dea7d848a3eb88f9521322b0d89650be3975d894 angie Sat Apr 4 13:44:50 2020 -0700 Get rid of requirement for vcf track to have < 3000 genotypes in order to do haplotype display. Nextstrain is already up to 3365. refs #25188 diff --git src/hg/hgTracks/vcfTrack.c src/hg/hgTracks/vcfTrack.c index 90b611f..804f1a6 100644 --- src/hg/hgTracks/vcfTrack.c +++ src/hg/hgTracks/vcfTrack.c @@ -1578,31 +1578,31 @@ if (isEmpty(fileOrUrl)) return; int vcfMaxErr = -1; struct vcfFile *vcff = NULL; boolean hapClustEnabled = cartOrTdbBoolean(cart, tg->tdb, VCF_HAP_ENABLED_VAR, TRUE); if (slCount(windows)>1) hapClustEnabled = FALSE; // haplotype sorting display not currently available with multiple windows. /* protect against temporary network error */ struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { vcff = vcfTabixFileAndIndexMayOpen(fileOrUrl, tbiFileOrUrl, chromName, winStart, winEnd, vcfMaxErr, -1); if (vcff != NULL) { filterRecords(vcff, tg->tdb); - if (hapClustEnabled && vcff->genotypeCount > 1 && vcff->genotypeCount < 3000 && + if (hapClustEnabled && vcff->genotypeCount > 1 && (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: tg->customInt = slCount(tg->items); } // Don't vcfFileFree here -- we are using its string pointers! } else { if (tbiFileOrUrl) errAbort("Unable to open VCF file/URL '%s' with tabix index '%s'", fileOrUrl, tbiFileOrUrl); else