9be83456f0cc46e79ebc460d75fe61ab9198c0c0 lrnassar Tue May 12 11:00:18 2020 -0700 Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479 diff --git src/utils/trackDbIndexBb/tests/in/trackDb.smallExample.txt src/utils/trackDbIndexBb/tests/in/trackDb.smallExample.txt new file mode 100644 index 0000000..2cb56d6 --- /dev/null +++ src/utils/trackDbIndexBb/tests/in/trackDb.smallExample.txt @@ -0,0 +1,127 @@ +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 +