098b0567c51ecc6e2098f17d8fbcf9dcf4f830ca angie Tue Nov 13 12:25:19 2012 -0800 Problem: when we have a BAM or VCF track with per-chromosome files,and then view a chromosome for which there is no file (e.g. a random or hap), hgTracks was hitting an early errAbort that is more appropriate for a single-big-file track that is missing its filename. Fix: allow bbiNameFromTableChrom to return NULL if there is a seqName column and there simply isn't a file for that seqName. diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c index f9fa729..b202065 100644 --- src/hg/lib/vcfUi.c +++ src/hg/lib/vcfUi.c @@ -1,335 +1,342 @@ /* vcfUi - Variant Call Format user interface controls that are shared * between more than one CGI. */ #include "common.h" #include "cheapcgi.h" #include "errCatch.h" #include "hCommon.h" #include "hui.h" #include "jsHelper.h" #include "vcf.h" #include "vcfUi.h" #if (defined USE_TABIX && defined KNETFILE_HOOKS) #include "knetUdc.h" #include "udc.h" #endif//def USE_TABIX && KNETFILE_HOOKS 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); } 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("<TABLE cellpadding=0><TR><TD>" "<B>Haplotype sorting order:</B> 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>"); vcfCfgHaplotypeCenterHiddens(track, thisName, thisChrom, thisPos); char label[256]; safef(label, sizeof(label), "Use %s", nameOrDefault(thisName, "this variant")); cgiMakeButton("submit", label); printf(" as anchor</TD></TR>\n"); } else printf("<TR><TD>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>\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</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>"); 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 ")</TD></TR>\n"); } puts("</TABLE>"); } } //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("<B>Enable Haplotype sorting display</B><BR>\n"); } 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>Haplotype coloring scheme:</B><BR>\n"); 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<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. */ { printf("<B>Haplotype clustering tree leaf shape:</B><BR>\n"); 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 <<BR>\n"); cgiMakeRadioButton(varName, VCF_HAP_TREEANGLE_RECTANGLE, sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE)); printf("draw leaf clusters as [<BR>\n"); } 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>Haplotype sorting display height:</B> \n"); 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("<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. */ { 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("<BR>"); } 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 = cartUsualBooleanClosestToHome(cart, tdb, parentLevel, 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 = 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("<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); 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 = 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("<BR>"); } 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) { puts("<H3>Haplotype sorting display</H3>"); puts("<P>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.</P>"); vcfCfgHapCluster(cart, tdb, vcff, name, parentLevel); } 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); }