0cbeed8fcb8eccd05e18cea41d4954f20d7698bd angie Wed Jul 9 13:45:50 2014 -0700 Added trackDb settings for initializing VCF track controls.This will be useful for CTs/hub tracks to turn off haplotype clustering or apply minimum QUAL score / minimum minor allele frequency filters. diff --git src/hg/hgTracks/vcfTrack.c src/hg/hgTracks/vcfTrack.c index dbd45af..07203bb9 100644 --- src/hg/hgTracks/vcfTrack.c +++ src/hg/hgTracks/vcfTrack.c @@ -10,36 +10,34 @@ #include "hacTree.h" #include "hdb.h" #include "hgColors.h" #include "hgTracks.h" #include "pgSnp.h" #include "trashDir.h" #include "vcf.h" #include "vcfUi.h" #include "knetUdc.h" #include "udc.h" static boolean getMinQual(struct trackDb *tdb, double *retMinQual) /* Return TRUE and set retMinQual if cart contains minimum QUAL filter */ { -if (cartUsualBooleanClosestToHome(cart, tdb, FALSE, - VCF_APPLY_MIN_QUAL_VAR, VCF_DEFAULT_APPLY_MIN_QUAL)) +if (cartOrTdbBoolean(cart, tdb, VCF_APPLY_MIN_QUAL_VAR, VCF_DEFAULT_APPLY_MIN_QUAL)) { if (retMinQual != NULL) - *retMinQual = cartUsualDoubleClosestToHome(cart, tdb, FALSE, VCF_MIN_QUAL_VAR, - VCF_DEFAULT_MIN_QUAL); + *retMinQual = cartOrTdbDouble(cart, tdb, VCF_MIN_QUAL_VAR, VCF_DEFAULT_MIN_QUAL); return TRUE; } return FALSE; } static boolean minQualFail(struct vcfRecord *record, double minQual) /* Return TRUE if record's QUAL column value is non-numeric or is less than minQual. */ { if (isEmpty(record->qual) || (record->qual[0] != '-' && !isdigit(record->qual[0])) || atof(record->qual) < minQual) return TRUE; return FALSE; } @@ -58,41 +56,37 @@ } static boolean filterColumnFail(struct vcfRecord *record, struct slName *filterValues) /* Return TRUE if record's FILTER column value(s) matches one of filterValues (from cart). */ { int i; for (i = 0; i < record->filterCount; i++) if (slNameInList(filterValues, record->filters[i])) return TRUE; return FALSE; } static boolean getMinFreq(struct trackDb *tdb, double *retMinFreq) /* Return TRUE and set retMinFreq if cart contains nonzero minimum minor allele frequency. */ { -if (cartVarExistsAnyLevel(cart, tdb, FALSE, VCF_MIN_ALLELE_FREQ_VAR)) - { - double minFreq = cartUsualDoubleClosestToHome(cart, tdb, FALSE, - VCF_MIN_ALLELE_FREQ_VAR, VCF_DEFAULT_MIN_ALLELE_FREQ); +double minFreq = cartOrTdbDouble(cart, tdb, VCF_MIN_ALLELE_FREQ_VAR, VCF_DEFAULT_MIN_ALLELE_FREQ); if (minFreq > 0) { if (retMinFreq != NULL) *retMinFreq = minFreq; return TRUE; } - } return FALSE; } static boolean minFreqFail(struct vcfRecord *record, double minFreq) /* Return TRUE if record's INFO include AF (alternate allele frequencies) or AC+AN * (alternate allele counts and total count of observed alleles) and the minor allele * frequency < minFreq -- or rather, major allele frequency > (1 - minFreq) because * variants with > 2 alleles might have some significant minor frequencies along with * tiny minor frequencies). */ { struct vcfFile *vcff = record->file; boolean gotInfo = FALSE; double refFreq = 1.0; double maxAltFreq = 0.0; int i; @@ -112,36 +106,36 @@ maxAltFreq = altFreq; } } else { // Calculate alternate allele freqs from AC and AN: const struct vcfInfoElement *acEl = vcfRecordFindInfo(record, "AC"); const struct vcfInfoDef *acDef = vcfInfoDefForKey(vcff, "AC"); const struct vcfInfoElement *anEl = vcfRecordFindInfo(record, "AN"); const struct vcfInfoDef *anDef = vcfInfoDefForKey(vcff, "AN"); if (acEl != NULL && acDef != NULL && acDef->type == vcfInfoInteger && anEl != NULL && anDef != NULL && anDef->type == vcfInfoInteger && anEl->count == 1 && anEl->missingData[0] == FALSE) { gotInfo = TRUE; - int totalCount = anEl->values[0].datFloat; + int totalCount = anEl->values[0].datInt; for (i = 0; i < acEl->count; i++) { if (acEl->missingData[i]) continue; - int altCount = acEl->values[i].datFloat; + int altCount = acEl->values[i].datInt; double altFreq = (double)altCount / totalCount; refFreq -= altFreq; if (altFreq < maxAltFreq) maxAltFreq = altFreq; } } else // Use MAF for alternate allele freqs from MAF: { const struct vcfInfoElement *mafEl = vcfRecordFindInfo(record, "MAF"); const struct vcfInfoDef *mafDef = vcfInfoDefForKey(vcff, "MAF"); if (mafEl != NULL && mafDef != NULL && mafDef->type == vcfInfoString && startsWith("Minor Allele Frequency",mafDef->description)) { // If INFO includes alt allele freqs, use them directly. @@ -1010,32 +1004,31 @@ // Restore the prior clipping: hvGfxUnclip(hvgLL); hvGfxSetClip(hvgLL, clipXBak, clipYBak, clipWidthBak, clipHeightBak); } static void ignoreEm(char *format, va_list args) /* Ignore warnings from genotype parsing -- when there's one, there * are usually hundreds more just like it. */ { } static enum hapColorMode getColorMode(struct trackDb *tdb) /* Get the hap-cluster coloring mode from cart & tdb. */ { enum hapColorMode colorMode = altOnlyMode; -char *colorBy = cartUsualStringClosestToHome(cart, tdb, FALSE, - VCF_HAP_COLORBY_VAR, VCF_DEFAULT_HAP_COLORBY); +char *colorBy = cartOrTdbString(cart, tdb, VCF_HAP_COLORBY_VAR, VCF_DEFAULT_HAP_COLORBY); if (sameString(colorBy, VCF_HAP_COLORBY_ALTONLY)) colorMode = altOnlyMode; else if (sameString(colorBy, VCF_HAP_COLORBY_REFALT)) colorMode = refAltMode; else if (sameString(colorBy, VCF_HAP_COLORBY_BASE)) colorMode = baseMode; return colorMode; } static void vcfHapClusterDraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) /* Split samples' chromosomes (haplotypes), cluster them by center-weighted * alpha similarity, and draw in the order determined by clustering. */ { @@ -1080,52 +1073,50 @@ if (ix != centerIx) drawOneRec(rec, gtHapOrder, gtHapCount, tg, hvg, xOff, yOff, width, isClustered, FALSE, colorMode); } // Draw the center rec on top, outlined with black lines, to make sure it is very visible: drawOneRec(centerRec, gtHapOrder, gtHapCount, tg, hvg, xOff, yOff, width, TRUE, TRUE, colorMode); // Draw as much of the tree as can fit in the left label area: int extraPixel = (colorMode == altOnlyMode) ? 1 : 0; int hapHeight = tg->height- CLIP_PAD - 2*extraPixel; struct yFromNodeHelper yHelper = {0, NULL, NULL}; initYFromNodeHelper(&yHelper, yOff+extraPixel, hapHeight, gtHapCount, gtHapOrder, vcff->genotypeCount); struct titleHelper titleHelper = { NULL, 0, 0, 0, 0, NULL, NULL }; initTitleHelper(&titleHelper, tg->track, startIx, centerIx, endIx, nRecords, vcff); -char *treeAngle = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, VCF_HAP_TREEANGLE_VAR, - VCF_DEFAULT_HAP_TREEANGLE); +char *treeAngle = cartOrTdbString(cart, tg->tdb, VCF_HAP_TREEANGLE_VAR, VCF_DEFAULT_HAP_TREEANGLE); boolean drawRectangle = sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE); drawTreeInLabelArea(ht, hvg, yOff+extraPixel, hapHeight+CLIP_PAD, &yHelper, &titleHelper, drawRectangle); } static int vcfHapClusterTotalHeight(struct track *tg, enum trackVisibility vis) /* Return height of haplotype graph (2 * #samples * lineHeight); * 2 because we're assuming diploid genomes here, no XXY, tetraploid etc. */ { const struct vcfFile *vcff = tg->extraUiData; if (vcff->records == NULL) return 0; int ploidy = sameString(chromName, "chrY") ? 1 : 2; int simpleHeight = ploidy * vcff->genotypeCount * tg->lineHeight; int defaultHeight = min(simpleHeight, VCF_DEFAULT_HAP_HEIGHT); char *tdbHeight = trackDbSettingOrDefault(tg->tdb, VCF_HAP_HEIGHT_VAR, NULL); if (isNotEmpty(tdbHeight)) defaultHeight = atoi(tdbHeight); -int cartHeight = cartUsualIntClosestToHome(cart, tg->tdb, FALSE, VCF_HAP_HEIGHT_VAR, - defaultHeight); +int cartHeight = cartOrTdbInt(cart, tg->tdb, VCF_HAP_HEIGHT_VAR, defaultHeight); if (tg->visibility == tvSquish) cartHeight /= 2; int extraPixel = (getColorMode(tg->tdb) == altOnlyMode) ? 1 : 0; int totalHeight = cartHeight + CLIP_PAD + 2*extraPixel; tg->height = min(totalHeight, maximumTrackHeight(tg)); return tg->height; } static char *vcfHapClusterTrackName(struct track *tg, void *item) /* If someone asks for itemName/mapItemName, just send name of track like wiggle. */ { return tg->track; } static void vcfHapClusterOverloadMethods(struct track *tg, struct vcfFile *vcff) @@ -1166,32 +1157,31 @@ if (tg->parallelLoading) { /* do not use mysql during parallel-fetch load */ fileOrUrl = trackDbSetting(tg->tdb, "bigDataUrl"); } else { struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb); fileOrUrl = bbiNameFromSettingOrTableChrom(tg->tdb, conn, tg->table, chromName); hFreeConn(&conn); } if (isEmpty(fileOrUrl)) return; int vcfMaxErr = -1; struct vcfFile *vcff = NULL; -boolean hapClustEnabled = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, - VCF_HAP_ENABLED_VAR, TRUE); +boolean hapClustEnabled = cartOrTdbBoolean(cart, tg->tdb, VCF_HAP_ENABLED_VAR, TRUE); /* protect against temporary network error */ struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { vcff = vcfTabixFileMayOpen(fileOrUrl, chromName, winStart, winEnd, vcfMaxErr, -1); if (vcff != NULL) { filterRecords(vcff, tg->tdb); if (hapClustEnabled && vcff->genotypeCount > 1 && vcff->genotypeCount < 3000 && (tg->visibility == tvPack || tg->visibility == tvSquish)) vcfHapClusterOverloadMethods(tg, vcff); else { tg->items = vcfFileToPgSnp(vcff, tg->tdb); // pgSnp bases coloring/display decision on count of items: @@ -1246,32 +1236,31 @@ void vcfTabixMethods(struct track *track) /* Methods for VCF alignment files, in absence of tabix lib. */ { // NOP warning method to warn users that tabix is not installed. messageLineMethods(track); track->drawItems = drawUseVcfTabixWarning; } #endif // no USE_TABIX static void vcfLoadItems(struct track *tg) /* Load items in window from VCF file. */ { int vcfMaxErr = -1; struct vcfFile *vcff = NULL; -boolean hapClustEnabled = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, - VCF_HAP_ENABLED_VAR, TRUE); +boolean hapClustEnabled = cartOrTdbBoolean(cart, tg->tdb, VCF_HAP_ENABLED_VAR, TRUE); char *table = tg->table; struct customTrack *ct = tg->customPt; struct sqlConnection *conn; if (ct == NULL) conn = hAllocConnTrack(database, tg->tdb); else { conn = hAllocConn(CUSTOM_TRASH); table = ct->dbTableName; } char *vcfFile = bbiNameFromSettingOrTable(tg->tdb, conn, table); hFreeConn(&conn); /* protect against parse error */ struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch))