE; + struct rgbColor *c = hashFindVal(cbi->valueToRgb, valStr); + if (c == NULL) + return FALSE; + *out = *c; + return TRUE; + } + +// Sub-field lookup: a record can carry many transcript annotations; collect +// every map key any of them matches, then walk the ordered list to return the +// earliest-declared (highest-priority) hit. +struct hash *seen = hashNew(4); +int v; +for (v = 0; v < ele->count; v++) + { + if (ele->missingData[v]) + continue; + char *annot = ele->values[v].datString; + if (isEmpty(annot)) + continue; + char *clone = cloneString(annot); + char *tokens[128]; + int nTok = chopByChar(clone, '|', tokens, ArraySize(tokens)); + if (cbi->subFieldIndex < nTok) + { + // The Consequence sub-field can be '&'-joined SO terms within one + // annotation; each term participates independently in the map lookup. + char *terms[16]; + int nTerms = chopByChar(tokens[cbi->subFieldIndex], '&', + terms, ArraySize(terms)); + int t; + for (t = 0; t < nTerms; t++) + if (hashLookup(cbi->valueToRgb, terms[t])) + hashStore(seen, terms[t]); + } + freeMem(clone); + } + +struct slPair *p; +for (p = cbi->orderedColors; p != NULL; p = p->next) + { + if (hashLookup(seen, p->name)) + { + *out = *(struct rgbColor *)p->val; + hashFree(&seen); + return TRUE; + } + } +hashFree(&seen); +return FALSE; +} + +struct vcfInfoFilter *buildVcfInfoFilters(struct vcfFile *vcff, struct cart *cart, struct trackDb *tdb) +/* Parse the cart/trackDb current filters into something we can filter the records on. + * Warns about and skips any filter whose INFO field is missing or has the wrong type. */ +{ +struct vcfInfoFilter *filters = NULL, *filter; + +struct trackDbFilter *tdbFilters = tdbGetTrackNumFilters(tdb); +for (; tdbFilters; tdbFilters = tdbFilters->next) + { + if ((filter = vcfInfoFilterMakeNumberFilter(cart, vcff, tdb, tdbFilters->name, NULL, tdbFilters->fieldName, FALSE)) != NULL) + slAddHead(&filters, filter); + } + +// then the text filters +tdbFilters = tdbGetTrackTextFilters(tdb); +for (; tdbFilters; tdbFilters = tdbFilters->next) + { + if ((filter = vcfInfoFilterMakeFilterText(cart, vcff, tdb, tdbFilters->name, tdbFilters->fieldName, FALSE)) != NULL) + slAddHead(&filters, filter); + } + +// finally the hash filters +filterBy_t *filterBySet = filterBySetGet(tdb, cart, NULL); +filterBy_t *filterBy = filterBySet; +for (; filterBy != NULL; filterBy = filterBy->next) + { + if (filterBy->slChoices && differentString(filterBy->slChoices->name, "All")) + { + if ((filter = vcfInfoFilterMakeFilterBy(cart, vcff, tdb, filterBy->column, filterBy->slChoices, FALSE)) != NULL) + slAddHead(&filters, filter); + } + } +return filters; +} + +boolean vcfInfoFilterOneRecord(struct vcfRecord *rec, struct vcfInfoFilter *vcfInfoFilters) +/* Return true if rec passes all the filters on the INFO fields defined in vcfInfoFilters */ +{ +struct vcfInfoFilter *filter; +for (filter = vcfInfoFilters; filter != NULL; filter = filter->next) + { + struct vcfInfoDef *def = filter->infoDef; + const struct vcfInfoElement *vcfInfoEle = vcfRecordFindInfo(rec, def->key); + // Records missing the filtered key, or with an explicit "." value, don't satisfy the filter. + if (vcfInfoEle == NULL || vcfInfoEle->count < 1 || vcfInfoEle->missingData[0]) + return FALSE; + if (filter->subFieldName != NULL) + { + // The filter targets a named sub-field of a pipe-separated INFO value (e.g. + // vep.Consequence). One VCF record can carry multiple transcript-level annotations; + // the variant passes if any annotation's indexed sub-field hits the value set. + boolean anyMatch = FALSE; + int v; + for (v = 0; v < vcfInfoEle->count && !anyMatch; v++) + { + if (vcfInfoEle->missingData[v]) + continue; + char *annot = vcfInfoEle->values[v].datString; + if (isEmpty(annot)) + continue; + char *clone = cloneString(annot); + char *tokens[128]; + int nTok = chopByChar(clone, '|', tokens, ArraySize(tokens)); + if (filter->subFieldIndex < nTok) + { + // Consequence and similar SO-term fields can be ampersand-joined within one + // annotation (e.g. splice_donor_variant&intron_variant); any term hit passes. + char *terms[16]; + int nTerms = chopByChar(tokens[filter->subFieldIndex], '&', + terms, ArraySize(terms)); + int t; + for (t = 0; t < nTerms; t++) + { + if (hashLookup(filter->valueHash, terms[t])) + { + anyMatch = TRUE; + break; + } + } + } + freeMem(clone); + } + if (!anyMatch) + return FALSE; + continue; + } + union vcfDatum val = vcfInfoEle->values[0]; + // vcfDatum is a union typed by def->type; pick the right member as a double for numeric ops. + double dval = 0; + if (def->type == vcfInfoInteger) + dval = (double)val.datInt; + else if (def->type == vcfInfoFloat) + dval = val.datFloat; + switch (filter->comparisonType) + { + case COMPARE_WILDCARD: + if (!wildMatch(filter->wildCardString, val.datString)) + return FALSE; + break; + case COMPARE_REGEXP: + if (regexec(&filter->regEx, val.datString, 0, NULL, 0) != 0) + return FALSE; + break; + case COMPARE_HASH_LIST_AND: + case COMPARE_HASH_LIST_OR: + { + // the VCF parser already split the comma-separated values into ele->values + unsigned found = 0; + struct hash *seenHash = newHash(3); + int v; + for (v = 0; v < vcfInfoEle->count; v++) + { + char *value = vcfInfoEle->values[v].datString; + if (vcfInfoEle->missingData[v] || isEmpty(value)) + continue; + if (hashLookup(seenHash, value)) + continue; + hashStore(seenHash, value); + if (hashLookup(filter->valueHash, value)) + { + found++; + if (filter->comparisonType == COMPARE_HASH_LIST_OR) + break; + } + } + hashFree(&seenHash); + if (filter->comparisonType == COMPARE_HASH_LIST_AND) + { + if (found < filter->numValuesInHash) + return FALSE; + } + else if (!found) + return FALSE; + } + break; + case COMPARE_HASH: + if (!hashLookup(filter->valueHash, val.datString)) + return FALSE;; + break; + case COMPARE_LESS: + if (!(dval <= filter->value1)) + return FALSE; + break; + case COMPARE_MORE: + if (!(dval >= filter->value1)) + return FALSE; + break; + case COMPARE_BETWEEN: + if (!((dval >= filter->value1) && (dval <= filter->value2))) + return FALSE; + break; + default: + break; + } + } +return TRUE; +} INLINE char *nameOrDefault(char *thisName, char *defaultVal) /* If thisName is not a placeholder value, return it; otherwise return default. */ { if (isNotEmpty(thisName) && !sameString(thisName, ".")) return thisName; return defaultVal; } #define VCF_HAPLOSORT_DEFAULT_DESC "middle variant in viewing window" static void vcfCfgHaplotypeCenterHiddens(char *track, char *ctrName, char *ctrChrom, int ctrPos) /* Make hidden form inputs and button for setting the center variant for haplotype * clustering/sorting in hgTracks. */ { char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s.centerVariantChrom", track); cgiMakeHiddenVar(cartVar, ctrChrom); safef(cartVar, sizeof(cartVar), "%s.centerVariantPos", track); char ctrPosStr[16]; safef(ctrPosStr, sizeof(ctrPosStr), "%d", ctrPos); cgiMakeHiddenVar(cartVar, ctrPosStr); safef(cartVar, sizeof(cartVar), "%s.centerVariantName", track); cgiMakeHiddenVar(cartVar, ctrName); } char *vcfHaplotypeOrSample(struct cart *cart) /* Return "Sample" if the current organism is uniploid (like SARS-CoV-2), "Haplotype" otherwise. */ { // We should make a better way of determining whether the organism is diploid, // but for now this will prevent David from being bothered by diploid terminology // when viewing SARS-CoV-2 variants: return sameOk(cartOptionalString(cart, "db"), "wuhCor1") ? "Sample" : "Haplotype"; } void vcfCfgHaplotypeCenter(struct cart *cart, struct trackDb *tdb, char *track, boolean parentLevel, struct vcfFile *vcff, char *thisName, char *thisChrom, int thisPos, char *formName) /* If vcff has genotype data, show status and controls for choosing the center variant * for haplotype clustering/sorting in hgTracks. */ { if (vcff != NULL && vcff->genotypeCount > 1) { printf("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.</TD></TR>\n"); if (isNotEmpty(thisChrom)) { // but we do have a candidate, so offer to make it the center: puts("<TR><TD></TD><TD>"); vcfCfgHaplotypeCenterHiddens(track, thisName, thisChrom, thisPos); char label[256]; safef(label, sizeof(label), "Use %s", nameOrDefault(thisName, "this variant")); cgiMakeButton("setCenterSubmit", label); printf(" as anchor</TD></TR>\n"); } else { printf("<TR><TD></TD><TD>"); char *hapOrSample = vcfHaplotypeOrSample(cart); if (sameString(hapOrSample, "Sample")) { puts("Samples are clustered by similarity around a central variant. " "Samples are reordered for display using the clustering tree, which is " "drawn in the left label area."); } else { puts("If this mode is selected and genotypes are phased or homozygous, " "then 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."); } printf("<br>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." "</TD></TR>\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.</TD></TR>\n"); else { // make a "use me" button printf("%s at %s:%d as anchor.</TD></TR>\n<TR><TD></TD><TD>\n", nameOrDefault(centerName, "variant"), centerChrom, centerPos+1); char label[256]; safef(label, sizeof(label), "Use %s", nameOrDefault(thisName, "this variant")); cgiMakeButton("replaceCenterSubmit", label); printf(" as anchor</TD></TR>\n"); } } else { // Form inputs (in case the clear button is clicked) vcfCfgHaplotypeCenterHiddens(track, centerName, centerChrom, centerPos); printf("%s at %s:%d as anchor.</TD></TR>\n", nameOrDefault(centerName, "variant"), centerChrom, centerPos+1); } // Make a clear button that modifies the hiddens using onClick puts("<TR><TD></TD><TD>"); 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("clearCenterSubmit", "Clear selection", NULL, onClick->string); printf(" (use " VCF_HAPLOSORT_DEFAULT_DESC ")</TD></TR>\n"); } } } static void vcfCfgHaplotypeMethod(struct cart *cart, struct trackDb *tdb, char *track, boolean parentLevel, struct vcfFile *vcff) /* If vcff has genotype data, offer the option of whether to cluster or just use the order * of genotypes in the VCF file. For clustering, show status and controls for choosing the * center variant for haplotype clustering/sorting in hgTracks. */ { if (vcff != NULL && vcff->genotypeCount > 1) { printf("<TABLE cellpadding=0><TR><TD colspan=2>" "<B>%s sorting order:</B></TD></TR>\n", vcfHaplotypeOrSample(cart)); // If trackDb specifies a treeFile, offer that as an option char *hapMethod = cartOrTdbString(cart, tdb, VCF_HAP_METHOD_VAR, VCF_DEFAULT_HAP_METHOD); char *hapMethodTdb = trackDbSetting(tdb, VCF_HAP_METHOD_VAR); char varName[1024]; safef(varName, sizeof(varName), "%s." VCF_HAP_METHOD_VAR, track); if (hapMethodTdb && startsWithWord("treeFile", hapMethodTdb)) { puts("<TR><TD>"); cgiMakeRadioButton(varName, VCF_HAP_METHOD_TREE_FILE, startsWithWord(VCF_HAP_METHOD_TREE_FILE, hapMethod)); printf("</TD><TD>using the tree specified in file associated with track</TD></TR>"); } printf("<TR><TD>"); cgiMakeRadioButton(varName, VCF_HAP_METHOD_CENTER_WEIGHTED, sameString(hapMethod, VCF_HAP_METHOD_CENTER_WEIGHTED)); printf("</TD><TD>"); vcfCfgHaplotypeCenter(cart, tdb, track, parentLevel, vcff, NULL, NULL, 0, "mainForm"); puts("<TR><TD>"); cgiMakeRadioButton(varName, VCF_HAP_METHOD_FILE_ORDER, sameString(hapMethod, VCF_HAP_METHOD_FILE_ORDER)); puts("</TD><TD>using the order in which samples appear in the underlying VCF file</TD></TR>"); puts("</TABLE>"); jsInlineF("$('input[type=radio][name=\"%s\"]').change(function() { " "if (this.value == '"VCF_HAP_METHOD_CENTER_WEIGHTED"') {" " $('#leafShapeContainer').show();" " $('#sampleColorContainer').hide();" "} else if (this.value == '"VCF_HAP_METHOD_TREE_FILE"') {" " $('#sampleColorContainer').show();" " $('#leafShapeContainer').hide();" "} else {" " $('#sampleColorContainer').hide();" " $('#leafShapeContainer').hide();" "}});\n", varName); } } //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. */ { knetUdcInstall(); if (udcCacheTimeout() < 300) udcSetCacheTimeout(300); char *fileOrUrl = trackDbSetting(tdb, "bigDataUrl"); if (isEmpty(fileOrUrl)) { char *db = cartString(cart, "db"); char *table = tdb->table; char *dbTableName = trackDbSetting(tdb, "dbTableName"); struct sqlConnection *conn; if (isCustomTrack(tdb->track) && isNotEmpty(dbTableName)) { conn = hAllocConn(CUSTOM_TRASH); table = dbTableName; } else conn = hAllocConnTrack(db, tdb); char *chrom = cartOptionalString(cart, "c"); if (chrom != NULL) fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, table, chrom); if (fileOrUrl == NULL) fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, 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)) { if (startsWithWord("vcfTabix", tdb->type)) vcff = vcfTabixFileMayOpen(fileOrUrl, NULL, 0, 0, vcfMaxErr, -1); else vcff = vcfFileMayOpen(fileOrUrl, NULL, 0, 0, vcfMaxErr, -1, FALSE); } 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 = cartOrTdbBoolean(cart, tdb, VCF_HAP_ENABLED_VAR, TRUE); char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s." VCF_HAP_ENABLED_VAR, name); cgiMakeCheckBox(cartVar, hapClustEnabled); printf("<B>Enable %s sorting display</B><BR>\n", vcfHaplotypeOrSample(cart)); } static void vcfCfgHapClusterColor(struct cart *cart, struct trackDb *tdb, char *name, boolean parentLevel) /* Let the user choose how to color the sorted haplotypes. */ { printf("<B>Allele coloring scheme:</B><BR>\n"); char *colorBy = cartOrTdbString(cart, tdb, 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<BR>\n"); char *geneTrack = cartOrTdbString(cart, tdb, "geneTrack", NULL); if (isNotEmpty(geneTrack)) { cgiMakeRadioButton(varName, VCF_HAP_COLORBY_FUNCTION, sameString(colorBy, VCF_HAP_COLORBY_FUNCTION)); printf("reference alleles invisible, alternate alleles in " "<span style='color:red'>red</span> for non-synonymous, " "<span style='color:green'>green</span> for synonymous, " "<span style='color:blue'>blue</span> for UTR/noncoding, " "black otherwise<BR>\n"); } cgiMakeRadioButton(varName, VCF_HAP_COLORBY_REFALT, sameString(colorBy, VCF_HAP_COLORBY_REFALT)); printf("reference alleles in blue, alternate alleles in red<BR>\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)<BR>\n"); } static void vcfCfgHapClusterSampleColor(struct cart *cart, struct trackDb *tdb, char *name, boolean parentLevel) /* If sampleColorFile specifies multiple files, when hapClusterMethod treeFile is selected, * let the user choose sample-coloring scheme for the tree. */ { char *tdbSetting = trackDbSetting(tdb, VCF_SAMPLE_COLOR_FILE); if (tdbSetting && strchr(tdbSetting, ' ')) { char *hapMethod = cartOrTdbString(cart, tdb, VCF_HAP_METHOD_VAR, VCF_DEFAULT_HAP_METHOD); printf("<div id='sampleColorContainer'%s>\n", startsWithWord(VCF_HAP_METHOD_TREE_FILE, hapMethod) ? "" : " style='display: none;'"); printf("<b>Sample coloring scheme for tree:</b><br>\n"); char *setting = cartOrTdbString(cart, tdb, VCF_SAMPLE_COLOR_FILE, tdbSetting); char *options[16]; int optionCount = chopLine(tdbSetting, options); char *labels[optionCount]; char *values[optionCount]; int i; for (i = 0; i < optionCount; i++) { char *eq = strchr(options[i], '='); if (eq) { *eq = '\0'; labels[i] = options[i]; replaceChar(options[i], '_', ' '); values[i] = eq+1; } else { labels[i] = values[i] = options[i]; } } char *selected = strchr(setting, ' ') ? values[0] : setting; char varName[1024]; safef(varName, sizeof varName, "%s." VCF_SAMPLE_COLOR_FILE, name); cgiMakeDropListWithVals(varName, labels, values, optionCount, selected); puts("</div>"); } } static void vcfCfgHapClusterTreeAngle(struct cart *cart, struct trackDb *tdb, char *name, boolean parentLevel) /* Let the user choose branch shape. */ { // This option applies only to center-weighted clustering; don't show option when some other // method is selected. char *hapMethod = cartOrTdbString(cart, tdb, VCF_HAP_METHOD_VAR, VCF_DEFAULT_HAP_METHOD); printf("<div id='leafShapeContainer'%s>\n", differentString(hapMethod, VCF_HAP_METHOD_CENTER_WEIGHTED) ? " style='display: none;'" : ""); printf("<B>%s clustering tree leaf shape:</B><BR>\n", vcfHaplotypeOrSample(cart)); char *treeAngle = cartOrTdbString(cart, tdb, 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 branches whose samples are all identical as <<BR>\n"); cgiMakeRadioButton(varName, VCF_HAP_TREEANGLE_RECTANGLE, sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE)); printf("draw branches whose samples are all identical as [<BR>\n"); puts("</div>"); } static void vcfCfgHapClusterHeight(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, char *name, boolean parentLevel) /* Let the user specify a height for the track. */ { if (vcff != NULL && vcff->genotypeCount > 1) { printf("<B>%s sorting display height:</B> \n", vcfHaplotypeOrSample(cart)); int cartHeight = cartOrTdbInt(cart, tdb, 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", "10000"); puts("<BR>"); } } static void vcfCfgHapCluster(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, char *name, boolean parentLevel) /* Show controls for haplotype-sorting display, which only makes sense to do when * the VCF file describes multiple genotypes. */ { char *hapOrSample = vcfHaplotypeOrSample(cart); printf("<H3>%s sorting display</H3>\n", hapOrSample); vcfCfgHapClusterEnable(cart, tdb, name, parentLevel); vcfCfgHaplotypeMethod(cart, tdb, name, parentLevel, vcff); vcfCfgHapClusterTreeAngle(cart, tdb, name, parentLevel); vcfCfgHapClusterSampleColor(cart, tdb, name, parentLevel); vcfCfgHapClusterColor(cart, tdb, name, parentLevel); vcfCfgHapClusterHeight(cart, tdb, vcff, name, parentLevel); } static void vcfCfgMinQual(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, 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 = cartOrTdbBoolean(cart, tdb, VCF_APPLY_MIN_QUAL_VAR, VCF_DEFAULT_APPLY_MIN_QUAL); cgiMakeCheckBox(cartVar, applyFilter); printf("<B>Exclude variants with Quality/confidence score (QUAL) score less than</B>\n"); double minQual = cartOrTdbDouble(cart, tdb, VCF_MIN_QUAL_VAR, VCF_DEFAULT_MIN_QUAL); safef(cartVar, sizeof(cartVar), "%s." VCF_MIN_QUAL_VAR, name); cgiMakeDoubleVar(cartVar, minQual, 10); printf("<BR>\n"); } static void vcfCfgFilterColumn(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, 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("<B>Exclude variants with these FILTER values:</B><BR>\n"); char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s."VCF_EXCLUDE_FILTER_VAR, name); if (slCount(vcff->filterDefs) > 1) { jsMakeCheckboxGroupSetClearButton(cartVar, TRUE); puts(" "); jsMakeCheckboxGroupSetClearButton(cartVar, FALSE); } char *values[filterCount]; char *labels[filterCount]; int i; struct vcfInfoDef *filt; for (i=0, filt=vcff->filterDefs; filt != NULL; i++, filt = filt->next) { 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 parentLevel) /* Show input for minimum allele frequency, if we can extract it from the VCF INFO column. */ { printf("<B>Minimum minor allele frequency (if INFO column includes AF or AC+AN):</B>\n"); double cartMinFreq = cartOrTdbDouble(cart, tdb, 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("<BR>"); } static void vcfCfgMinAc(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, char *name, boolean parentLevel) /* Show input for minimum alternate allele count, if INFO column includes AC. This lets * the user filter on a whole-number count (e.g. 2 to hide singletons) instead of having to * enter a tiny frequency cutoff. */ { printf("<B>Minimum allele count (if INFO column includes AC), e.g. 2 to hide singletons:</B>\n"); int cartMinAc = cartOrTdbInt(cart, tdb, VCF_MIN_AC_VAR, VCF_DEFAULT_MIN_AC); char varName[1024]; safef(varName, sizeof(varName), "%s." VCF_MIN_AC_VAR, name); cgiMakeIntVarWithMin(varName, cartMinAc, "minimum allele count", 5, 0); puts("<BR>"); } static char *getChildSample(struct trackDb *tdb) /* Return just the VCF sample name of the phased trio child setting */ { char *childSampleMaybeAlias = cloneString(trackDbLocalSetting(tdb, VCF_PHASED_CHILD_SAMPLE_SETTING)); char *pt = strchr(childSampleMaybeAlias, '|'); if (pt != NULL) *pt = '\0'; return childSampleMaybeAlias; } static struct slPair *vcfPhasedGetSamplesFromTdb(struct trackDb *tdb, boolean hideOtherSamples) /* Get the different VCF Phased Trio setings out of trackDb onto a list */ { // cloneString here because we will be munging the result if there are alternate labels char *childSampleMaybeAlias = cloneString(trackDbLocalSetting(tdb, VCF_PHASED_CHILD_SAMPLE_SETTING)); char *parentSamplesMaybeAlias = cloneString(trackDbLocalSetting(tdb, VCF_PHASED_PARENTS_SAMPLE_SETTING)); char *samples[VCF_PHASED_MAX_OTHER_SAMPLES+1]; // for now only allow at most two parents int numOthers = 0; if (parentSamplesMaybeAlias && !hideOtherSamples) { numOthers = chopCommas(cloneString(parentSamplesMaybeAlias), samples); if (numOthers > VCF_PHASED_MAX_OTHER_SAMPLES) { warn("More than %d other samples specified for phased trio", VCF_PHASED_MAX_OTHER_SAMPLES); numOthers = VCF_PHASED_MAX_OTHER_SAMPLES; } // shove child into middle of array, and if there are two parents, scoot the second one to the end int lastParentIx = VCF_PHASED_MAX_OTHER_SAMPLES - 1; if (samples[lastParentIx] != NULL) samples[VCF_PHASED_MAX_OTHER_SAMPLES] = cloneString(samples[lastParentIx]); samples[lastParentIx] = cloneString(childSampleMaybeAlias); } else samples[0] = cloneString(childSampleMaybeAlias); boolean gotAlias = strchr(samples[0], '|') != NULL; // default to whatever is first struct slPair *ret = NULL; int i; for (i = 0; i < numOthers+1; i++) { char *val = strchr(samples[i], '|'); boolean foundAlias = val != NULL; if (val != NULL) { if (foundAlias != gotAlias) errAbort("Either all samples have aliases or none."); else *val++ = 0; } char *name = samples[i]; struct slPair *temp = slPairNew(cloneString(name), cloneString(val)); slAddHead(&ret, temp); } slReverse(&ret); return ret; } struct slPair *vcfPhasedGetSampleOrder(struct cart *cart, struct trackDb *tdb, boolean parentLevel, boolean hideOtherSamples) /* Parse out a trio sample order from either trackDb or the cart. * If the trackName.sortChildBelow cart variable is true, then ensure * the vcfChildSample sample is last in the order, otherwise, use what's * in the trackName.vcfSampleOrder cart variable. */ { char sampleOrderVar[1024]; safef(sampleOrderVar, sizeof(sampleOrderVar), "%s.%s", tdb->track, VCF_PHASED_SAMPLE_ORDER_VAR); char *cartOrder = cartOptionalString(cart, sampleOrderVar); boolean childBelow = cartUsualBooleanClosestToHome(cart, tdb, parentLevel, VCF_PHASED_CHILD_BELOW_VAR, FALSE); struct slPair *tdbOrder = vcfPhasedGetSamplesFromTdb(tdb, hideOtherSamples); if (!hideOtherSamples) { // if the user used drag and drop to reorder the trios then that takes precedence // over the childBelow checkbox if (cartOrder != NULL) { struct slName *name, *fromCart = slNameListFromComma(cartOrder); struct slPair *ret = NULL; for (name = fromCart; name != NULL; name = name->next) { struct slPair *temp = slPairFind(tdbOrder, name->name); struct slPair *toAdd = slPairNew(temp->name, temp->val); slAddHead(&ret, toAdd); } slReverse(&ret); return ret; } else if (childBelow) { char *childName = getChildSample(tdb); struct slPair *ret = NULL, *child = NULL, *temp = NULL; for (temp = tdbOrder; temp != NULL; temp = temp->next) { struct slPair *toAdd = slPairNew(temp->name, temp->val); if (sameString(temp->name, childName)) child = toAdd; else slAddHead(&ret, toAdd); } if (child) slAddHead(&ret, child); slReverse(&ret); return ret; } } // we're hiding the parents OR (we unchecked the childBelow checkbox AND we didn't drag reorder) return tdbOrder; } static boolean hasSampleAliases(struct trackDb *tdb) /* Check whether trackDb has aliases for the sample names */ { struct slPair *nameVals = vcfPhasedGetSamplesFromTdb(tdb,FALSE); return nameVals->val != NULL; } static void vcfPhasedSampleSortUi(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, char *name, boolean parentLevel) /* Put up the UI for sorting the samples */ { struct dyString *sortOrder = dyStringNew(0); struct slPair *pair, *tdbOrder = vcfPhasedGetSampleOrder(cart, tdb, parentLevel, FALSE); if (slCount(tdbOrder) == 1) // no sorting if there are no parents return; char childBelowSortOrder[1024]; safef(childBelowSortOrder, sizeof(childBelowSortOrder), "%s.%s", name, VCF_PHASED_CHILD_BELOW_VAR); boolean isBelowChecked = cartUsualBooleanClosestToHome(cart, tdb, parentLevel, VCF_PHASED_CHILD_BELOW_VAR, FALSE); printf("<b>Show child haplotypes below parents:</b>\n"); cgiMakeCheckBox(childBelowSortOrder, isBelowChecked); char *infoText = "Check this box to sort the child haplotypes below the parents, leave unchecked" " to use the default sort order of the child in the middle. Click into each subtrack to arbitrarily" " order the samples which overrides this setting."; printInfoIcon(infoText); printf("<br>"); if (!parentLevel) { printf("<b>or:</b><br>\n"); printf("<b>Drag to change order:</b>\n"); printf("<div>\n"); printf("<table id=\"%s_table\" class=\"tableWithDragAndDrop\">\n", tdb->track); for (pair = tdbOrder; pair != NULL; pair = pair->next) { char id[256]; safef(id, sizeof(id), "%s_drag", pair->name); printf("<tr id=\"%s_row\" class=\"trDraggable\"><td id=\"%s\" class=\"dragHandle\">%s - %s</td></tr>\n", pair->name, id, pair->name, (char *)pair->val); dyStringPrintf(sortOrder, "%s,", pair->name); } printf("</table>\n"); printf("</div>\n"); printf("<input type=\"hidden\" name=\"%s.%s\" value=\"%s\">",tdb->track, VCF_PHASED_SAMPLE_ORDER_VAR, dyStringCannibalize(&sortOrder)); // add the hidden variable for setting the order and the javascript to change it jsInlineF("" "dragReorder.init();\n" "var imgTable = $(\"#%s_table\");\n" "if ($(imgTable).length > 0) {\n" " $(imgTable).tableDnD({\n" " onDragClass: \"trDrag\",\n" " dragHandle: \"dragHandle\",\n" " scrollAmount: 40,\n" " onDragStart: function(ev, table, row) {\n" " mouse.saveOffset(ev);\n" " table.tableDnDConfig.dragObjects = [ row ]; // defaults to just the one\n" " },\n" " onDrop: function(table, row, dragStartIndex) {\n" " if ($(row).attr('rowIndex') !== dragStartIndex) {\n" " // NOTE Even if dragging a contiguous set of rows,\n" " // still only need to check the one under the cursor.\n" " if (dragReorder.setOrder) {\n" " dragReorder.setOrder(table);\n" " }\n" " // save the order of the samples into the input variable named above\n" " var newVal = \"\";\n" " var inp = $(\"input[name='%s.%s']\")[0];\n" " for (i = 0; i < table.rows.length; i++) {\n" " newVal += table.rows[i].id.slice(0,-4) + \",\";\n" " }\n" " if (newVal.slice(-1) === \",\") {\n" " newVal = newVal.slice(0,-1);\n" " }\n" " inp.value = newVal;\n" " }\n" " }\n" " });\n" "}\n" "", tdb->track, tdb->track, VCF_PHASED_SAMPLE_ORDER_VAR); } } static void vcfCfgPhasedTrioUi(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, char *name, boolean parentLevel) /* Put up the phased trio specific config settings */ { //if (!parentLevel) // don't put up this display at the composite level vcfPhasedSampleSortUi(cart, tdb, vcff, name, parentLevel); if (hasSampleAliases(tdb)) { printf("<b>Label samples by:</b>"); char defaultLabel[1024], aliasLabel[1024]; safef(defaultLabel, sizeof(defaultLabel), "%s.%s", name, VCF_PHASED_DEFAULT_LABEL_VAR); safef(aliasLabel, sizeof(aliasLabel), "%s.%s", name, VCF_PHASED_ALIAS_LABEL_VAR); boolean isDefaultChecked = cartUsualBooleanClosestToHome(cart, tdb, parentLevel, VCF_PHASED_DEFAULT_LABEL_VAR, FALSE); boolean isAliasChecked = cartUsualBooleanClosestToHome(cart, tdb, parentLevel, VCF_PHASED_ALIAS_LABEL_VAR, TRUE); cgiMakeCheckBox(defaultLabel, isDefaultChecked); printf("VCF file sample names "); cgiMakeCheckBox(aliasLabel, isAliasChecked); printf("Family Labels"); printf("<br>"); } if (trackDbSetting(tdb,VCF_PHASED_PARENTS_SAMPLE_SETTING)) { printf("<b>Hide parent sample(s)"); char hideVarName[1024]; safef(hideVarName, sizeof(hideVarName), "%s.%s", name, VCF_PHASED_HIDE_OTHER_VAR); boolean hidingOtherSamples = cartUsualBooleanClosestToHome(cart, tdb, parentLevel, VCF_PHASED_HIDE_OTHER_VAR, FALSE); cgiMakeCheckBox(hideVarName, hidingOtherSamples); } printf("<br>"); printf("Allele coloring scheme:"); printf("<br>"); char *colorBy = cartOrTdbString(cart, tdb, VCF_PHASED_COLORBY_VAR, VCF_PHASED_COLORBY_DEFAULT); char varName[1024]; safef(varName, sizeof(varName), "%s.%s", name, VCF_PHASED_COLORBY_VAR); cgiMakeRadioButton(varName, VCF_PHASED_COLORBY_DEFAULT, sameString(colorBy, VCF_PHASED_COLORBY_DEFAULT)); printf("No color<br>"); char *geneTrack = cartOrTdbString(cart, tdb, "geneTrack", NULL); if (isNotEmpty(geneTrack)) { cgiMakeRadioButton(varName, VCF_PHASED_COLORBY_FUNCTION, sameString(colorBy, VCF_PHASED_COLORBY_FUNCTION)); printf("predicted functional affect: "); printf("reference alleles invisible, alternate alleles in " "<span style='color:red'>red</span> for non-synonymous, " "<span style='color:green'>green</span> for synonymous, " "<span style='color:blue'>blue</span> for UTR/noncoding, " "black otherwise<BR>\n"); } cgiMakeRadioButton(varName, VCF_PHASED_COLORBY_DE_NOVO, sameString(colorBy, VCF_PHASED_COLORBY_DE_NOVO)); printf("predicted de novo child mutations <span style='color:red'>red</span>"); char *deNovoInfoText = "Check this box to color child variants red if they are unique to the child"; printInfoIcon(deNovoInfoText); printf("<br>"); cgiMakeRadioButton(varName, VCF_PHASED_COLORBY_MENDEL_DIFF, sameString(colorBy, VCF_PHASED_COLORBY_MENDEL_DIFF)); printf("child variants that are inconsistent with phasing <span style='color:red'>red</span>"); char *phasedInfoText = "Check this box to color child variants red if they do not agree with the implied " "parental transmitted allele at this location. This configuration is only available when parent " "haplotypes are displayed."; printInfoIcon(phasedInfoText); } +static void vcfCfgInfoFilterUi(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, char *name, boolean parentLevel) +/* Show the filters on the INFO fields, if any */ +{ +if (cartOptionalString(cart, "ajax") == NULL) + { + webIncludeResourceFile("ui.dropdownchecklist.css"); + jsIncludeFile("ui.dropdownchecklist.js",NULL); + jsIncludeFile("ddcl.js",NULL); + } + +if (parentLevel) + if (trackDbSettingOn(tdb->parent, "noParentConfig")) + return; + +// Skip everything (including the heading) when no INFO filters are defined. +struct trackDbFilter *numFilters = tdbGetTrackNumFilters(tdb); +struct trackDbFilter *textFilters = tdbGetTrackTextFilters(tdb); +filterBy_t *filterBySet = filterBySetGet(tdb, cart, name); +if (numFilters == NULL && textFilters == NULL && filterBySet == NULL) + return; + +printf("<B>Filter on INFO fields:</B><BR>\n"); + +char *db = cartString(cart, "db"); +boolean isBoxOpened = FALSE; +numericFiltersShowAll(db, cart, tdb, &isBoxOpened, TRUE, parentLevel, name, NULL, FALSE); + +textFiltersShowAll(db, cart, tdb, FALSE); + +if (filterBySet != NULL) + { + if (!tdbIsComposite(tdb) && cartOptionalString(cart, "ajax") == NULL) + jsIncludeFile("hui.js",NULL); + + if (!isBoxOpened) // filterBy boxes are not double "boxed" when alone + printf("<BR>"); + filterBySetCfgUi(cart, tdb, filterBySet, TRUE, name); + filterBySetFree(&filterBySet); + } +} + 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("<TABLE%s><TR><TD>", boxed ? " width='100%'" : ""); struct vcfFile *vcff = vcfHopefullyOpenHeader(cart, tdb); if (vcff != NULL) { boolean parentLevel = isNameAtParentLevel(tdb, name); boolean doVcfFilterUi = cartOrTdbBoolean(cart, tdb, VCF_DO_FILTER_UI, TRUE); boolean doVcfQualUi = cartOrTdbBoolean(cart, tdb, VCF_DO_QUAL_UI, TRUE); boolean doVcfMafUi = cartOrTdbBoolean(cart, tdb, VCF_DO_MAF_UI, TRUE); boolean doVcfMinAcUi = cartOrTdbBoolean(cart, tdb, VCF_DO_MIN_AC_UI, TRUE); + boolean doVcfInfoFilterUi = cartOrTdbBoolean(cart, tdb, VCF_DO_INFOFILTER_UI, TRUE) + && bedHasFilters(tdb); if (vcff->genotypeCount > 1 && !sameString(tdb->type, "vcfPhasedTrio")) { vcfCfgHapCluster(cart, tdb, vcff, name, parentLevel); } if (sameString(tdb->type, "vcfPhasedTrio")) { vcfCfgPhasedTrioUi(cart, tdb, vcff, name, parentLevel); } - if (differentString(tdb->track,"evsEsp6500") && (doVcfFilterUi || doVcfQualUi)) - { + boolean isEvsEsp = sameString(tdb->track, "evsEsp6500"); + boolean printFiltersH3 = (!isEvsEsp && (doVcfQualUi || doVcfFilterUi)) + || doVcfMafUi || doVcfMinAcUi || doVcfInfoFilterUi; + if (printFiltersH3) puts("<H3>Filters</H3>"); + if (!isEvsEsp) + { if (doVcfQualUi) vcfCfgMinQual(cart, tdb, vcff, name, parentLevel); if (doVcfFilterUi) vcfCfgFilterColumn(cart, tdb, vcff, name, parentLevel); } if (doVcfMafUi) vcfCfgMinAlleleFreq(cart, tdb, vcff, name, parentLevel); if (doVcfMinAcUi) vcfCfgMinAc(cart, tdb, vcff, name, parentLevel); + if (doVcfInfoFilterUi) + vcfCfgInfoFilterUi(cart, tdb, vcff, name, parentLevel); } else { printf("Sorry, couldn't access VCF file.<BR>\n"); } puts("</TD>"); if (boxed && fileExists(hHelpFile("hgVcfTrackHelp"))) printf("<TD style='text-align:right'><A HREF=\"../goldenPath/help/hgVcfTrackHelp.html\" " "TARGET=_BLANK>VCF configuration help</A></TD>"); printf("</TR></TABLE>"); wigOption(cart, name, title, tdb); if (!boxed && fileExists(hHelpFile("hgVcfTrackHelp"))) printf("<P><A HREF=\"../goldenPath/help/hgVcfTrackHelp.html\" TARGET=_BLANK>VCF " "configuration help</A></P>"); cfgEndBox(boxed); } -