e7c53e49485ab14146a43157c4eba77bda38e7e0
chmalee
  Fri Jul 24 16:11:34 2020 -0700
Work in progress combination of the clingen dosage tracks

diff --git src/hg/makeDb/trackDb/human/trackDb.clinGen.ra src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
index 8592c4f..91d387f 100644
--- src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
+++ src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
@@ -1,61 +1,70 @@
-track clinGenSuper
-shortLabel ClinGen
-longLabel Clinical Genome Resource (ClinGen)
-group phenDis
-superTrack on
-html clinGen 
-
-    track dosageSensitivity
-    parent clinGenSuper on
-    shortLabel ClinGen Dosage Sensitivity
-    longLabel Clinical Genome Resource (ClinGen) Dosage Sensitivity Map 
+track clinGenComp
+shortLabel ClinGen CNV and Dosage
+longLabel Clinical Genome Resource (ClinGen) Dosage Sensitivity Map and Structural Variants
 visibility pack
 type bigBed 9 +
+group phenDis
 itemRgb on
 compositeTrack on
 html clinGenDosage
 
     track clinGenHaplo
-        parent dosageSensitivity
-        shortLabel ClinGen Haploinsufficiency
-        longLabel ClinGen Dosage Sensitivity Map - Haploinsufficiency
-        visibility dense
+    parent clinGenComp on
+    shortLabel ClinGen Haploinsufficiency Old
+    longLabel ClinGen Dosage Sensitivity Map - Haploinsufficiency Old
+    visibility pack
     type bigBed 9 +
     bigDataUrl /gbdb/$D/bbi/clinGen/clinGenHaplo.bb
     mouseOverField _mouseOver
     filterValues.haploScore 0|No evidence available,1|Little evidence for dosage pathogenicity,2|Some evidence for dosage pathogenicity,3|Sufficient evidence for dosage pathogenicity,30|Gene associated with autosomal recessive phenotype,40|Dosage sensitivity unlikely
     filterLabel.haploScore Dosage Sensitivity Score
     urls haploPMID1="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" haploPMID2="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" haploPMID3="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$"
 
     track clinGenTriplo
-        parent dosageSensitivity
-        shortLabel ClinGen Triplosensitivity
-        longLabel ClinGen Dosage Sensitivity Map - Triplosensitivity
-        visibility dense
+    parent clinGenComp on
+    shortLabel ClinGen Triplosensitivity Old
+    longLabel ClinGen Dosage Sensitivity Map - Triplosensitivity Old
+    visibility pack
     type bigBed 9 +
     bigDataUrl /gbdb//$D/bbi/clinGen/clinGenTriplo.bb
     mouseOverField _mouseOver
     filterValues.triploScore 0|No evidence available,1|Little evidence for dosage pathogenicity,2|Some evidence for dosage pathogenicity,3|Sufficient evidence for dosage pathogenicity,30|Gene associated with autosomal recessive phenotype,40|Dosage sensitivity unlikely
     filterLabel.triploScore Dosage Sensitivity Score
     urls triploPMID1="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" triploPMID2="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" triploPMID3="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$"
 
+    track clinGenDosage
+    parent clinGenComp on
+    shortLabel ClinGen Dosage Sensitivity
+    longLabel ClinGen Dosage Sensitivity
+    visibility pack
+    type bigBed 9 +
+    bigDataUrl /gbdb//$D/bbi/clinGen/clinGenDosage.bb
+    mouseOverField _mouseOver
+    filterValues.dosageType haplo|Likely Haplosensitive (Haploinsufficiency score >= 2 and Triplosensitivity score < 2),triplo|Likely Triplosensitive (Triplosensitivity score >= 2 and Haploinsufficiency score < 2),both|Haplo and Triplo Sensitive (Both scores >= 2),none|Little to no evidence for dosage sensitivity (Both scores < 2)
+    filterLabel.dosageType Type of dosage sensitivity
+    filterValues.haploScore 0|0 - No evidence available,1|1 - Little evidence for dosage pathogenicity,2|2 - Some evidence for dosage pathogenicity,3|3 - Sufficient evidence for dosage pathogenicity,30|30 - Gene associated with autosomal recessive phenotype,40|40 - Dosage sensitivity unlikely
+    filterLabel.haploScore Haplosensitivity Score
+    filterValues.triploScore 0|0 - No evidence available,1|1 - Little evidence for dosage pathogenicity,2|2 - Some evidence for dosage pathogenicity,3|3 - Sufficient evidence for dosage pathogenicity,30|30 - Gene associated with autosomal recessive phenotype,40|40 - Dosage sensitivity unlikely
+    filterLabel.triploScore Triplosensitivity Score
+    urls clinGenUrl="$$" haploPMID1="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" haploPMID2="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" haploPMID3="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" triploPMID1="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" triploPMID2="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" triploPMID3="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$"
+
     track clinGenCnv
-    parent clinGenSuper off
+    parent clinGenComp on
     shortLabel ClinGen Structural Variants
     longLabel Clinical Genome Resource (ClinGen) Structural Variants
     html clinGenSv
     type bigBed 9 +
     itemRgb on
     visibility dense
     mergeSpannedItems off
     bigDataUrl /gbdb/$D/bbi/clinGen/clinGenCnv.bb
     mouseOverField _mouseOver
     filterByRange.size on
     filterLabel.size Variant Size
     filterValues.variantType copy_number_loss|loss,copy_number_gain|gain
     filterLabel.variantType Variant Type
     filterValues.clinicalInterpretation Pathogenic|pathogenic,Benign|benign
     filterLabel.clinicalInterpretation Clinical Significance
     url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$
     urlLabel NCBI DbVar:
     urls pubMed="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" clinGenId="$$"