kent: changes by commit

branch to review (2009-12-01 to 2009-12-09) v221

• Adding lmCloneFirstWord
  • src/inc/localmem.h 1.8 - lines changed: 3, context: html, text, full: html, text
  • src/lib/localmem.c 1.12 - lines changed: 14, context: html, text, full: html, text
• Decluttering genes section. Hiding MGC genes by default. Putting hg19's RefSeq Genes back to dense.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.71 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.541 - lines changed: 3, context: html, text, full: html, text
• Making the this=that option parsing smart about not trying to parse code, filenames, and other things as option. Previously it knew not to treat URLs with = as options.
  • src/lib/options.c 1.28 - lines changed: 12, context: html, text, full: html, text
• Initial commit of tdbQuery. Still has clones of some files from raSqlQuery that will eventually end up in library when more stable.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.1 - lines changed: 245, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbRecord.c 1.1 - lines changed: 156, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbRecord.h 1.1 - lines changed: 47, context: html, text, full: html, text
• Handling include files. CHecking for duplicate tags (in non-include stanzas)
  • src/hg/utils/tdbQuery/tdbQuery.c 1.2 - lines changed: 63, context: html, text, full: html, text
• Removing duplicate tags within same stanza.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChip.ra 1.24 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChrom.ra 1.8 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.encodeGenes.ra 1.7 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.694 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.encode.ra 1.99 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.542 - lines changed: 1, context: html, text, full: html, text
• Removing duplicate track records at same level of directory hierarchy, in many cases by adding a missing release tag.
  • src/hg/makeDb/trackDb/human/trackDb.encode.ra 1.100 - lines changed: 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.475 - lines changed: 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.543 - lines changed: 31, context: html, text, full: html, text
• Adding check for duplicate records including handling of different records for different releases. Merging together records from root/organism/assembly tree.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.3 - lines changed: 116, context: html, text, full: html, text
• Adding rql parser and evaluator to library.
  • src/inc/rql.h 1.1 - lines changed: 118, context: html, text, full: html, text
  • src/lib/makefile 1.157 - lines changed: 1, context: html, text, full: html, text
  • src/lib/rqlEval.c 1.1 - lines changed: 289, context: html, text, full: html, text
  • src/lib/rqlParse.c 1.1 - lines changed: 643, context: html, text, full: html, text
• Fixing bug where options was no longer handling -this=that, just this=that.
  • src/lib/options.c 1.29 - lines changed: 1, context: html, text, full: html, text
• Librarifying RQL parser and interpreter.
  • src/utils/raSqlQuery/makefile 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/utils/raSqlQuery/raRecord.c 1.9 - lines changed: 13, context: html, text, full: html, text
  • src/utils/raSqlQuery/raSqlQuery.c 1.25 - lines changed: 12, context: html, text, full: html, text
  • src/utils/raSqlQuery/rql.h 1.3 - lines changed: 99, context: html, text, full: html, text
  • src/utils/raSqlQuery/rqlEval.c 1.3 - lines changed: 288, context: html, text, full: html, text
  • src/utils/raSqlQuery/rqlParse.c 1.9 - lines changed: 643, context: html, text, full: html, text
• Adding rqlStatementFree.
  • src/lib/rqlParse.c 1.2 - lines changed: 26, context: html, text, full: html, text
• Starting to work. Lots of debugging code still in.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.4 - lines changed: 368, context: html, text, full: html, text
• Cleaning up debugging statements and also db and filePos pseudo-field handling.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.5 - lines changed: 42, context: html, text, full: html, text
• Oops, forgot makefile in initial commit off of laptop.
  • src/hg/utils/tdbQuery/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
• Fixing linux compiler complaints.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbRecord.c 1.2 - lines changed: 2, context: html, text, full: html, text
• Improving usage message.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.7 - lines changed: 2, context: html, text, full: html, text
• Massaging handling of duplicate record detection to handle a tricky case in danRer6 involving inheritence and inherited releases.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.8 - lines changed: 243, context: html, text, full: html, text
• Fixing some duplicates found by tdbQuery
  • src/hg/makeDb/trackDb/ancestor/homIni14/trackDb.ra 1.6 - lines changed: 73, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ancestor/priMat13/trackDb.ra 1.6 - lines changed: 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ancestor/rodEnt13/trackDb.ra 1.4 - lines changed: 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/h1n1/h1n1/trackDb.ra 1.12 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg12/trackDb.ra 1.16 - lines changed: 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg13/trackDb.ra 1.47 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg16/trackDb.ra 1.577 - lines changed: 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/trackDb.encode.ra 1.179 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/trackDb.ra 1.429 - lines changed: 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/loadTracks 1.16 - lines changed: 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lowelab/haloHalo1/trackDb.ra 1.25 - lines changed: 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lowelab/joseCoat_042308/trackDb.ra 1.6 - lines changed: 0, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lowelab/pyrFur2/trackDb.ra 1.34 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lowelab/pyroArse1/trackDb.ra 1.29 - lines changed: 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lowelab/pyroIsla1/trackDb.ra 1.32 - lines changed: 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lowelab/trackDb.ra 1.91 - lines changed: 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/trackDb.ra 1.32 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/stickleback/trackDb.ra 1.18 - lines changed: 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.ra 1.18 - lines changed: 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra 1.52 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/trackDb.ra 1.54 - lines changed: 0, context: html, text, full: html, text
• Fixing more dupes in trackDb.
  • src/hg/makeDb/trackDb/ancestor/borEut13/trackDb.ra 1.8 - lines changed: 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ancestor/canHg12/trackDb.ra 1.6 - lines changed: 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ancestor/catArr1/trackDb.ra 1.5 - lines changed: 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ancestor/euaGli13/trackDb.ra 1.4 - lines changed: 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ancestor/gliRes13/trackDb.ra 1.4 - lines changed: 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ancestor/homIni13/trackDb.ra 1.7 - lines changed: 61, context: html, text, full: html, text
• Freen tests rqlStatementDump
  • src/hg/oneShot/freen/freen.c 1.95 - lines changed: 8, context: html, text, full: html, text
• Adding in visibility.ra and priority.ra handling.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.9 - lines changed: 70, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbRecord.c 1.3 - lines changed: 3, context: html, text, full: html, text
• Making -strict leave in parents when their children exist.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.10 - lines changed: 16, context: html, text, full: html, text
• Adding limit clause to RQL parsing.
  • src/inc/rql.h 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/lib/rqlParse.c 1.3 - lines changed: 36, context: html, text, full: html, text
• Implementing limit clause.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.11 - lines changed: 3, context: html, text, full: html, text
• Adding integer unary minus.
  • src/inc/rql.h 1.3 - lines changed: 4, context: html, text, full: html, text
  • src/lib/rqlEval.c 1.2 - lines changed: 6, context: html, text, full: html, text
  • src/lib/rqlParse.c 1.4 - lines changed: 12, context: html, text, full: html, text
• Making rqlParser handle arrays and field-separating-dots. Evaluation handles arrays but not dots yet.
  • src/inc/rql.h 1.4 - lines changed: 17, context: html, text, full: html, text
  • src/lib/rqlEval.c 1.3 - lines changed: 91, context: html, text, full: html, text
  • src/lib/rqlParse.c 1.5 - lines changed: 77, context: html, text, full: html, text
• Adding lmCloneSomeWord.
  • src/inc/localmem.h 1.9 - lines changed: 4, context: html, text, full: html, text
  • src/lib/localmem.c 1.13 - lines changed: 17, context: html, text, full: html, text
• Adding lm parameter to rqlEvalOnRecord since array operation uses memory.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.12 - lines changed: 4, context: html, text, full: html, text
  • src/inc/rql.h 1.5 - lines changed: 4, context: html, text, full: html, text
  • src/lib/rqlEval.c 1.4 - lines changed: 28, context: html, text, full: html, text
  • src/lib/rqlParse.c 1.6 - lines changed: 16, context: html, text, full: html, text
  • src/utils/raSqlQuery/raSqlQuery.c 1.26 - lines changed: 3, context: html, text, full: html, text
  • src/utils/raSqlQuery/test.ra 1.2 - lines changed: 3, context: html, text, full: html, text
• Removing unimplemented 'file' option from usage statement.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.13 - lines changed: 7, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbQuery.doc 1.1 - lines changed: 12, context: html, text, full: html, text
• Adding to documentation.
  • src/hg/utils/tdbQuery/tdbQuery.doc 1.2 - lines changed: 56, context: html, text, full: html, text
• Little fixes to trackDb.ra
  • src/hg/makeDb/trackDb/chicken/trackDb.ra 1.13 - lines changed: 0, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/trackDb.ra 1.61 - lines changed: 0, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.432 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lizard/trackDb.ra 1.6 - lines changed: 0, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/malaria/falciparum/trackDb.ra 1.3 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/trackDb.ra 1.17 - lines changed: 0, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.162 - lines changed: 0, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/platypus/trackDb.ra 1.6 - lines changed: 0, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/stickleback/trackDb.ra 1.20 - lines changed: 0, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tetraodon/trackDb.ra 1.41 - lines changed: 0, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebraFinch/trackDb.ra 1.5 - lines changed: 0, context: html, text, full: html, text
• Adding tdbQuery to build.
  • src/hg/utils/makefile 1.19 - lines changed: 1, context: html, text, full: html, text
• Improving docs.
  • src/hg/utils/tdbQuery/tdbQuery.doc 1.3 - lines changed: 22, context: html, text, full: html, text
• Did some testing, took out debugging statements, and polished interface a little.
  • src/hg/makeDb/trackDbPatch/trackDbPatch.c 1.3 - lines changed: 38, context: html, text, full: html, text
• Adding trackDbPatch.
  • src/hg/makeDb/makefile 1.42 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/loadTracks 1.17 - lines changed: 1, context: html, text, full: html, text
• correcting altcolor to altColor
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.433 - lines changed: 5, context: html, text, full: html, text
• Removing unused track stanza with unusual tag.
  • src/hg/makeDb/trackDb/human/hg16/trackDb.ra 1.578 - lines changed: 10, context: html, text, full: html, text
• Fixing visibililty typo
  • src/hg/makeDb/trackDb/xenTro/trackDb.ra 1.22 - lines changed: 2, context: html, text, full: html, text
• removing unused track stanza with weird field.
  • src/hg/makeDb/trackDb/human/hg17/trackDb.ra 1.430 - lines changed: 12, context: html, text, full: html, text
• Fixing dataversion that should be dataVersion.
  • src/hg/makeDb/trackDb/human/hg17/trackDb.encode.ra 1.180 - lines changed: 12, context: html, text, full: html, text
• Fixing viewLimts that should be viewLimits
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.703 - lines changed: 1, context: html, text, full: html, text
• Adding file that list all available tags and the types they can appear in.
  • src/hg/makeDb/trackDb/tagTypes.tab 1.1 - lines changed: 270, context: html, text, full: html, text
• Making -check do something, specifically look for tagTypes.tab and check tags against it.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.14 - lines changed: 74, context: html, text, full: html, text
• Utility to make first cut of tagTypes.tab seems to work.
  • src/hg/oneShot/makeTrackDbTypeTags/makeTrackDbTypeTags.c 1.1 - lines changed: 110, context: html, text, full: html, text
  • src/hg/oneShot/makeTrackDbTypeTags/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
• Fixing bug in -strict logic for parent tables.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.15 - lines changed: 48, context: html, text, full: html, text
• Adding -noBlank option
  • src/hg/utils/tdbQuery/tdbQuery.c 1.16 - lines changed: 8, context: html, text, full: html, text
• Adding whereVarList to rqlStatement structure.
  • src/lib/rqlParse.c 1.7 - lines changed: 20, context: html, text, full: html, text
• Adding in whereVarList to rqlStatement
  • src/inc/rql.h 1.6 - lines changed: 1, context: html, text, full: html, text
• When you do a -check also does check of query.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.17 - lines changed: 15, context: html, text, full: html, text
• Making check for tag names in RQL query existing happen even without -check
  • src/hg/utils/tdbQuery/tdbQuery.c 1.18 - lines changed: 27, context: html, text, full: html, text
• Moving around some subtracks that weren't directly under their parents. Adding some indentation to subtracks.
  • src/hg/makeDb/trackDb/hiv/trackDb.ra 1.5 - lines changed: 321, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.434 - lines changed: 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab 1.2 - lines changed: 2, context: html, text, full: html, text
• Adding additional checks on child/parent relationships. Forcing children to be close to parent in file.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.19 - lines changed: 158, context: html, text, full: html, text
• Adding optional dyString parameter.
  • src/inc/ra.h 1.8 - lines changed: 6, context: html, text, full: html, text
  • src/lib/ra.c 1.15 - lines changed: 37, context: html, text, full: html, text
• Making tdbRecord have start and end lineIx, and also text representation of stanza.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.20 - lines changed: 27, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbRecord.c 1.4 - lines changed: 16, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbRecord.h 1.2 - lines changed: 12, context: html, text, full: html, text
• Fixing some problems with the new dyString parameter to the ra readers.
  • src/lib/ra.c 1.16 - lines changed: 17, context: html, text, full: html, text
• Starting to experiment with some rewriting. Not very far along.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.21 - lines changed: 51, context: html, text, full: html, text
• Removing empty visibility.ra file.
  • src/hg/makeDb/trackDb/armadillo/visibility.ra 1.3 - lines changed: 0, context: html, text, full: html, text
• Removing empty visibility.ra
  • src/hg/makeDb/trackDb/elephant/visibility.ra 1.3 - lines changed: 0, context: html, text, full: html, text
• Moving visibility.ra contents to new trackDb.ra file for rabbit.
  • src/hg/makeDb/trackDb/rabbit/trackDb.ra 1.1 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rabbit/visibility.ra 1.3 - lines changed: 2, context: html, text, full: html, text
• Rewriting to get rid of visibility.ra and priority.ra files.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.22 - lines changed: 176, context: html, text, full: html, text
• Merging visibility.ra and priority.ra files back into trackDb.ra
  • src/hg/makeDb/trackDb/anopheles/trackDb.ra 1.18 - lines changed: 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/anopheles/visibility.ra 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/apiMel2/trackDb.ra 1.25 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/apiMel2/visibility.ra 1.3 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/priority.ra 1.9 - lines changed: 42, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/trackDb.ra 1.14 - lines changed: 45, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/priority.ra 1.8 - lines changed: 66, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/trackDb.ra 1.26 - lines changed: 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra 1.58 - lines changed: 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm2/visibility.ra 1.2 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droAna2/trackDb.ra 1.11 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droAna2/visibility.ra 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droEre1/trackDb.ra 1.12 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droEre1/visibility.ra 1.2 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droGri1/trackDb.ra 1.7 - lines changed: 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droGri1/visibility.ra 1.2 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/priority.ra 1.2 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/trackDb.ra 1.62 - lines changed: 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/visibility.ra 1.7 - lines changed: 38, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/trackDb.ra 1.12 - lines changed: 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/visibility.ra 1.3 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg16/priority.ra 1.2 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg16/trackDb.ra 1.579 - lines changed: 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/priority.ra 1.3 - lines changed: 131, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/trackDb.ra 1.431 - lines changed: 59, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/priority.ra 1.11 - lines changed: 232, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.476 - lines changed: 225, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac1/trackDb.ra 1.13 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac1/visibility.ra 1.2 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/priority.ra 1.5 - lines changed: 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/trackDb.ra 1.5 - lines changed: 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/priority.ra 1.4 - lines changed: 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/trackDb.ra 1.18 - lines changed: 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/priority.ra 1.13 - lines changed: 230, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.163 - lines changed: 178, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/visibility.ra 1.3 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/platypus/ornAna1/priority.ra 1.6 - lines changed: 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/platypus/ornAna1/trackDb.ra 1.14 - lines changed: 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/priority.ra 1.6 - lines changed: 112, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/priority.ra 1.2 - lines changed: 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/trackDb.ra 1.44 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/trackDb.ra 1.58 - lines changed: 127, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/visibility.ra 1.7 - lines changed: 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/priority.ra 1.3 - lines changed: 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac1/trackDb.ra 1.7 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac1/visibility.ra 1.3 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/trackDb.ra 1.13 - lines changed: 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/trackDb.ra 1.13 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/visibility.ra 1.2 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/stickleback/priority.ra 1.3 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/stickleback/trackDb.ra 1.21 - lines changed: 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tetraodon/priority.ra 1.2 - lines changed: 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tetraodon/trackDb.ra 1.42 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tetraodon/visibility.ra 1.2 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeJap1/trackDb.ra 1.4 - lines changed: 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeJap1/visibility.ra 1.2 - lines changed: 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caePb2/trackDb.ra 1.5 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caePb2/visibility.ra 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeRem2/priority.ra 1.2 - lines changed: 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeRem2/trackDb.ra 1.8 - lines changed: 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeRem3/trackDb.ra 1.4 - lines changed: 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeRem3/visibility.ra 1.2 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce4/trackDb.ra 1.39 - lines changed: 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce4/visibility.ra 1.2 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce6/priority.ra 1.2 - lines changed: 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce6/trackDb.ra 1.15 - lines changed: 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/priPac1/priority.ra 1.2 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/priPac1/trackDb.ra 1.8 - lines changed: 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/priority.ra 1.3 - lines changed: 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/trackDb.ra 1.23 - lines changed: 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer3/priority.ra 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra 1.53 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer4/priority.ra 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.ra 1.36 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer5/priority.ra 1.7 - lines changed: 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra 1.24 - lines changed: 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/trackDb.ra 1.56 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/visibility.ra 1.2 - lines changed: 2, context: html, text, full: html, text
• Fixing a few little places where the automatic rewrite left duplicate records.
  • src/hg/makeDb/trackDb/fugu/trackDb.ra 1.63 - lines changed: 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/trackDb.ra 1.59 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.545 - lines changed: 5, context: html, text, full: html, text
• Adding a little more comment.
  • src/hg/makeDb/trackDb/trackDb.ra 1.546 - lines changed: 1, context: html, text, full: html, text
• Avoiding generating a duplicate record for vis when there is both priority and vis.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.23 - lines changed: 4, context: html, text, full: html, text
• Fixed linux-specific compiler warning.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.24 - lines changed: 1, context: html, text, full: html, text
• Making trackDb pass tdbQuery -check -alpha
  • src/hg/makeDb/trackDb/tagTypes.tab 1.3 - lines changed: 9, context: html, text, full: html, text
• Utility to extract values of tags actually seen seems to work.
  • src/hg/oneShot/makeTrackDbTagVals/makeTrackDbTagVals.c 1.1 - lines changed: 109, context: html, text, full: html, text
  • src/hg/oneShot/makeTrackDbTagVals/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
• Rewriter that alphabetizes tags after the first one in a stanza. Not totally sure I like result, but worth bouncing off other people.
  • src/hg/oneShot/tdbRewriteSortTags/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
  • src/hg/oneShot/tdbRewriteSortTags/tdbRewriteSortTags.c 1.1 - lines changed: 172, context: html, text, full: html, text
• Making it so that don't lose blank terminating lines in raNextTagVal. Simplifying logic in raSkipLeadingEmptyLines.
  • src/lib/ra.c 1.17 - lines changed: 25, context: html, text, full: html, text
• Rewriter that adds 'replace' on track lines in subdirectories where are redefining an old track rather than defining a new track at that level.
  • src/hg/oneShot/tdbRewriteAddReplaces/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
  • src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c 1.1 - lines changed: 501, context: html, text, full: html, text
• Getting rid of debugging statements.
  • src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c 1.2 - lines changed: 16, context: html, text, full: html, text
• Rewriter that will convert replacement records to override records when possible, and otherwise add comment that it is a replacement record seems to work.
  • src/hg/oneShot/tdbRewriteReduceReplaces/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
  • src/hg/oneShot/tdbRewriteReduceReplaces/tdbRewriteReduceReplaces.c 1.1 - lines changed: 572, context: html, text, full: html, text
• Fixing bug that limited to no more than 4 settings in a settingsByLimit for any view.
  • src/utils/raSqlQuery/raRecord.c 1.10 - lines changed: 1, context: html, text, full: html, text
• Fixing bug that limited to no more than 4 settings in a settingsByLimit for any view. Sharpening line number reporting in error messages.
  • src/hg/utils/tdbQuery/tdbRecord.c 1.5 - lines changed: 3, context: html, text, full: html, text
• Rewriter to take out views and put in a new layer of hierarchy seems to work.
  • src/hg/oneShot/tdbRewriteViewsToSubtracks/makefile 1.1 - lines changed: 17, context: html, text, full: html, text
  • src/hg/oneShot/tdbRewriteViewsToSubtracks/tdbRewriteViewsToSubtracks.c 1.1 - lines changed: 762, context: html, text, full: html, text
• Removing details page when clicking on RepeatMasker but not on a specific repeat.
  • src/hg/hgTracks/rmskTrack.c 1.13 - lines changed: 1, context: html, text, full: html, text