30ee8eb43a22ad344e07f8f86816914d6c3a5cf7 tdreszer Fri Mar 28 15:04:40 2014 -0700 Limit vcf filtering for a particular track evsEsp6500, which has slighltly non-conforming vcf fields. Really this code should be changed to not be track specific, but to only offer vcf filters that are requested in trackDb.ra. Redmine #9329. diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c index 9caed6d..f310afb 100644 --- src/hg/lib/vcfUi.c +++ src/hg/lib/vcfUi.c @@ -312,33 +312,36 @@ struct vcfFile *vcff = vcfHopefullyOpenHeader(cart, tdb); if (vcff != NULL) { boolean parentLevel = isNameAtParentLevel(tdb, name); if (vcff->genotypeCount > 1) { puts("

Haplotype sorting display

"); puts("

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.

"); vcfCfgHapCluster(cart, tdb, vcff, name, parentLevel); } + if (differentString(tdb->track,"evsEsp6500")) + { puts("

Filters

"); 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.
\n"); } puts(""); if (boxed && fileExists(hHelpFile("hgVcfTrackHelp"))) printf("VCF configuration help"); printf(""); if (!boxed && fileExists(hHelpFile("hgVcfTrackHelp")))