791097ea7589f6fadcf825c5c3a8934054917a28 angie Thu Jul 9 14:38:12 2020 -0700 VCF haplotype display: trackDb setting geneTrack adds option to color by function (red for non-synon, green for synon, blue for UTR/NC). refs #25870 diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c index 8702fd6..52a7e2f 100644 --- src/hg/lib/vcfUi.c +++ src/hg/lib/vcfUi.c @@ -1,655 +1,666 @@ /* 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 README in this or parent directory for licensing information. */ #include "common.h" #include "cheapcgi.h" #include "errCatch.h" #include "hCommon.h" #include "hui.h" #include "jsHelper.h" #include "vcf.h" #include "vcfUi.h" #include "knetUdc.h" #include "udc.h" 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();" "} else {" " $('#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 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); 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 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("Highlight child variants that are inconsistent with phasing"); char shadeByDiffs[1024]; safef(shadeByDiffs, sizeof(shadeByDiffs), "%s.%s", name, VCF_PHASED_HIGHLIGHT_INCONSISTENT); boolean highlightChildDiffs = cartUsualBooleanClosestToHome(cart, tdb, FALSE, VCF_PHASED_HIGHLIGHT_INCONSISTENT, FALSE); cgiMakeCheckBox(shadeByDiffs, highlightChildDiffs); char *infoText = "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(infoText); } 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); 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")) { puts("<H3>Filters</H3>"); 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.<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>"); if (!boxed && fileExists(hHelpFile("hgVcfTrackHelp"))) printf("<P><A HREF=\"../goldenPath/help/hgVcfTrackHelp.html\" TARGET=_BLANK>VCF " "configuration help</A></P>"); cfgEndBox(boxed); }