a21526733fec1b6e7930fae4758e1688aa125383
chmalee
  Tue Apr 23 10:30:40 2024 -0700
Removing test gnomad v3.1.1 track that was for QA testing only

diff --git src/hg/makeDb/trackDb/human/hg38/gnomad.ra src/hg/makeDb/trackDb/human/hg38/gnomad.ra
index a21529b..dc8857a 100644
--- src/hg/makeDb/trackDb/human/hg38/gnomad.ra
+++ src/hg/makeDb/trackDb/human/hg38/gnomad.ra
@@ -71,66 +71,30 @@
     filterValues.annot pLoF,missense,synonymous,other
     filterType.annot multiple
     filterValues.FILTER PASS,InbreedingCoeff,RF,AC0
     filterType.FILTER multipleListAnd
     filterValuesDefault.FILTER PASS
     filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,TFBS_ablation,TF_binding_site_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intergenic_variant,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation
     filterType.variation_type multipleListOr
     filter.AF 0.0
     filterLabel.AF Minor Allele Frequency Filter
     maxItems 50000
     mouseOver Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt); Genes: $genes; Type: $annot; Tag: $FILTER; Allele Frequency: $AF ($AC/$AN)
     url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r3&ignore=$<rsId>
     urlLabel View this variant at gnomAD
     detailsStaticTable Population Frequencies|/gbdb/hg38/gnomAD/v3.1/variants/v3.1.genomes.popTable.txt
 
-    track gnomadV311Test
-    release alpha
-    bigDataUrl /hive/data/inside/gnomAD/v3.1.1/2024-02-12/genomes.bb
-    parent gnomadVariants
-    visibility squish
-    shortLabel TEST gnomAD v3.1.1
-    longLabel TEST Genome Aggregation Database (gnomAD) Genome Variants v3.1.1
-    dataVersion Release v3.1.1 (March 20, 2021) and v3.1 chrM Release (November 17, 2020)
-    type bigBed 9 +
-    itemRgb on
-    searchIndex name,_displayName,rsId
-    html gnomadV3_1_1
-    priority 2
-    labelFields rsId,_displayName
-    defaultLabelFields _displayName
-    skipFields _displayName
-    skipEmptyFields on
-    filterValues.AC_non_cancer Non-Cancer
-    filterValuesDefault.AC_non_cancer Non-Cancer
-    filterType.AC_non_cancer single
-    filterValues.annot pLoF,missense,synonymous,other
-    filterValuesDefault.annot pLoF,missense,synonymous
-    filterValues.FILTER PASS,InbreedingCoeff,RF,AC0,AS_VQSR,indel_stack (chrM only),npg (chrM only)
-    filterType.FILTER multipleListAnd
-    filterValuesDefault.FILTER PASS
-    filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,start_retained_variant,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation
-    filterType.variation_type multipleListOr
-    filter.AF 0.0
-    filterLabel.AF Minor Allele Frequency Filter
-    maxItems 50000
-    mouseOver Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt); rsId: $rsId; Genes: $genes; Annotation: $annot; FILTER: $FILTER; Variation: $variation_type
-    url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r3&ignore=$<rsId>
-    urlLabel View this variant at gnomAD
-    detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies
-    detailsTabUrls _dataOffset=/hive/data/inside/gnomAD/v3.1.1/2024-02-12/gnomad.v3.1.1.details.tab.gz
-
     track gnomadGenomesVariantsV3_1_1
     parent gnomadVariants
     visibility squish
     shortLabel gnomAD v3.1.1
     longLabel Genome Aggregation Database (gnomAD) Genome Variants v3.1.1
     dataVersion Release v3.1.1 (March 20, 2021) and v3.1 chrM Release (November 17, 2020)
     type bigBed 9 +
     itemRgb on
     searchIndex name,_displayName,rsId
     html gnomadV3_1_1
     bigDataUrl /gbdb/hg38/gnomAD/v3.1.1/genomes.bb
     priority 2
     labelFields rsId,_displayName
     defaultLabelFields _displayName
     skipFields _displayName