1c32191759769c28cf763342f5e405420add0170 markd Thu Oct 1 21:20:54 2026 -0700 Make the TSS tracks superTracks of multiWig overlays. refs #35528 The composite held the multiWig overlays as children, which drew correctly but left two faults, both from hgTrackUi listing descendant leaves rather than containers: an overlay got no configuration block of its own, and hiding both strands of a cell line left an empty row where the overlay had been. That is #38441. As superTrack members the overlays are tracks in their own right. Each gets a full configuration page, including overlay method and negate values, and hiding one hides the whole overlay. Verified: hiding proCapNet_K562_pred removes the row and leaves the other five. Two top-level superTracks, PRO-cap and ProCapNet, rather than one transcriptionStart folder holding both. superTracks do not nest. A superTrack given a parent passes tdbQuery -check -strict and is then dropped at load, since trackDbSuperMarkup refuses to set a parent on a superTrack and hgTrackDb only writes a superTrack that some track names as its parent. Filed as #38460, with the test case; transcriptionStart.html stays in the tree unused in case it is fixed. What this costs: the subtrack matrix and the sample class filter, which a superTrack does not offer. Each overlay now carries its own wiggle settings and its own html, neither being inherited from a container any more. diff --git src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra index c3986df4797..a2eb9d3574c 100644 --- src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra +++ src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra @@ -1,495 +1,515 @@ # Generated by hg/makeDb/outside/proCapNet/proCapNetTrackDb for hg38. # Do not edit by hand, edit the script and regenerate. -track transcriptionStart +track encode4ProCap superTrack on show -shortLabel Transcription Initiation (TSS) -longLabel Transcription initiation (TSS) group rna - - track encode4ProCap - parent transcriptionStart - compositeTrack on - type bigWig shortLabel PRO-cap longLabel PRO-cap nascent RNA transcription start sites from ENCODE 4 - subGroup1 cellLine Cell_line A673=A673 Caco2=Caco-2 Calu3=Calu3 HUVEC=HUVEC K562=K562 MCF10A=MCF10A - subGroup2 dataType Data_type procapPos=PRO-cap_+ procapNeg=PRO-cap_- - subGroup3 sampleClass Sample_class Cancer=Cancer Noncancer=Non-cancer - dimensions dimensionX=dataType dimensionY=cellLine dimA=sampleClass - filterComposite dimA - sortOrder cellLine=+ dataType=+ - configurable on - autoScale group - alwaysZero on - maxHeightPixels 100:40:8 - windowingFunction maximum - noInherit on - visibility hide priority 1 +track proCapNet +superTrack on show +group rna +shortLabel ProCapNet +longLabel ProCapNet predicted PRO-cap +priority 2 + track encode4ProCap_A673_procap - parent encode4ProCap on +superTrack encode4ProCap full container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +windowingFunction maximum +configurable on +html encode4ProCap color 0,114,178 shortLabel A673 PRO-cap longLabel A673 (ENCSR046BCI) PRO-cap transcription start sites, plus up minus down - onlyVisibility full priority 1 track encode4ProCap_A673_procap_pos parent encode4ProCap_A673_procap - subGroups cellLine=A673 dataType=procapPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/A673.ENCSR046BCI.pos.bw color 0,114,178 shortLabel A673 PRO-cap + longLabel A673 (ENCSR046BCI) PRO-cap transcription start sites, plus strand track encode4ProCap_A673_procap_neg parent encode4ProCap_A673_procap - subGroups cellLine=A673 dataType=procapNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/A673.ENCSR046BCI.neg.bw color 0,114,178 altColor 0,114,178 shortLabel A673 PRO-cap - longLabel A673 (ENCSR046BCI) PRO-cap transcription start sites, minus strand track encode4ProCap_Caco-2_procap - parent encode4ProCap on +superTrack encode4ProCap full container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +windowingFunction maximum +configurable on +html encode4ProCap color 213,94,0 shortLabel Caco-2 PRO-cap longLabel Caco-2 (ENCSR100LIJ) PRO-cap transcription start sites, plus up minus down - onlyVisibility full priority 2 track encode4ProCap_Caco-2_procap_pos parent encode4ProCap_Caco-2_procap - subGroups cellLine=Caco2 dataType=procapPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Caco-2.ENCSR100LIJ.pos.bw color 213,94,0 shortLabel Caco-2 PRO-cap + longLabel Caco-2 (ENCSR100LIJ) PRO-cap transcription start sites, plus strand track encode4ProCap_Caco-2_procap_neg parent encode4ProCap_Caco-2_procap - subGroups cellLine=Caco2 dataType=procapNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Caco-2.ENCSR100LIJ.neg.bw color 213,94,0 altColor 213,94,0 shortLabel Caco-2 PRO-cap - longLabel Caco-2 (ENCSR100LIJ) PRO-cap transcription start sites, minus strand track encode4ProCap_Calu3_procap - parent encode4ProCap on +superTrack encode4ProCap full container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +windowingFunction maximum +configurable on +html encode4ProCap color 0,158,115 shortLabel Calu3 PRO-cap longLabel Calu3 (ENCSR935RNW) PRO-cap transcription start sites, plus up minus down - onlyVisibility full priority 3 track encode4ProCap_Calu3_procap_pos parent encode4ProCap_Calu3_procap - subGroups cellLine=Calu3 dataType=procapPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Calu3.ENCSR935RNW.pos.bw color 0,158,115 shortLabel Calu3 PRO-cap + longLabel Calu3 (ENCSR935RNW) PRO-cap transcription start sites, plus strand track encode4ProCap_Calu3_procap_neg parent encode4ProCap_Calu3_procap - subGroups cellLine=Calu3 dataType=procapNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Calu3.ENCSR935RNW.neg.bw color 0,158,115 altColor 0,158,115 shortLabel Calu3 PRO-cap - longLabel Calu3 (ENCSR935RNW) PRO-cap transcription start sites, minus strand track encode4ProCap_HUVEC_procap - parent encode4ProCap on +superTrack encode4ProCap full container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +windowingFunction maximum +configurable on +html encode4ProCap color 204,121,167 shortLabel HUVEC PRO-cap longLabel HUVEC (ENCSR098LLB) PRO-cap transcription start sites, plus up minus down - onlyVisibility full priority 4 track encode4ProCap_HUVEC_procap_pos parent encode4ProCap_HUVEC_procap - subGroups cellLine=HUVEC dataType=procapPos sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/HUVEC.ENCSR098LLB.pos.bw color 204,121,167 shortLabel HUVEC PRO-cap + longLabel HUVEC (ENCSR098LLB) PRO-cap transcription start sites, plus strand track encode4ProCap_HUVEC_procap_neg parent encode4ProCap_HUVEC_procap - subGroups cellLine=HUVEC dataType=procapNeg sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/HUVEC.ENCSR098LLB.neg.bw color 204,121,167 altColor 204,121,167 shortLabel HUVEC PRO-cap - longLabel HUVEC (ENCSR098LLB) PRO-cap transcription start sites, minus strand track encode4ProCap_K562_procap - parent encode4ProCap on +superTrack encode4ProCap full container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +windowingFunction maximum +configurable on +html encode4ProCap color 230,159,0 shortLabel K562 PRO-cap longLabel K562 (ENCSR261KBX) PRO-cap transcription start sites, plus up minus down - onlyVisibility full priority 5 track encode4ProCap_K562_procap_pos parent encode4ProCap_K562_procap - subGroups cellLine=K562 dataType=procapPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/K562.ENCSR261KBX.pos.bw color 230,159,0 shortLabel K562 PRO-cap + longLabel K562 (ENCSR261KBX) PRO-cap transcription start sites, plus strand track encode4ProCap_K562_procap_neg parent encode4ProCap_K562_procap - subGroups cellLine=K562 dataType=procapNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/K562.ENCSR261KBX.neg.bw color 230,159,0 altColor 230,159,0 shortLabel K562 PRO-cap - longLabel K562 (ENCSR261KBX) PRO-cap transcription start sites, minus strand track encode4ProCap_MCF10A_procap - parent encode4ProCap on +superTrack encode4ProCap full container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +windowingFunction maximum +configurable on +html encode4ProCap color 86,180,233 shortLabel MCF10A PRO-cap longLabel MCF10A (ENCSR799DGV) PRO-cap transcription start sites, plus up minus down - onlyVisibility full priority 6 track encode4ProCap_MCF10A_procap_pos parent encode4ProCap_MCF10A_procap - subGroups cellLine=MCF10A dataType=procapPos sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/MCF10A.ENCSR799DGV.pos.bw color 86,180,233 shortLabel MCF10A PRO-cap + longLabel MCF10A (ENCSR799DGV) PRO-cap transcription start sites, plus strand track encode4ProCap_MCF10A_procap_neg parent encode4ProCap_MCF10A_procap - subGroups cellLine=MCF10A dataType=procapNeg sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/MCF10A.ENCSR799DGV.neg.bw color 86,180,233 altColor 86,180,233 shortLabel MCF10A PRO-cap - longLabel MCF10A (ENCSR799DGV) PRO-cap transcription start sites, minus strand - track proCapNet - parent transcriptionStart - compositeTrack on - type bigWig - shortLabel ProCapNet - longLabel ProCapNet predicted PRO-cap - subGroup1 cellLine Cell_line A673=A673 Caco2=Caco-2 Calu3=Calu3 HUVEC=HUVEC K562=K562 MCF10A=MCF10A - subGroup2 dataType Data_type predPos=Predicted_+ predNeg=Predicted_- contrib=Contribution_scores - subGroup3 sampleClass Sample_class Cancer=Cancer Noncancer=Non-cancer - dimensions dimensionX=dataType dimensionY=cellLine dimA=sampleClass - filterComposite dimA - sortOrder cellLine=+ dataType=+ - configurable on - autoScale group - alwaysZero on - maxHeightPixels 100:40:8 - windowingFunction maximum - noInherit on - visibility hide - priority 2 - track proCapNet_A673_pred - parent proCapNet on +superTrack proCapNet full container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +windowingFunction maximum +configurable on +html proCapNet color 0,114,178 shortLabel A673 Predicted longLabel A673 (ENCSR072YCM) ProCapNet predicted PRO-cap, plus up minus down - onlyVisibility full priority 1 track proCapNet_A673_pred_pos parent proCapNet_A673_pred - subGroups cellLine=A673 dataType=predPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/A673.proCapNet.pos.bw color 0,114,178 shortLabel A673 Predicted + longLabel A673 (ENCSR072YCM) ProCapNet predicted PRO-cap, plus strand track proCapNet_A673_pred_neg parent proCapNet_A673_pred - subGroups cellLine=A673 dataType=predNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/A673.proCapNet.neg.bw color 0,114,178 altColor 0,114,178 shortLabel A673 Predicted - longLabel A673 (ENCSR072YCM) ProCapNet predicted PRO-cap, minus strand track proCapNet_Caco-2_pred - parent proCapNet on +superTrack proCapNet full container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +windowingFunction maximum +configurable on +html proCapNet color 213,94,0 shortLabel Caco-2 Predicted longLabel Caco-2 (ENCSR182QNJ) ProCapNet predicted PRO-cap, plus up minus down - onlyVisibility full priority 2 track proCapNet_Caco-2_pred_pos parent proCapNet_Caco-2_pred - subGroups cellLine=Caco2 dataType=predPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/Caco-2.proCapNet.pos.bw color 213,94,0 shortLabel Caco-2 Predicted + longLabel Caco-2 (ENCSR182QNJ) ProCapNet predicted PRO-cap, plus strand track proCapNet_Caco-2_pred_neg parent proCapNet_Caco-2_pred - subGroups cellLine=Caco2 dataType=predNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/Caco-2.proCapNet.neg.bw color 213,94,0 altColor 213,94,0 shortLabel Caco-2 Predicted - longLabel Caco-2 (ENCSR182QNJ) ProCapNet predicted PRO-cap, minus strand track proCapNet_Calu3_pred - parent proCapNet on +superTrack proCapNet full container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +windowingFunction maximum +configurable on +html proCapNet color 0,158,115 shortLabel Calu3 Predicted longLabel Calu3 (ENCSR797DEF) ProCapNet predicted PRO-cap, plus up minus down - onlyVisibility full priority 3 track proCapNet_Calu3_pred_pos parent proCapNet_Calu3_pred - subGroups cellLine=Calu3 dataType=predPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/Calu3.proCapNet.pos.bw color 0,158,115 shortLabel Calu3 Predicted + longLabel Calu3 (ENCSR797DEF) ProCapNet predicted PRO-cap, plus strand track proCapNet_Calu3_pred_neg parent proCapNet_Calu3_pred - subGroups cellLine=Calu3 dataType=predNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/Calu3.proCapNet.neg.bw color 0,158,115 altColor 0,158,115 shortLabel Calu3 Predicted - longLabel Calu3 (ENCSR797DEF) ProCapNet predicted PRO-cap, minus strand track proCapNet_HUVEC_pred - parent proCapNet on +superTrack proCapNet full container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +windowingFunction maximum +configurable on +html proCapNet color 204,121,167 shortLabel HUVEC Predicted longLabel HUVEC (ENCSR801ECP) ProCapNet predicted PRO-cap, plus up minus down - onlyVisibility full priority 4 track proCapNet_HUVEC_pred_pos parent proCapNet_HUVEC_pred - subGroups cellLine=HUVEC dataType=predPos sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/HUVEC.proCapNet.pos.bw color 204,121,167 shortLabel HUVEC Predicted + longLabel HUVEC (ENCSR801ECP) ProCapNet predicted PRO-cap, plus strand track proCapNet_HUVEC_pred_neg parent proCapNet_HUVEC_pred - subGroups cellLine=HUVEC dataType=predNeg sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/HUVEC.proCapNet.neg.bw color 204,121,167 altColor 204,121,167 shortLabel HUVEC Predicted - longLabel HUVEC (ENCSR801ECP) ProCapNet predicted PRO-cap, minus strand track proCapNet_K562_pred - parent proCapNet on +superTrack proCapNet full container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +windowingFunction maximum +configurable on +html proCapNet color 230,159,0 shortLabel K562 Predicted longLabel K562 (ENCSR740IPL) ProCapNet predicted PRO-cap, plus up minus down - onlyVisibility full priority 5 track proCapNet_K562_pred_pos parent proCapNet_K562_pred - subGroups cellLine=K562 dataType=predPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/K562.proCapNet.pos.bw color 230,159,0 shortLabel K562 Predicted + longLabel K562 (ENCSR740IPL) ProCapNet predicted PRO-cap, plus strand track proCapNet_K562_pred_neg parent proCapNet_K562_pred - subGroups cellLine=K562 dataType=predNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/K562.proCapNet.neg.bw color 230,159,0 altColor 230,159,0 shortLabel K562 Predicted - longLabel K562 (ENCSR740IPL) ProCapNet predicted PRO-cap, minus strand track proCapNet_MCF10A_pred - parent proCapNet on +superTrack proCapNet full container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +windowingFunction maximum +configurable on +html proCapNet color 86,180,233 shortLabel MCF10A Predicted longLabel MCF10A (ENCSR860TYZ) ProCapNet predicted PRO-cap, plus up minus down - onlyVisibility full priority 6 track proCapNet_MCF10A_pred_pos parent proCapNet_MCF10A_pred - subGroups cellLine=MCF10A dataType=predPos sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/MCF10A.proCapNet.pos.bw color 86,180,233 shortLabel MCF10A Predicted + longLabel MCF10A (ENCSR860TYZ) ProCapNet predicted PRO-cap, plus strand track proCapNet_MCF10A_pred_neg parent proCapNet_MCF10A_pred - subGroups cellLine=MCF10A dataType=predNeg sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/MCF10A.proCapNet.neg.bw color 86,180,233 altColor 86,180,233 shortLabel MCF10A Predicted - longLabel MCF10A (ENCSR860TYZ) ProCapNet predicted PRO-cap, minus strand track proCapNet_A673_contrib - subGroups cellLine=A673 dataType=contrib sampleClass=Cancer - parent proCapNet off +superTrack proCapNet hide type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/A673.proCapNet-contrib.bw logo on +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +configurable on +html proCapNet color 0,114,178 shortLabel A673 Contribution longLabel A673 (ENCSR072YCM) ProCapNet sequence-contribution scores - onlyVisibility full priority 11 track proCapNet_Caco-2_contrib - subGroups cellLine=Caco2 dataType=contrib sampleClass=Cancer - parent proCapNet off +superTrack proCapNet hide type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/Caco-2.proCapNet-contrib.bw logo on +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +configurable on +html proCapNet color 213,94,0 shortLabel Caco-2 Contribution longLabel Caco-2 (ENCSR182QNJ) ProCapNet sequence-contribution scores - onlyVisibility full priority 12 track proCapNet_Calu3_contrib - subGroups cellLine=Calu3 dataType=contrib sampleClass=Cancer - parent proCapNet off +superTrack proCapNet hide type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/Calu3.proCapNet-contrib.bw logo on +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +configurable on +html proCapNet color 0,158,115 shortLabel Calu3 Contribution longLabel Calu3 (ENCSR797DEF) ProCapNet sequence-contribution scores - onlyVisibility full priority 13 track proCapNet_HUVEC_contrib - subGroups cellLine=HUVEC dataType=contrib sampleClass=Noncancer - parent proCapNet off +superTrack proCapNet hide type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/HUVEC.proCapNet-contrib.bw logo on +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +configurable on +html proCapNet color 204,121,167 shortLabel HUVEC Contribution longLabel HUVEC (ENCSR801ECP) ProCapNet sequence-contribution scores - onlyVisibility full priority 14 track proCapNet_K562_contrib - subGroups cellLine=K562 dataType=contrib sampleClass=Cancer - parent proCapNet off +superTrack proCapNet hide type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/K562.proCapNet-contrib.bw logo on +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +configurable on +html proCapNet color 230,159,0 shortLabel K562 Contribution longLabel K562 (ENCSR740IPL) ProCapNet sequence-contribution scores - onlyVisibility full priority 15 track proCapNet_MCF10A_contrib - subGroups cellLine=MCF10A dataType=contrib sampleClass=Noncancer - parent proCapNet off +superTrack proCapNet hide type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/MCF10A.proCapNet-contrib.bw logo on +autoScale on +alwaysZero on +maxHeightPixels 100:40:8 +configurable on +html proCapNet color 86,180,233 shortLabel MCF10A Contribution longLabel MCF10A (ENCSR860TYZ) ProCapNet sequence-contribution scores - onlyVisibility full priority 16