98b25e3170373c357d24b1cbf66d04bf74396112 lrnassar Wed May 27 16:44:41 2020 -0700 Fixing up trackDbIndexBb based on CR feedback, refs #25590 diff --git src/utils/trackDbIndexBb/tests/in/trackDb.smallExample.txt src/utils/trackDbIndexBb/tests/in/trackDb.smallExample.txt deleted file mode 100644 index 2cb56d6..0000000 --- src/utils/trackDbIndexBb/tests/in/trackDb.smallExample.txt +++ /dev/null @@ -1,127 +0,0 @@ -track uniformDnase -noInherit on -type bed 3 -longLabel ENCODE DNase-seq Peaks and Signal of Open Chromatin based on Uniform processing pipeline -priority 4 -dragAndDrop subTracks -dimensions dimX=lab dimY=cellType dimA=tier -compositeTrack on -pennantIcon encodeThumbnail.jpg http://genome.ucsc.edu/ENCODE/ "ENCODE Project" -subGroup4 lab Lab Duke=Duke UW=UW UWDuke=UW-Duke -subGroup3 view View Peaks=Peaks Signal=Signal -subGroup2 cellType Cell_Line GM12878=GM12878 H1hESC=H1-hESC K562=K562 HeLaS3=HeLa-S3 HepG2=HepG2 HUVEC=HUVEC T8988T=8988T A549=A549 AG04449=AG04449 AG04450=AG04450 AG09309=AG09309 AG09319=AG09319 AG10803=AG10803 AoAF=AoAF AoSMC=AoSMC BE2C=BE2_C BJ=BJ Caco2=Caco-2 CD20=CD20+ CD34Mobilized=CD34+_Mobilized Chorion=Chorion CLL=CLL CMK=CMK Fibrobl=Fibrobl FibroP=FibroP Gliobla=Gliobla GM06990=GM06990 GM12864=GM12864 GM12865=GM12865 GM12891=GM12891 GM12892=GM12892 GM18507=GM18507 GM19238=GM19238 GM19239=GM19239 GM19240=GM19240 H7hESC=H7-hESC H9ES=H9ES HAh=HA-h HAsp=HA-sp HAc=HAc HAEpiC=HAEpiC HBMEC=HBMEC HCF=HCF HCFaa=HCFaa HCM=HCM HConF=HConF HCPEpiC=HCPEpiC HCT116=HCT-116 HEEpiC=HEEpiC Hepatocytes=Hepatocytes HFF=HFF HFFMyc=HFF-Myc HGF=HGF HIPEpiC=HIPEpiC HL60=HL-60 HMEC=HMEC HMF=HMF HMVECdAd=HMVEC-dAd HMVECdBlAd=HMVEC-dBl-Ad HMVECdBlNeo=HMVEC-dBl-Neo HMVECdLyAd=HMVEC-dLy-Ad HMVECdLyNeo=HMVEC-dLy-Neo HMVECdNeo=HMVEC-dNeo HMVECLBl=HMVEC-LBl HMVECLLy=HMVEC-LLy HNPCEpiC=HNPCEpiC HPAEC=HPAEC HPAF=HPAF HPDE6E6E7=HPDE6-E6E7 HPdLF=HPdLF HPF=HPF HRCEpiC=HRCEpiC HRE=HRE HRGEC=HRGEC HRPEpiC=HRPEpiC HSMM=HSMM HSMMemb=HSMM_emb HSMMtube=HSMMtube HTR8svn=HTR8svn Huh7=Huh-7 Huh75=Huh-7.5 HVMF=HVMF iPS=iPS Ishikawa=Ishikawa Jurkat=Jurkat K562=K562 LNCaP=LNCaP MCF7=MCF-7 Medullo=Medullo Melano=Melano MonocytesCD14RO01746=Monocytes-CD14+_RO01746 Myometr=Myometr NB4=NB4 NHA=NH-A NHDFAd=NHDF-Ad NHDFneo=NHDF-neo NHEK=NHEK NHLF=NHLF NT2D1=NT2-D1 Osteobl=Osteobl PANC1=PANC-1 PanIsletD=PanIsletD PanIslets=PanIslets pHTE=pHTE PrEC=PrEC ProgFib=ProgFib RPTEC=RPTEC RWPE1=RWPE1 SAEC=SAEC SKNMC=SK-N-MC SKNSHRA=SK-N-SH_RA SkMC=SkMC Stellate=Stellate T47D=T-47D Th0=Th0 Th1=Th1 Th2=Th2 Urothelia=Urothelia WERIRb1=WERI-Rb-1 WI38=WI-38 -filterComposite dimA -visibility dense -shortLabel ENCODE DNase-seq -subGroup1 tier Tier t1=1 t2=2 t3=3 -sortOrder view=+ tier=+ cellType=+ lab=+ -hideEmptySubtracks on -hideEmptySubtracksMultiBedUrl uniformDnase.multiBed.bb -hideEmptySubtracksSourcesUrl uniformDnase.multiBedSources.tab - -track uniformDnasePeaks -type bigBed 6 + -parent uniformDnase -view Peaks -shortLabel ENCODE DNase-seq Peaks -visibility dense - -track wgEncodeUWDukeDnaseGM12878FdrPeaks -type bigBed 6 + -longLabel GM12878 DNaseI FDR 1% Uniform Peak Calls from UW-Duke -color 8,104,172 -parent uniformDnasePeaks on -bigDataUrl wgEncodeUWDukeDnaseGM12878.fdr01peaks.hg19.bb -subGroups view=Peaks tier=t1 cellType=GM12878 lab=UWDuke -metadata cell=GM12878 -shortLabel GM12878 - -track wgEncodeUWDukeDnaseH1hESCFdrPeaks -type bigBed 6 + -longLabel H1-hESC DNaseI FDR 1% Uniform Peak Calls from UW-Duke -color 8,104,172 -parent uniformDnasePeaks off -bigDataUrl wgEncodeUWDukeDnaseH1hESC.fdr01peaks.hg19.bb -subGroups view=Peaks tier=t1 cellType=H1hESC lab=UWDuke -metadata cell=H1-hESC -shortLabel H1-hESC - -track wgEncodeUWDukeDnaseK562FdrPeaks -type bigBed 6 + -longLabel K562 DNaseI FDR 1% Uniform Peak Calls from UW-Duke -color 8,104,172 -parent uniformDnasePeaks on -bigDataUrl wgEncodeUWDukeDnaseK562.fdr01peaks.hg19.bb -subGroups view=Peaks tier=t1 cellType=K562 lab=UWDuke -metadata cell=K562 -shortLabel K562 - -track uniformDnaseSignal -type bigWig -parent uniformDnase -view Signal -maxHeightPixels 64:32:16 -shortLabel ENCODE DNase-seq Signal -visibility dense -autoscale off - -track wgEncodeDukeDnaseGM12878FdrSignal -type bigWig -longLabel GM12878 DNaseI signals from Duke -color 8,104,172 -parent uniformDnaseSignal on -bigDataUrl wgEncodeOpenChromDnaseGm12878Aln_5Reps.norm5.rawsignal.bw -subGroups view=Signal tier=t1 cellType=GM12878 lab=Duke -metadata cell=GM12878 lab=Duke -shortLabel GM12878 Duke - -track wgEncodeUWDnaseGM12878FdrSignal -type bigWig -longLabel GM12878 DNaseI signals from UW -color 8,104,172 -parent uniformDnaseSignal on -bigDataUrl wgEncodeUwDnaseGm12878Aln_2Reps.norm5.rawsignal.bw -subGroups view=Signal tier=t1 cellType=GM12878 lab=UW -metadata cell=GM12878 lab=UW -shortLabel GM12878 UW - -track wgEncodeDukeDnaseH1hESCFdrSignal -type bigWig -longLabel H1-hESC DNaseI signals from Duke -color 8,104,172 -parent uniformDnaseSignal off -bigDataUrl wgEncodeOpenChromDnaseH1hescAln_2Reps.norm5.rawsignal.bw -subGroups view=Signal tier=t1 cellType=H1hESC lab=Duke -metadata cell=H1-hESC lab=Duke -shortLabel H1-hESC Duke - -track wgEncodeUWDnaseH1hESCFdrSignal -type bigWig -longLabel H1-hESC DNaseI signals from UW -color 8,104,172 -parent uniformDnaseSignal off -bigDataUrl wgEncodeUwDnaseH1hescAln_1Reps.norm5.rawsignal.bw -subGroups view=Signal tier=t1 cellType=H1hESC lab=UW -metadata cell=H1-hESC lab=UW -shortLabel H1-hESC UW - -track wgEncodeDukeDnaseK562FdrSignal -type bigWig -longLabel K562 DNaseI signals from Duke -color 8,104,172 -parent uniformDnaseSignal on -bigDataUrl wgEncodeOpenChromDnaseK562Aln_2Reps.norm5.rawsignal.bw -subGroups view=Signal tier=t1 cellType=K562 lab=Duke -metadata cell=K562 lab=Duke -shortLabel K562 Duke - -track wgEncodeUWDnaseK562FdrSignal -type bigWig -longLabel K562 DNaseI signals from UW -color 8,104,172 -parent uniformDnaseSignal on -bigDataUrl wgEncodeUwDnaseK562Aln_2Reps.norm5.rawsignal.bw -subGroups view=Signal tier=t1 cellType=K562 lab=UW -metadata cell=K562 lab=UW -shortLabel K562 UW -