4fd9f828f80a223799ce69d7078ee22ffe8aabc5 max Wed Apr 15 07:22:19 2026 -0700 fixing up after claude, refs #35059 diff --git src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra index 6de1bbb4010..97f6f10a769 100644 --- src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra +++ src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra @@ -1,423 +1,440 @@ track cloneEndSuper compositeTrack on shortLabel Clone Ends longLabel Mapping of clone libraries end placements group map visibility hide type bed 3 noInherit on dragAndDrop on subGroup1 source Source agencourt=Agencourt chori=Chori corielle=Coriell caltech=CalTech rpci=RPCI wibr=WIBR placements=Placements dimensions dimensionX=source sortOrder source=+ track cloneEndABC10 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC10 longLabel Agencourt fosmid library 10 colorByStrand 0,0,128 0,128,0 type bed 12 visibility pack priority 1 track cloneEndABC11 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC11 longLabel Agencourt fosmid library 11 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 2 track cloneEndABC12 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC12 longLabel Agencourt fosmid library 12 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 3 track cloneEndABC13 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC13 longLabel Agencourt fosmid library 13 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 4 track cloneEndABC14 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC14 longLabel Agencourt fosmid library 14 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 5 track cloneEndABC16 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC16 longLabel Agencourt fosmid library 16 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 6 track cloneEndABC18 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC18 longLabel Agencourt fosmid library 18 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 7 track cloneEndABC20 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC20 longLabel Agencourt fosmid library 20 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 8 track cloneEndABC21 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC21 longLabel Agencourt fosmid library 21 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 9 track cloneEndABC22 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC22 longLabel Agencourt fosmid library 22 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 10 track cloneEndABC23 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC23 longLabel Agencourt fosmid library 23 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 11 track cloneEndABC24 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC24 longLabel Agencourt fosmid library 24 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 12 track cloneEndABC27 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC27 longLabel Agencourt fosmid library 27 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 13 track cloneEndABC7 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC7 longLabel Agencourt fosmid library 7 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 14 track cloneEndABC8 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC8 longLabel Agencourt fosmid library 8 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 15 track cloneEndABC9 parent cloneEndSuper off subGroups source=agencourt shortLabel ABC9 longLabel Agencourt fosmid library 9 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 16 track cloneEndCH17 parent cloneEndSuper on subGroups source=chori shortLabel CH17 longLabel CHORI BAC hydatidiform mole colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 17 track cloneEndCOR02 parent cloneEndSuper off subGroups source=corielle shortLabel COR02 longLabel NHGRI-CORIELLE CORIELL-02-F-39-40KB colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 18 track cloneEndCOR2A parent cloneEndSuper off subGroups source=corielle shortLabel COR2A longLabel NHGRI-CORIELLE CORIELL-02A-F-39-40KB colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 19 track cloneEndCTD parent cloneEndSuper on subGroups source=caltech shortLabel CTD longLabel CalTech BAC library D colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 20 track cloneEndRP11 parent cloneEndSuper on subGroups source=rpci shortLabel RP11 longLabel RPCI BAC library 11 colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 21 track cloneEndWI2 parent cloneEndSuper off subGroups source=wibr shortLabel WI2 longLabel WIBR-2 Fosmid library colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 22 track cloneEndmultipleMaps parent cloneEndSuper off subGroups source=placements shortLabel Multiple mappings longLabel Clone end placements that map to multiple locations in the genome colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 23 track cloneEndbadEnds parent cloneEndSuper off subGroups source=placements shortLabel Bad end mappings longLabel Clone end placements dropped at UCSC, map distance 3X median library size colorByStrand 0,0,128 0,128,0 type bed 12 visibility hide priority 24 track cloneEndcoverageForward parent cloneEndSuper off subGroups source=placements shortLabel Coverage forward longLabel Clone end placements overlap coverage on the forward strand type bigWig 0 5377 visibility full autoScale on alwaysZero on maxHeightPixels 128:35:16 windowingFunction mean priority 25 track cloneEndcoverageReverse parent cloneEndSuper off subGroups source=placements shortLabel Coverage reverse longLabel Clone end placements overlap coverage on the reverse strand type bigWig 0 4112 visibility full negateValues 1 alwaysZero on maxHeightPixels 128:35:16 windowingFunction mean autoScale on priority 26 -searchTable cloneEndABC10 -searchType bed -searchMethod prefix -searchPriority 50 -termRegex ABC10-([0-9A-Z])+ + track bacRearray32k + parent cloneEndSuper on + subGroups source=chori + shortLabel BCGSC 32k rearray + longLabel BCGSC Human BAC Rearray (32k minimal tiling set, mostly RP11 and CTD) + type bigBed 5 + bigDataUrl /gbdb/$D/bbi/cloneEnd/bacRearray32k.bb + color 0,60,120 + priority 27 + visibility pack searchTable cloneEndABC11 searchType bed searchMethod prefix searchPriority 50 termRegex ABC11-([0-9A-Z])+ searchTable cloneEndABC12 searchType bed searchMethod prefix searchPriority 50 termRegex ABC12-([0-9A-Z])+ searchTable cloneEndABC13 searchType bed searchMethod prefix searchPriority 50 termRegex ABC13-([0-9A-Z])+ searchTable cloneEndABC14 searchType bed searchMethod prefix searchPriority 50 termRegex ABC14-([0-9A-Z])+ searchTable cloneEndABC16 searchType bed searchMethod prefix searchPriority 50 termRegex ABC16-([0-9A-Z])+ searchTable cloneEndABC18 searchType bed searchMethod prefix searchPriority 50 termRegex ABC18-([0-9A-Z])+ searchTable cloneEndABC20 searchType bed searchMethod prefix searchPriority 50 termRegex ABC20-([0-9A-Z])+ searchTable cloneEndABC21 searchType bed searchMethod prefix searchPriority 50 termRegex ABC21-([0-9A-Z])+ searchTable cloneEndABC22 searchType bed searchMethod prefix searchPriority 50 termRegex ABC22-([0-9A-Z])+ searchTable cloneEndABC23 searchType bed searchMethod prefix searchPriority 50 termRegex ABC23-([0-9A-Z])+ searchTable cloneEndABC24 searchType bed searchMethod prefix searchPriority 50 termRegex ABC24-([0-9A-Z])+ searchTable cloneEndABC27 searchType bed searchMethod prefix searchPriority 50 termRegex ABC27-([0-9A-Z])+ searchTable cloneEndABC7 searchType bed searchMethod prefix searchPriority 50 termRegex ABC7-([0-9A-Z])+ searchTable cloneEndABC8 searchType bed searchMethod prefix searchPriority 50 termRegex ABC8-([0-9A-Z])+ searchTable cloneEndABC9 searchType bed searchMethod prefix searchPriority 50 termRegex ABC9-([0-9A-Z])+ searchTable cloneEndCH17 searchType bed searchMethod prefix searchPriority 50 termRegex CH17-([0-9A-Z])+ searchTable cloneEndCOR02 searchType bed searchMethod prefix searchPriority 50 termRegex COR02-DD0002([0-9A-Z_])+ searchTable cloneEndCOR2A searchType bed searchMethod prefix searchPriority 50 termRegex COR2A-DD000([0-9A-Z_])+ searchTable cloneEndCTD searchType bed searchMethod prefix searchPriority 50 termRegex CTD-([0-9A-Z])+ searchTable cloneEndRP11 searchType bed searchMethod prefix searchPriority 50 termRegex RP11-([0-9A-Z])+ searchTable cloneEndWI2 searchType bed searchMethod prefix searchPriority 50 termRegex [GW][2I][24][-8]([0-9A-Z])+ searchTable cloneEndmultipleMaps searchType bed searchMethod prefix searchPriority 50 termRegex [ACGRW][BHIOPT2]([-0-9A-Z_])+ searchTable cloneEndbadEnds searchType bed searchMethod prefix searchPriority 50 termRegex [ACGRW][BHIOPT2]([-0-9A-Z_])+ + +searchTable bacRearray32k +searchType bigBed +searchMethod prefix +searchPriority 50 +termRegex (CTD|RP11|RP13)-([0-9A-Z])+ + +searchTable cloneEndABC10 +searchType bed +searchMethod prefix +searchPriority 50 +termRegex ABC10-([0-9A-Z])+