CVS changes by file

branch to review (2009-12-14 to 2010-01-04) v222

• java/build
  • 1.4 lines changed: 10, context: html, text, full: html, text
    setting environment variables if they are not already set
• src/hg/archaeStuff/data/Genome-info-mods
  • 1.92 lines changed: 2, context: html, text, full: html, text
    change Baci_subt to release dated Nov 9 2009
• src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm
  • 1.24 lines changed: 2, context: html, text, full: html, text
    remove temp COG file
  • 1.23 lines changed: 18, context: html, text, full: html, text
    fix loading COG function due to change in file format of .ptt from NCBI
• src/hg/das/das.c
  • 1.46 lines changed: 1, context: html, text, full: html, text
    change content-type for DAS results to text/xml
• src/hg/encode/DAFs/HAIBChIPseq.daf
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fix my mistake in 'variables' line
• src/hg/encode/encodePatchTdb/encodePatchTdb.c
  • 1.2 lines changed: 803, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.1 lines changed: 803, context: html, text, full: html, text
    file encodePatchTdb.c was initially added on branch viewInTheMiddle.
• src/hg/encode/encodePatchTdb/makefile
  • 1.2 lines changed: 18, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.1 lines changed: 18, context: html, text, full: html, text
    file makefile was initially added on branch viewInTheMiddle.
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.168 lines changed: 2, context: html, text, full: html, text
    fix some strings
  • 1.167 lines changed: 1, context: html, text, full: html, text
    change tag for longPolyA
  • 1.166 lines changed: 154, context: html, text, full: html, text
    Added 14 new tier 3 cell lines for Snyder and Stam labs
  • 1.165 lines changed: 5, context: html, text, full: html, text
    add 1x75
  • 1.164 lines changed: 5, context: html, text, full: html, text
    add new maapping protocol
  • 1.163 lines changed: 6, context: html, text, full: html, text
    add new mapping algorithm BB2
  • 1.162 lines changed: 4, context: html, text, full: html, text
    Add datatype for SUNY
  • 1.161 lines changed: 7, context: html, text, full: html, text
    Add CV term for submissions versions (used by reporting)
  • 1.160 lines changed: 86, context: html, text, full: html, text
    Add labels and CV of data types, for use in automated reporting
  • 1.159 lines changed: 2, context: html, text, full: html, text
    Fix BTO term for myotubes
  • 1.158 lines changed: 49, context: html, text, full: html, text
    Added 2 cell types for Broad
  • 1.157 lines changed: 8, context: html, text, full: html, text
    Shortened more tags because tableNames and sorting
  • 1.156 lines changed: 3, context: html, text, full: html, text
    Shortened some tags because tableNames are over-flowing
• src/hg/encode/encodeValidate/config/pi.ra
  • 1.6 lines changed: 5, context: html, text, full: html, text
    Remove problem entry for now
  • 1.5 lines changed: 13, context: html, text, full: html, text
    Add labels for automated reporting
• src/hg/encode/encodeValidate/doEncodeReport.pl
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Ignore revoked entries
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Restore proper lib path
  • 1.7 lines changed: 57, context: html, text, full: html, text
    More successful at sniffing out release date
  • 1.6 lines changed: 52, context: html, text, full: html, text
    Pretty close to duplicating the manual spreadsheet
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.210 lines changed: 1, context: html, text, full: html, text
    Add check for missing DDF file
  • 1.209 lines changed: 8, context: html, text, full: html, text
    Special case code for cleaning up tablenames that are too long
  • 1.208 lines changed: 114, context: html, text, full: html, text
    Simplified controlled vocab validation, tableNames based on cv tags not terms, tag 'None' not included in naem, special case replicate subGroup
• src/hg/encode/hgEncodeSubmit/app/views/user_notifier/failure_notification.rhtml
  • 1.3 lines changed: 1, context: html, text, full: html, text
    adding project.id to email as requested by a user
• src/hg/encode/validateFiles/validateFiles.c
  • 1.34 lines changed: 21, context: html, text, full: html, text
    Added 'privateData' option and require tab delimit instead of white space delimit
  • 1.33 lines changed: 14, context: html, text, full: html, text
    Never do in 1 checkin what can be spread out into 2
  • 1.32 lines changed: 5, context: html, text, full: html, text
    Exception for chrM should not be an option. If end > chromSize and chrM, then make sure start <= chromSize
• src/hg/hgChroms/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/compositeTrack.c
  • 1.18 lines changed: 6, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/hgTables.c
  • 1.188 lines changed: 6, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/intersect.c
  • 1.52 lines changed: 10, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/maf.c
  • 1.18 lines changed: 5, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/mainPage.c
  • 1.145 lines changed: 5, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/schema.c
  • 1.61 lines changed: 4, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTables/wiggle.c
  • 1.76 lines changed: 11, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.511 lines changed: 13, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgTracks/bamTrack.c
  • 1.21 lines changed: 2, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
  • 1.20 lines changed: 19, context: html, text, full: html, text
    For pairSearchRange, don't do two bamFetch's -- very inefficient. Just expand the search range up front.
• src/hg/hgTracks/bedTrack.c
  • 1.21 lines changed: 1, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
• src/hg/hgTracks/cgapSageTrack.c
  • 1.14 lines changed: 5, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
• src/hg/hgTracks/chainTrack.c
  • 1.38 lines changed: 5, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
• src/hg/hgTracks/encode.c
  • 1.23 lines changed: 1, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
• src/hg/hgTracks/hgTracks.c
  • 1.1617 lines changed: 37, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.1616 lines changed: 2, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
  • 1.1615 lines changed: 5, context: html, text, full: html, text
    Add count of sequences to chromInfo page (hg19 has greatly expanded the count over hg18)
• src/hg/hgTracks/hgTracks.h
  • 1.195 lines changed: 5, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.194 lines changed: 2, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
• src/hg/hgTracks/imageV2.c
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Changed verbose messages from js developers only to hgwdev only
  • 1.18 lines changed: 6, context: html, text, full: html, text
    Warning only for javascriipt developers
• src/hg/hgTracks/loweLabTracks.c
  • 1.31 lines changed: 2, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
• src/hg/hgTracks/pslTrack.c
  • 1.33 lines changed: 4, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
• src/hg/hgTracks/retroGene.c
  • 1.18 lines changed: 1, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
• src/hg/hgTracks/sampleTracks.c
  • 1.9 lines changed: 1, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
• src/hg/hgTracks/simpleTracks.c
  • 1.118 lines changed: 128, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.117 lines changed: 7, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
• src/hg/hgTracks/switchGear.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
• src/hg/hgTracks/wigTrack.c
  • 1.101 lines changed: 4, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.100 lines changed: 8, context: html, text, full: html, text
    Allow whisker plots to show colors in positive and negative tracks
• src/hg/hgc/hgc.c
  • 1.1584 lines changed: 36, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/hgc/wiggleClick.c
  • 1.33 lines changed: 2, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/inc/trackDb.h
  • 1.52 lines changed: 57, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/instinct/bioInt2/makeClusterFiles.c
  • 1.5 lines changed: 52, context: html, text, full: html, text
    Added db batch number support
  • 1.4 lines changed: 259, context: html, text, full: html, text
    Deal with an arbitrary number of data types, rather than just CGH expression; Changed output names; fixed bug with withinPathway permutation
• src/hg/instinct/bioInt2/makefile
  • 1.14 lines changed: 8, context: html, text, full: html, text
    Added populateDbFromFile
• src/hg/instinct/bioInt2/populateDb.c
  • 1.12 lines changed: 5, context: html, text, full: html, text
    Aborts rather than crashes when number of data labels doesn't match data
• src/hg/instinct/bioInt2/populateDbFromFile.c
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Added populateDbFromFile
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenMinGBMBio.ra
  • 1.4 lines changed: 205, context: html, text, full: html, text
    Updated open access clinical info
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenMinOVBio.ra
  • 1.5 lines changed: 2, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenOVBio.ra
  • 1.13 lines changed: 127, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAPublicBrowser.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    add public browser TCGA ra file
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
  • 1.22 lines changed: 70, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.32 lines changed: 125, context: html, text, full: html, text
    add public browser TCGA ra file
• src/hg/js/README
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Need this to note the obscure hg.conf setting required to test changes
• src/hg/js/hgTracks.js
  • 1.51 lines changed: 11, context: html, text, full: html, text
    use auto for dialog heights and widths; fixes MSIE problems
  • 1.50 lines changed: 31, context: html, text, full: html, text
    retrieve new image when user chooses viewImg
  • 1.49 lines changed: 156, context: html, text, full: html, text
    handle changes to track buttons
• src/hg/js/hui.js
  • 1.47 lines changed: 7, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/js/jquery.contextmenu.js
  • 1.3 lines changed: 6, context: html, text, full: html, text
    hide menu when user presses the escape key
• src/hg/js/makefile
  • 1.13 lines changed: 1, context: html, text, full: html, text
    add jquery-ui.js and jquery.contextmenu.js
• src/hg/lib/cart.c
  • 1.115 lines changed: 40, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/lib/hVarSubst.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/lib/hdb.c
  • 1.417 lines changed: 208, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/lib/hui.c
  • 1.253 lines changed: 299, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/lib/trackDbCustom.c
  • 1.73 lines changed: 324, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/lib/wigDataStream.c
  • 1.87 lines changed: 3, context: html, text, full: html, text
    Raising the HUGE_LIMIT to 4280000000 caused a very large slow down in some custom tracks. Doesn't make any sense.
  • 1.86 lines changed: 17, context: html, text, full: html, text
    Raise memory limit for data fetch operations
• src/hg/lib/wiggleCart.c
  • 1.37 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/doc/ailMel1.txt
  • 1.2 lines changed: 41, context: html, text, full: html, text
    ready for genbank run
  • 1.1 lines changed: 41, context: html, text, full: html, text
    Initial sequence for Panda
• src/hg/makeDb/doc/bosTau4.txt
  • 1.21 lines changed: 4, context: html, text, full: html, text
    one more detail
  • 1.20 lines changed: 11, context: html, text, full: html, text
    adding liftover to MD3
• src/hg/makeDb/doc/danRer5.txt
  • 1.19 lines changed: 7, context: html, text, full: html, text
    LiftOver to danRer6
• src/hg/makeDb/doc/danRer6.txt
  • 1.15 lines changed: 44, context: html, text, full: html, text
    danRer6 xentro2 chains
  • 1.14 lines changed: 8, context: html, text, full: html, text
    added transmap build doc
  • 1.13 lines changed: 44, context: html, text, full: html, text
    danRer6/gas
  • 1.12 lines changed: 52, context: html, text, full: html, text
    danRer6 to mmm9 chains
• src/hg/makeDb/doc/encodeDccHg18/broadChipSeq.notes.txt
  • 1.9 lines changed: 287, context: html, text, full: html, text
    Fix captitaliZation in paths
  • 1.8 lines changed: 51, context: html, text, full: html, text
    Kayla found some mangled names
• src/hg/makeDb/doc/encodeDccHg18/uwDnaseSeq.release2.notes.txt
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Notes for the 2nd release of UW DNase
• src/hg/makeDb/doc/gasAcu1.txt
  • 1.41 lines changed: 2, context: html, text, full: html, text
    fixed typo
  • 1.40 lines changed: 20, context: html, text, full: html, text
    danRer6/gas
• src/hg/makeDb/doc/hg18.txt
  • 1.392 lines changed: 16, context: html, text, full: html, text
    Changed cdsStart and cdsEnd to be 0 in Burge RNA-seq data and moved track data to directory for hg18 genome assembly.
• src/hg/makeDb/doc/hg19.txt
  • 1.69 lines changed: 16, context: html, text, full: html, text
    Added track of new Exoniphy predictions.
  • 1.68 lines changed: 17, context: html, text, full: html, text
    Changed cdsStart and cdsEnd to be 0 in Burge RNA-seq data and moved track data to directory for hg19 genome assembly.
• src/hg/makeDb/doc/mm9.txt
  • 1.118 lines changed: 2, context: html, text, full: html, text
    danRer6 chain swap
  • 1.117 lines changed: 21, context: html, text, full: html, text
    danRer6 to mmm9 chains
• src/hg/makeDb/doc/xenTro2.txt
  • 1.16 lines changed: 19, context: html, text, full: html, text
    danRer6/xenTro2 chainswap
• src/hg/makeDb/genbank/doc/to-do.txt
  • 1.119 lines changed: 2, context: html, text, full: html, text
    added problem case example
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.107 lines changed: 1, context: html, text, full: html, text
    don't align dropped database
  • 1.106 lines changed: 6, context: html, text, full: html, text
    don't align for genomes no longer being updated
  • 1.105 lines changed: 11, context: html, text, full: html, text
    put database update lists in alphabetical order to make comparisons easy
  • 1.104 lines changed: 1, context: html, text, full: html, text
    added panda
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.355 lines changed: 3, context: html, text, full: html, text
    changed panda params
  • 1.354 lines changed: 1, context: html, text, full: html, text
    need ailMel1.lift = no
  • 1.353 lines changed: 14, context: html, text, full: html, text
    adding panda ailMel1
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.103 lines changed: 2, context: html, text, full: html, text
    sort to make finding differences easy
  • 1.102 lines changed: 2, context: html, text, full: html, text
    put database update lists in alphabetical order to make comparisons easy
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.111 lines changed: 1, context: html, text, full: html, text
    don't update danRer1
  • 1.110 lines changed: 16, context: html, text, full: html, text
    put database update lists in alphabetical order to make comparisons easy
  • 1.109 lines changed: 5, context: html, text, full: html, text
    added panda
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.85 lines changed: 1, context: html, text, full: html, text
    don't align dropped database
  • 1.84 lines changed: 10, context: html, text, full: html, text
    put database update lists in alphabetical order to make comparisons easy
• src/hg/makeDb/genbank/src/extFileUpdate/extFileTool
  • 1.10 lines changed: 1, context: html, text, full: html, text
    fix path for hgnfs1 (fixed premature commit)
  • 1.9 lines changed: 2, context: html, text, full: html, text
    modified extFile updating to match new server configuration
  • 1.8 lines changed: 41, context: html, text, full: html, text
    modified extFile updating to match new server configuration
• src/hg/makeDb/genbank/src/extFileUpdate/extFileUpdate.c
  • 1.13 lines changed: 42, context: html, text, full: html, text
    modified extFile updating to match new server configuration
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • 1.74 lines changed: 4, context: html, text, full: html, text
    adding ailMel - Panda with Dog specifications
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.56 lines changed: 364, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/hgTrackDb/makefile
  • 1.32 lines changed: 1, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/schema/all.joiner
  • 1.757 lines changed: 1, context: html, text, full: html, text
    added table to galGal ignore list
  • 1.756 lines changed: 1, context: html, text, full: html, text
    Added exoniphy to list of tables to be ignored.
  • 1.755 lines changed: 1, context: html, text, full: html, text
    added danRer6 as a database covered by xrg variable; danRer6 is first danRer db to have xenoRefGene
  • 1.754 lines changed: 2, context: html, text, full: html, text
    moved danRer6 from '#transMapDb not public...' to a database covered by transMapDb variable
• src/hg/makeDb/trackDb/armadillo/trackDb.chainNet.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.1 lines changed: 1, context: html, text, full: html, text
    catching up chain and net composites for hgwdev only bosTau1 dasNov1 echTel1 loxAfr1 dasNov2 loxAfr3
• src/hg/makeDb/trackDb/armadillo/trackDb.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    catching up chain and net composites for hgwdev only bosTau1 dasNov1 echTel1 loxAfr1 dasNov2 loxAfr3
• src/hg/makeDb/trackDb/bushbaby/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
• src/hg/makeDb/trackDb/bushbaby/trackDb.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
• src/hg/makeDb/trackDb/cat/trackDb.chainNet.ra
  • 1.3 lines changed: 9, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.2 lines changed: 9, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.1 lines changed: 18, context: html, text, full: html, text
    all canFam chain net tracks are now composites
• src/hg/makeDb/trackDb/cat/trackDb.ra
  • 1.9 lines changed: 2, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.8 lines changed: 2, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.7 lines changed: 4, context: html, text, full: html, text
    all canFam chain net tracks are now composites
• src/hg/makeDb/trackDb/chicken/galGal2/trackDb.chainNet.ra
  • 1.4 lines changed: 5, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.3 lines changed: 3, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.2 lines changed: 5, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.1 lines changed: 11, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/chicken/galGal2/trackDb.ra
  • 1.74 lines changed: 4, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.73 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/chicken/galGal3/caCondor454.html
  • 1.5 lines changed: 7, context: html, text, full: html, text
    a few more tweaks
  • 1.4 lines changed: 108, context: html, text, full: html, text
    initial draft of changes
  • 1.3 lines changed: 1, context: html, text, full: html, text
    added credit
• src/hg/makeDb/trackDb/chicken/galGal3/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
• src/hg/makeDb/trackDb/chicken/galGal3/trackDb.ra
  • 1.17 lines changed: 7, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
• src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra
  • 1.18 lines changed: 7, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.17 lines changed: 6, context: html, text, full: html, text
    all zebrafinch taeGut1 chain net tracks are composite
  • 1.16 lines changed: 3, context: html, text, full: html, text
    all lanclet braFlo1 chain net tracks are composite
  • 1.15 lines changed: 6, context: html, text, full: html, text
    all guinea pig cavPor3 and 2 chain net tracks are composite
  • 1.14 lines changed: 7, context: html, text, full: html, text
    all horse equCab1 and 2 chain net tracks are composite
  • 1.13 lines changed: 3, context: html, text, full: html, text
    all lamprey petMar1 chain and net tracks are composites
  • 1.12 lines changed: 3, context: html, text, full: html, text
    all lizard anoCar1 chain and net tracks are now composite
  • 1.11 lines changed: 9, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.10 lines changed: 6, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.9 lines changed: 6, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.8 lines changed: 5, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.7 lines changed: 6, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.6 lines changed: 4, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.5 lines changed: 6, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.4 lines changed: 6, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.3 lines changed: 13, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.2 lines changed: 13, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.1 lines changed: 109, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/chicken/trackDb.ra
  • 1.17 lines changed: 4, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.chainNet.ra
  • 1.2 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.1 lines changed: 3, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.ra
  • 1.40 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
  • 1.10 lines changed: 3, context: html, text, full: html, text
    do not need individual chain net entries for hgwdev specific genomes sorAra1 eriEur1 tupBel1 otoGar1 oryCun1 gorGor1
  • 1.9 lines changed: 3, context: html, text, full: html, text
    all horse equCab1 and 2 chain net tracks are composite
  • 1.8 lines changed: 8, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Marmoset calJac1 chain and net tracks are now all composites
  • 1.6 lines changed: 8, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.5 lines changed: 3, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.4 lines changed: 7, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.3 lines changed: 9, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.2 lines changed: 3, context: html, text, full: html, text
    all canFam chain net tracks are now composites
  • 1.1 lines changed: 47, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/chimp/trackDb.ra
  • 1.27 lines changed: 2, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.26 lines changed: 3, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.25 lines changed: 4, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/cow/bosTau2/trackDb.chainNet.ra
  • 1.2 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.1 lines changed: 3, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/cow/bosTau2/trackDb.ra
  • 1.10 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/cow/bosTau3/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/cow/bosTau3/trackDb.ra
  • 1.9 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/cow/trackDb.chainNet.ra
  • 1.9 lines changed: 3, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.8 lines changed: 4, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.7 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.6 lines changed: 17, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.5 lines changed: 4, context: html, text, full: html, text
    eliminate duplicate entry for chainNetCanFam2
  • 1.4 lines changed: 3, context: html, text, full: html, text
    all canFam chain net tracks are now composites
  • 1.3 lines changed: 2, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/dog/canFam1/trackDb.chainNet.ra
  • 1.2 lines changed: 3, context: html, text, full: html, text
    chainNetHg17 is needed for canFam1 and monDom1 to complete human business
  • 1.1 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/dog/canFam1/trackDb.ra
  • 1.38 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.chainNet.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.1 lines changed: 1, context: html, text, full: html, text
    shorLabel monDom4 for hgwdev
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.42 lines changed: 6, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.41 lines changed: 7, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
  • 1.12 lines changed: 9, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.11 lines changed: 3, context: html, text, full: html, text
    catching up chain and net composites for hgwdev only bosTau1 dasNov1 echTel1 loxAfr1 dasNov2 loxAfr3
  • 1.10 lines changed: 6, context: html, text, full: html, text
    all horse equCab1 and 2 chain net tracks are composite
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Marmoset calJac1 chain and net tracks are now all composites
  • 1.8 lines changed: 4, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.7 lines changed: 9, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.6 lines changed: 4, context: html, text, full: html, text
    chainNetHg17 is needed for canFam1 and monDom1 to complete human business
  • 1.5 lines changed: 7, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.4 lines changed: 9, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.3 lines changed: 13, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/dog/trackDb.ra
  • 1.30 lines changed: 6, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.29 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.28 lines changed: 4, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • 1.84 lines changed: 911, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/elephant/loxAfr3/trackDb.ra
  • 1.3 lines changed: 15, context: html, text, full: html, text
    Fixed matrix parameters for mm9 chain
• src/hg/makeDb/trackDb/elephant/trackDb.chainNet.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.1 lines changed: 1, context: html, text, full: html, text
    catching up chain and net composites for hgwdev only bosTau1 dasNov1 echTel1 loxAfr1 dasNov2 loxAfr3
• src/hg/makeDb/trackDb/elephant/trackDb.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    catching up chain and net composites for hgwdev only bosTau1 dasNov1 echTel1 loxAfr1 dasNov2 loxAfr3
• src/hg/makeDb/trackDb/fugu/fr1/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composite
• src/hg/makeDb/trackDb/fugu/fr1/trackDb.ra
  • 1.3 lines changed: 4, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
• src/hg/makeDb/trackDb/fugu/fr2/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    all mouse human net tracks are now composites
• src/hg/makeDb/trackDb/fugu/fr2/trackDb.ra
  • 1.10 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/fugu/trackDb.chainNet.ra
  • 1.7 lines changed: 18, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.6 lines changed: 6, context: html, text, full: html, text
    all Medaka oryLat2 chain and net tracks are now composites
  • 1.5 lines changed: 5, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.4 lines changed: 10, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.3 lines changed: 12, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.2 lines changed: 13, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.1 lines changed: 64, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/fugu/trackDb.ra
  • 1.70 lines changed: 6, context: html, text, full: html, text
    all Medaka oryLat2 chain and net tracks are now composites
  • 1.69 lines changed: 2, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.68 lines changed: 14, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.67 lines changed: 2, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.66 lines changed: 6, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.65 lines changed: 4, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/guineaPig/trackDb.chainNet.ra
  • 1.5 lines changed: 3, context: html, text, full: html, text
    do not need individual chain net entries for hgwdev specific genomes sorAra1 eriEur1 tupBel1 otoGar1 oryCun1 gorGor1
  • 1.4 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.3 lines changed: 9, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.2 lines changed: 6, context: html, text, full: html, text
    all galGal chain net tracks are now composite
  • 1.1 lines changed: 21, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/guineaPig/trackDb.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/horse/equCab1/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/horse/equCab1/trackDb.ra
  • 1.7 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/horse/trackDb.chainNet.ra
  • 1.8 lines changed: 5, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.7 lines changed: 4, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.6 lines changed: 3, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.5 lines changed: 9, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.4 lines changed: 9, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.3 lines changed: 3, context: html, text, full: html, text
    all galGal chain net tracks are now composite
  • 1.2 lines changed: 3, context: html, text, full: html, text
    all canFam chain net tracks are now composites
  • 1.1 lines changed: 36, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/horse/trackDb.ra
  • 1.21 lines changed: 1, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.20 lines changed: 2, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.19 lines changed: 3, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.18 lines changed: 7, context: html, text, full: html, text
    eliminate duplicate chainNetMonDom5 override
  • 1.17 lines changed: 4, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/human/encodeAffyChipSuper.html
  • 1.2 lines changed: 9, context: html, text, full: html, text
    these links require logins -- so, we are removing (ok by Kate)
  • 1.1 lines changed: 9, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/encodeGencodeSuper.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/encodeStanfordChipSuper.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/encodeUvaDnaRepSuper.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg16/trackDb.chainNet.ra
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.2 lines changed: 5, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.1 lines changed: 8, context: html, text, full: html, text
    all mouse human net tracks are now composites
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
  • 1.581 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/human/hg17/trackDb.chainNet.ra
  • 1.9 lines changed: 3, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.7 lines changed: 4, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.6 lines changed: 4, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.5 lines changed: 4, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.4 lines changed: 6, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.3 lines changed: 3, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.2 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.1 lines changed: 31, context: html, text, full: html, text
    all canFam chain net tracks are now composites
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • 1.433 lines changed: 5, context: html, text, full: html, text
    all canFam chain net tracks are now composites
• src/hg/makeDb/trackDb/human/hg18/burgeRnaSeqGemMapperAlign.html
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Minor edits.
  • 1.3 lines changed: 21, context: html, text, full: html, text
    Moved links to labs to first paragraph, changed paper link to Nature instead of pubmed, small tweaks everywhere.
• src/hg/makeDb/trackDb/human/hg18/encodeAffyChipSuper.html
  • 1.9 lines changed: 56, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/encodeEgaspSuper.html
  • 1.11 lines changed: 257, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/encodeGencodeSuper.html
  • 1.9 lines changed: 160, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/encodeStanfordChipSuper.html
  • 1.9 lines changed: 33, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/encodeUvaDnaRepSuper.html
  • 1.10 lines changed: 43, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/trackDb.chainNet.ra
  • 1.9 lines changed: 12, context: html, text, full: html, text
    clean up chain net composites for non-released genomes on hg18
  • 1.8 lines changed: 6, context: html, text, full: html, text
    all horse equCab1 and 2 chain net tracks are composite
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Marmoset calJac1 chain and net tracks are now all composites
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.5 lines changed: 7, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.4 lines changed: 3, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.3 lines changed: 3, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.2 lines changed: 3, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.1 lines changed: 41, context: html, text, full: html, text
    all rat chain and net tracks are now composites
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChip.ra
  • 1.29 lines changed: 22, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.28 lines changed: 2, context: html, text, full: html, text
    Adding comment as to nature of work-around.
  • 1.27 lines changed: 33, context: html, text, full: html, text
    Moving encodeAffyChipSuper back down a level in directory to hg18 to serve as a test case that we can have supertracks in levels below their tracks. Have to keep the single child as well as the workaround for over-eager pruning in -strict mode in hgTrackDb.
  • 1.26 lines changed: 18, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChrom.ra
  • 1.10 lines changed: 9, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeCompAndVar.ra
  • 1.23 lines changed: 17, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeGenes.ra
  • 1.9 lines changed: 18, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeTxLevels.ra
  • 1.16 lines changed: 9, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.446 lines changed: 302, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.445 lines changed: 8, context: html, text, full: html, text
    clean up chain net composites for non-released genomes on hg18
  • 1.444 lines changed: 2, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.443 lines changed: 3, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.442 lines changed: 7, context: html, text, full: html, text
    Removed the priority setting from the rn4, monDom4 and canFam2 chain and net tracks. The settings were formerly overridden by human/priority.ra.
  • 1.441 lines changed: 3, context: html, text, full: html, text
    Updated search terms for 3 new Illumina SNP arrays.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.736 lines changed: 18312, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.735 lines changed: 2, context: html, text, full: html, text
    Fix some labels to match metadata and tablenames
  • 1.734 lines changed: 7, context: html, text, full: html, text
    Correct some submission IDs so reporting works properly
  • 1.733 lines changed: 2, context: html, text, full: html, text
    Roll back default wiggle height for UW tracks for consistency w/ other ENCODE tracks
  • 1.732 lines changed: 9, context: html, text, full: html, text
    Add some missing protocol metadata
  • 1.731 lines changed: 3, context: html, text, full: html, text
    Stay with V2 convention
  • 1.730 lines changed: 1, context: html, text, full: html, text
    Fix dataVersion on Broad during the 13th hour
  • 1.729 lines changed: 1, context: html, text, full: html, text
    fix controlled vocabulary links
  • 1.728 lines changed: 1, context: html, text, full: html, text
    Fix UW ChipSeq settings
  • 1.727 lines changed: 1, context: html, text, full: html, text
    moving ENCODE Gencode so that it doesn't appear first in the genes group
  • 1.726 lines changed: 264, context: html, text, full: html, text
    Broads 14 for Jan 2010
  • 1.725 lines changed: 36, context: html, text, full: html, text
    removed release alpha lines for ENCODE CSHL Sm RNA
  • 1.724 lines changed: 36, context: html, text, full: html, text
    change A+ to tot in Hannon small RNA-seq
  • 1.723 lines changed: 35, context: html, text, full: html, text
    change H1-hESC cell compartment to cell rather than cytosol for GIS RNA tracks
  • 1.722 lines changed: 151, context: html, text, full: html, text
    Added 4 more HAIB ChIP submissions
  • 1.721 lines changed: 38, context: html, text, full: html, text
    change labels for Cshl Short RNA-seq to Cshl Small Rna-seq
  • 1.720 lines changed: 115, context: html, text, full: html, text
    add A+ to Transcriptome tracks where polyA+ is the default
  • 1.719 lines changed: 5, context: html, text, full: html, text
    fix big bed filename for Cshl Long tracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.html
  • 1.3 lines changed: 5, context: html, text, full: html, text
    correcting minor errors
• src/hg/makeDb/trackDb/human/hg19/burgeRnaSeqGemMapperAlign.html
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Minor edits.
  • 1.3 lines changed: 21, context: html, text, full: html, text
    Moved links to labs to first paragraph, changed paper link to Nature instead of pubmed, small tweaks everywhere.
• src/hg/makeDb/trackDb/human/hg19/exoniphy.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Description for hg19 exoniphy predictions track.
• src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.79 lines changed: 956, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.78 lines changed: 5, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.77 lines changed: 12, context: html, text, full: html, text
    swapped out danRer5 and in danRer6 in vertChainNet composite
  • 1.76 lines changed: 20, context: html, text, full: html, text
    Added track entry for RetroFiner retrogenes, version 2.
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • 1.28 lines changed: 9, context: html, text, full: html, text
    catching up chain and net composites for hgwdev only bosTau1 dasNov1 echTel1 loxAfr1 dasNov2 loxAfr3
  • 1.27 lines changed: 3, context: html, text, full: html, text
    do not need individual chain net entries for hgwdev specific genomes sorAra1 eriEur1 tupBel1 otoGar1 oryCun1 gorGor1
  • 1.26 lines changed: 24, context: html, text, full: html, text
    clean up chain net composites for non-released genomes on hg18
  • 1.25 lines changed: 3, context: html, text, full: html, text
    all zebrafinch taeGut1 chain net tracks are composite
  • 1.24 lines changed: 4, context: html, text, full: html, text
    all lanclet braFlo1 chain net tracks are composite
  • 1.23 lines changed: 6, context: html, text, full: html, text
    all guinea pig cavPor3 and 2 chain net tracks are composite
  • 1.22 lines changed: 6, context: html, text, full: html, text
    all horse equCab1 and 2 chain net tracks are composite
  • 1.21 lines changed: 3, context: html, text, full: html, text
    all lamprey petMar1 chain and net tracks are composites
  • 1.20 lines changed: 3, context: html, text, full: html, text
    all lizard anoCar1 chain and net tracks are now composite
  • 1.19 lines changed: 15, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.18 lines changed: 10, context: html, text, full: html, text
    all Medaka oryLat2 chain and net tracks are now composites
  • 1.17 lines changed: 5, context: html, text, full: html, text
    Marmoset calJac1 chain and net tracks are now all composites
  • 1.16 lines changed: 6, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.15 lines changed: 10, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.14 lines changed: 6, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.13 lines changed: 5, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.12 lines changed: 6, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.11 lines changed: 6, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.10 lines changed: 8, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.9 lines changed: 7, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.8 lines changed: 7, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.7 lines changed: 12, context: html, text, full: html, text
    all galGal chain net tracks are now composite
  • 1.6 lines changed: 3, context: html, text, full: html, text
    all canFam chain net tracks are now composites
  • 1.5 lines changed: 18, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/human/trackDb.encode.ra
  • 1.103 lines changed: 31, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.102 lines changed: 7, context: html, text, full: html, text
    Moving encodeAffyChipSuper back down a level in directory to hg18 to serve as a test case that we can have supertracks in levels below their tracks. Have to keep the single child as well as the workaround for over-eager pruning in -strict mode in hgTrackDb.
  • 1.101 lines changed: 46, context: html, text, full: html, text
    Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.485 lines changed: 25, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.484 lines changed: 47, context: html, text, full: html, text
    catching up chain and net composites for hgwdev only bosTau1 dasNov1 echTel1 loxAfr1 dasNov2 loxAfr3
  • 1.483 lines changed: 8, context: html, text, full: html, text
    do not need individual chain net entries for hgwdev specific genomes sorAra1 eriEur1 tupBel1 otoGar1 oryCun1 gorGor1
  • 1.482 lines changed: 5, context: html, text, full: html, text
    clean up chain net composites for non-released genomes on hg18
  • 1.481 lines changed: 15, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.480 lines changed: 1, context: html, text, full: html, text
    Added setting for subtracks drag and drop for Burge RNA-seq.
• src/hg/makeDb/trackDb/lamprey/trackDb.chainNet.ra
  • 1.4 lines changed: 3, context: html, text, full: html, text
    all lanclet braFlo1 chain net tracks are composite
  • 1.3 lines changed: 7, context: html, text, full: html, text
    all Medaka oryLat2 chain and net tracks are now composites
  • 1.2 lines changed: 13, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.1 lines changed: 23, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/lamprey/trackDb.ra
  • 1.7 lines changed: 4, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/lancelet/trackDb.chainNet.ra
  • 1.3 lines changed: 3, context: html, text, full: html, text
    all lamprey petMar1 chain and net tracks are composites
  • 1.2 lines changed: 6, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.1 lines changed: 9, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/lancelet/trackDb.ra
  • 1.2 lines changed: 4, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/lizard/trackDb.chainNet.ra
  • 1.6 lines changed: 3, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.5 lines changed: 5, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.4 lines changed: 6, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.3 lines changed: 7, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.2 lines changed: 13, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.1 lines changed: 34, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/lizard/trackDb.ra
  • 1.8 lines changed: 4, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.7 lines changed: 4, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
  • 1.92 lines changed: 6, context: html, text, full: html, text
    hide blastx track by default
• src/hg/makeDb/trackDb/makefile
  • 1.281 lines changed: 1, context: html, text, full: html, text
    Add ailMel1 panda to the build
• src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra
  • 1.7 lines changed: 1, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.6 lines changed: 3, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.5 lines changed: 1, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.4 lines changed: 4, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.3 lines changed: 2, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/marmoset/trackDb.ra
  • 1.8 lines changed: 1, context: html, text, full: html, text
    It does no good to have a release beta in an override
• src/hg/makeDb/trackDb/medaka/oryLat2/trackDb.ra
  • 1.7 lines changed: 8, context: html, text, full: html, text
    changed danRer5 chains/nets to db name. now replaced by danRer6
• src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra
  • 1.7 lines changed: 5, context: html, text, full: html, text
    all lamprey petMar1 chain and net tracks are composites
  • 1.6 lines changed: 10, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.5 lines changed: 5, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.4 lines changed: 3, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.3 lines changed: 10, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.2 lines changed: 6, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.1 lines changed: 39, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/medaka/trackDb.ra
  • 1.22 lines changed: 2, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.21 lines changed: 1, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.20 lines changed: 11, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.chainNet.ra
  • 1.7 lines changed: 3, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.5 lines changed: 3, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.4 lines changed: 3, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.3 lines changed: 3, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.2 lines changed: 4, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.1 lines changed: 19, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra
  • 1.58 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.chainNet.ra
  • 1.8 lines changed: 9, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.7 lines changed: 3, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.5 lines changed: 3, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.4 lines changed: 3, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.3 lines changed: 1, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.2 lines changed: 3, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.1 lines changed: 22, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.62 lines changed: 475, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.61 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.74 lines changed: 117, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.73 lines changed: 3, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • 1.26 lines changed: 20, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.25 lines changed: 15, context: html, text, full: html, text
    catching up chain and net composites for hgwdev only bosTau1 dasNov1 echTel1 loxAfr1 dasNov2 loxAfr3
  • 1.24 lines changed: 15, context: html, text, full: html, text
    do not need individual chain net entries for hgwdev specific genomes sorAra1 eriEur1 tupBel1 otoGar1 oryCun1 gorGor1
  • 1.23 lines changed: 3, context: html, text, full: html, text
    all lanclet braFlo1 chain net tracks are composite
  • 1.22 lines changed: 6, context: html, text, full: html, text
    all guinea pig cavPor3 and 2 chain net tracks are composite
  • 1.21 lines changed: 3, context: html, text, full: html, text
    all lamprey petMar1 chain and net tracks are composites
  • 1.20 lines changed: 3, context: html, text, full: html, text
    all lizard anoCar1 chain and net tracks are now composite
  • 1.19 lines changed: 12, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.18 lines changed: 10, context: html, text, full: html, text
    all Medaka oryLat2 chain and net tracks are now composites
  • 1.17 lines changed: 3, context: html, text, full: html, text
    Marmoset calJac1 chain and net tracks are now all composites
  • 1.16 lines changed: 6, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.15 lines changed: 7, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.14 lines changed: 7, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.13 lines changed: 5, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.12 lines changed: 6, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.11 lines changed: 6, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.10 lines changed: 9, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.9 lines changed: 9, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.8 lines changed: 9, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.7 lines changed: 6, context: html, text, full: html, text
    all galGal chain net tracks are now composite
  • 1.6 lines changed: 3, context: html, text, full: html, text
    all canFam chain net tracks are now composites
  • 1.5 lines changed: 12, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.175 lines changed: 4, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.174 lines changed: 75, context: html, text, full: html, text
    catching up chain and net composites for hgwdev only bosTau1 dasNov1 echTel1 loxAfr1 dasNov2 loxAfr3
  • 1.173 lines changed: 36, context: html, text, full: html, text
    do not need individual chain net entries for hgwdev specific genomes sorAra1 eriEur1 tupBel1 otoGar1 oryCun1 gorGor1
  • 1.172 lines changed: 2, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.171 lines changed: 1, context: html, text, full: html, text
    revised termRegex in komp table search block so that searches of komp.name work
  • 1.170 lines changed: 4, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.169 lines changed: 4, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.168 lines changed: 2, context: html, text, full: html, text
    all rat chain and net tracks are now composites
• src/hg/makeDb/trackDb/opossum/monDom1/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    chainNetHg17 is needed for canFam1 and monDom1 to complete human business
• src/hg/makeDb/trackDb/opossum/monDom1/trackDb.ra
  • 1.25 lines changed: 4, context: html, text, full: html, text
    chainNetHg17 is needed for canFam1 and monDom1 to complete human business
• src/hg/makeDb/trackDb/opossum/monDom4/trackDb.chainNet.ra
  • 1.8 lines changed: 4, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.7 lines changed: 3, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.6 lines changed: 7, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.5 lines changed: 3, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.4 lines changed: 5, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.3 lines changed: 5, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.2 lines changed: 3, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.1 lines changed: 29, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/opossum/monDom4/trackDb.ra
  • 1.26 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
  • 1.4 lines changed: 3, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.3 lines changed: 3, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.2 lines changed: 3, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.1 lines changed: 9, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • 1.24 lines changed: 7, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.23 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
  • 1.15 lines changed: 4, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.14 lines changed: 6, context: html, text, full: html, text
    all guinea pig cavPor3 and 2 chain net tracks are composite
  • 1.13 lines changed: 6, context: html, text, full: html, text
    all horse equCab1 and 2 chain net tracks are composite
  • 1.12 lines changed: 11, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Marmoset calJac1 chain and net tracks are now all composites
  • 1.10 lines changed: 11, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.9 lines changed: 4, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.8 lines changed: 5, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.7 lines changed: 6, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.6 lines changed: 3, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.5 lines changed: 7, context: html, text, full: html, text
    chainNetHg17 is needed for canFam1 and monDom1 to complete human business
  • 1.4 lines changed: 18, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.3 lines changed: 14, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.2 lines changed: 12, context: html, text, full: html, text
    all galGal chain net tracks are now composite
  • 1.1 lines changed: 112, context: html, text, full: html, text
    all canFam chain net tracks are now composites
• src/hg/makeDb/trackDb/opossum/trackDb.ra
  • 1.40 lines changed: 2, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.39 lines changed: 2, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.38 lines changed: 2, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.37 lines changed: 1, context: html, text, full: html, text
    chainNetHg17 is needed for canFam1 and monDom1 to complete human business
  • 1.36 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.35 lines changed: 3, context: html, text, full: html, text
    all canFam chain net tracks are now composites
• src/hg/makeDb/trackDb/orangutan/ponAbe2/trackDb.ra
  • 1.19 lines changed: 3, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
• src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra
  • 1.8 lines changed: 6, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.7 lines changed: 3, context: html, text, full: html, text
    all Medaka oryLat2 chain and net tracks are now composites
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Marmoset calJac1 chain and net tracks are now all composites
  • 1.5 lines changed: 3, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.4 lines changed: 6, context: html, text, full: html, text
    all platypus ornAna1 chain and net tracks are composites
  • 1.3 lines changed: 4, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.2 lines changed: 9, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.1 lines changed: 34, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/orangutan/trackDb.ra
  • 1.8 lines changed: 4, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/panda/ailMel1/description.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/panda/ailMel1/gap.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/panda/ailMel1/gold.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/panda/ailMel1/trackDb.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
  • 1.10 lines changed: 14, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.9 lines changed: 6, context: html, text, full: html, text
    all horse equCab1 and 2 chain net tracks are composite
  • 1.8 lines changed: 4, context: html, text, full: html, text
    all lizard anoCar1 chain and net tracks are now composite
  • 1.7 lines changed: 6, context: html, text, full: html, text
    Marmoset calJac1 chain and net tracks are now all composites
  • 1.6 lines changed: 6, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.5 lines changed: 6, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.4 lines changed: 13, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.3 lines changed: 6, context: html, text, full: html, text
    all galGal chain net tracks are now composite
  • 1.2 lines changed: 7, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/platypus/trackDb.ra
  • 1.12 lines changed: 3, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.11 lines changed: 3, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.10 lines changed: 8, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/rabbit/trackDb.chainNet.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.1 lines changed: 1, context: html, text, full: html, text
    all guinea pig cavPor3 and 2 chain net tracks are composite
• src/hg/makeDb/trackDb/rabbit/trackDb.ra
  • 1.3 lines changed: 4, context: html, text, full: html, text
    all guinea pig cavPor3 and 2 chain net tracks are composite
• src/hg/makeDb/trackDb/rat/rn3/trackDb.chainNet.ra
  • 1.3 lines changed: 2, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.2 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.1 lines changed: 4, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/rat/rn3/trackDb.ra
  • 1.65 lines changed: 2, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.64 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.46 lines changed: 2, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
• src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra
  • 1.14 lines changed: 6, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.13 lines changed: 3, context: html, text, full: html, text
    all guinea pig cavPor3 and 2 chain net tracks are composite
  • 1.12 lines changed: 3, context: html, text, full: html, text
    all horse equCab1 and 2 chain net tracks are composite
  • 1.11 lines changed: 11, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.10 lines changed: 3, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.9 lines changed: 8, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.8 lines changed: 4, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.7 lines changed: 14, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.6 lines changed: 9, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.5 lines changed: 13, context: html, text, full: html, text
    all galGal chain net tracks are now composite
  • 1.4 lines changed: 5, context: html, text, full: html, text
    all canFam chain net tracks are now composites
  • 1.3 lines changed: 11, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • 1.64 lines changed: 45, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.63 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.62 lines changed: 4, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • 1.51 lines changed: 28, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
• src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
  • 1.8 lines changed: 11, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Marmoset calJac1 chain and net tracks are now all composites
  • 1.6 lines changed: 4, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.5 lines changed: 5, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.4 lines changed: 3, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.3 lines changed: 7, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.2 lines changed: 11, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.1 lines changed: 44, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
  • 1.18 lines changed: 2, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
  • 1.17 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.16 lines changed: 4, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.15 lines changed: 4, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • 1.46 lines changed: 22, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/stickleback/trackDb.chainNet.ra
  • 1.7 lines changed: 3, context: html, text, full: html, text
    all lizard anoCar1 chain and net tracks are now composite
  • 1.6 lines changed: 9, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.5 lines changed: 6, context: html, text, full: html, text
    all Medaka oryLat2 chain and net tracks are now composites
  • 1.4 lines changed: 8, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.3 lines changed: 9, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.2 lines changed: 13, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.1 lines changed: 48, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/stickleback/trackDb.ra
  • 1.24 lines changed: 2, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.23 lines changed: 12, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.5 lines changed: 13, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/tenrec/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
• src/hg/makeDb/trackDb/tenrec/trackDb.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
• src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
• src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.ra
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
• src/hg/makeDb/trackDb/tetraodon/trackDb.chainNet.ra
  • 1.7 lines changed: 7, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.6 lines changed: 9, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.5 lines changed: 8, context: html, text, full: html, text
    all Medaka oryLat2 chain and net tracks are now composites
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.3 lines changed: 5, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.2 lines changed: 27, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.1 lines changed: 60, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
  • 1.48 lines changed: 7, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.47 lines changed: 6, context: html, text, full: html, text
    all Medaka oryLat2 chain and net tracks are now composites
  • 1.46 lines changed: 5, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.45 lines changed: 5, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.44 lines changed: 18, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.32 lines changed: 3, context: html, text, full: html, text
    Need release alpha and beta on Mm5
  • 1.31 lines changed: 76, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.30 lines changed: 1105, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
  • 1.29 lines changed: 245, context: html, text, full: html, text
    catching up chain and net composites for hgwdev only bosTau1 dasNov1 echTel1 loxAfr1 dasNov2 loxAfr3
  • 1.28 lines changed: 19, context: html, text, full: html, text
    do not need individual chain net entries for hgwdev specific genomes sorAra1 eriEur1 tupBel1 otoGar1 oryCun1 gorGor1
  • 1.27 lines changed: 364, context: html, text, full: html, text
    clean up chain net composites for non-released genomes on hg18
  • 1.26 lines changed: 55, context: html, text, full: html, text
    all zebrafinch taeGut1 chain net tracks are composite
  • 1.25 lines changed: 42, context: html, text, full: html, text
    all lanclet braFlo1 chain net tracks are composite
  • 1.24 lines changed: 84, context: html, text, full: html, text
    all guinea pig cavPor3 and 2 chain net tracks are composite
  • 1.23 lines changed: 41, context: html, text, full: html, text
    all horse equCab1 and 2 chain net tracks are composite
  • 1.22 lines changed: 42, context: html, text, full: html, text
    all lamprey petMar1 chain and net tracks are composites
  • 1.21 lines changed: 42, context: html, text, full: html, text
    all lizard anoCar1 chain and net tracks are now composite
  • 1.20 lines changed: 273, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.19 lines changed: 43, context: html, text, full: html, text
    all Medaka oryLat2 chain and net tracks are now composites
  • 1.18 lines changed: 40, context: html, text, full: html, text
    Marmoset calJac1 chain and net tracks are now all composites
  • 1.17 lines changed: 42, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.16 lines changed: 40, context: html, text, full: html, text
    rhesus and orangutan chain and net tracks are now all composites
  • 1.15 lines changed: 82, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.14 lines changed: 41, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.13 lines changed: 40, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.12 lines changed: 42, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.11 lines changed: 40, context: html, text, full: html, text
    chainNetHg17 is needed for canFam1 and monDom1 to complete human business
  • 1.10 lines changed: 126, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.9 lines changed: 42, context: html, text, full: html, text
    all galGal chain net tracks are now composite
  • 1.8 lines changed: 41, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.578 lines changed: 2, context: html, text, full: html, text
    Need release alpha and beta on Mm5
  • 1.577 lines changed: 24, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.576 lines changed: 22, context: html, text, full: html, text
    catching up chain and net composites for hgwdev only bosTau1 dasNov1 echTel1 loxAfr1 dasNov2 loxAfr3
  • 1.575 lines changed: 150, context: html, text, full: html, text
    do not need individual chain net entries for hgwdev specific genomes sorAra1 eriEur1 tupBel1 otoGar1 oryCun1 gorGor1
  • 1.574 lines changed: 12, context: html, text, full: html, text
    clean up chain net composites for non-released genomes on hg18
  • 1.573 lines changed: 34, context: html, text, full: html, text
    all zebrafinch taeGut1 chain net tracks are composite
  • 1.572 lines changed: 3, context: html, text, full: html, text
    all lanclet braFlo1 chain net tracks are composite
  • 1.571 lines changed: 6, context: html, text, full: html, text
    all guinea pig cavPor3 and 2 chain net tracks are composite
  • 1.570 lines changed: 4, context: html, text, full: html, text
    all horse equCab1 and 2 chain net tracks are composite
  • 1.569 lines changed: 2, context: html, text, full: html, text
    all lamprey petMar1 chain and net tracks are composites
  • 1.568 lines changed: 3, context: html, text, full: html, text
    all lizard anoCar1 chain and net tracks are now composite
  • 1.567 lines changed: 18, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.566 lines changed: 4, context: html, text, full: html, text
    all Medaka oryLat2 chain and net tracks are now composites
  • 1.565 lines changed: 3, context: html, text, full: html, text
    Marmoset calJac1 chain and net tracks are now all composites
  • 1.564 lines changed: 3, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.563 lines changed: 6, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.562 lines changed: 3, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.561 lines changed: 4, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.560 lines changed: 25, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.559 lines changed: 2, context: html, text, full: html, text
    chainNetHg17 is needed for canFam1 and monDom1 to complete human business
  • 1.558 lines changed: 8, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.557 lines changed: 3, context: html, text, full: html, text
    all galGal chain net tracks are now composite
  • 1.556 lines changed: 5, context: html, text, full: html, text
    all monDom chain nets are now composites
  • 1.555 lines changed: 1, context: html, text, full: html, text
    removing alpha from transMapAlnSplicedEst track
• src/hg/makeDb/trackDb/transMap.html
  • 1.15 lines changed: 2, context: html, text, full: html, text
    removed references to specific assemblies
• src/hg/makeDb/trackDb/transMapAlnMRna.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    removed references to specific assemblies
• src/hg/makeDb/trackDb/transMapAlnRefSeq.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    removed references to specific assemblies
• src/hg/makeDb/trackDb/transMapAlnSplicedEst.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    removed references to specific assemblies
• src/hg/makeDb/trackDb/transMapAlnUcscGenes.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    removed references to specific assemblies
• src/hg/makeDb/trackDb/treeShrew/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
• src/hg/makeDb/trackDb/treeShrew/trackDb.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    cleaning rough edges around chain net composite conversion
• src/hg/makeDb/trackDb/worm/ce6/trackDb.ra
  • 1.18 lines changed: 15, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • 1.40 lines changed: 85, context: html, text, full: html, text
    Merging viewInTheMiddle branch.
• src/hg/makeDb/trackDb/xenTro/trackDb.chainNet.ra
  • 1.8 lines changed: 7, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.7 lines changed: 3, context: html, text, full: html, text
    all lizard anoCar1 chain and net tracks are now composite
  • 1.6 lines changed: 10, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.5 lines changed: 6, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.4 lines changed: 27, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.3 lines changed: 13, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.2 lines changed: 12, context: html, text, full: html, text
    all galGal chain net tracks are now composite
  • 1.1 lines changed: 78, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/xenTro/trackDb.ra
  • 1.27 lines changed: 2, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.26 lines changed: 2, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.25 lines changed: 4, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.chainNet.ra
  • 1.3 lines changed: 5, context: html, text, full: html, text
    all zebrafish chain and net tracks are now composites
  • 1.2 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.1 lines changed: 7, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.ra
  • 1.41 lines changed: 1, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.40 lines changed: 3, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.chainNet.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.1 lines changed: 1, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.ra
  • 1.21 lines changed: 8, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.20 lines changed: 3, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/zebraFinch/trackDb.chainNet.ra
  • 1.2 lines changed: 13, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.1 lines changed: 13, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/zebraFinch/trackDb.ra
  • 1.8 lines changed: 3, context: html, text, full: html, text
    all galGal chain net tracks are now composite
• src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.chainNet.ra
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.2 lines changed: 2, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.1 lines changed: 5, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra
  • 1.56 lines changed: 9, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.55 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.chainNet.ra
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.2 lines changed: 2, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.1 lines changed: 5, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
• src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.ra
  • 1.40 lines changed: 5, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.39 lines changed: 2, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.38 lines changed: 4, context: html, text, full: html, text
    all mouse chain net tracks are now composites
• src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
  • 1.28 lines changed: 8, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.27 lines changed: 5, context: html, text, full: html, text
    need to bring in some other of the zebrafish trackDb for affyZebrafish
  • 1.26 lines changed: 1, context: html, text, full: html, text
    take out override on a track that is composite in danRer5, but not in zebrafish
• src/hg/makeDb/trackDb/zebrafish/danRer6/trackDb.ra
  • 1.10 lines changed: 6, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
• src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra
  • 1.12 lines changed: 13, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.11 lines changed: 8, context: html, text, full: html, text
    all Medaka oryLat2 chain and net tracks are now composites
  • 1.10 lines changed: 6, context: html, text, full: html, text
    Fugu fr1 and fr2 chain net tracks are now all composite
  • 1.9 lines changed: 3, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.8 lines changed: 5, context: html, text, full: html, text
    all stickleback chain and net tracks are now composite
  • 1.7 lines changed: 3, context: html, text, full: html, text
    all Tetraodon chain and net tracks are now composites
  • 1.6 lines changed: 6, context: html, text, full: html, text
    all chimp chain net tracks are now composites
  • 1.5 lines changed: 9, context: html, text, full: html, text
    all rat chain and net tracks are now composites
  • 1.4 lines changed: 13, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.3 lines changed: 13, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
  • 1.2 lines changed: 6, context: html, text, full: html, text
    all galGal chain net tracks are now composite
  • 1.1 lines changed: 85, context: html, text, full: html, text
    all monDom chain nets are now composites
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.63 lines changed: 5, context: html, text, full: html, text
    some more edge clean up of chainNet composites for hgwdev
  • 1.62 lines changed: 33, context: html, text, full: html, text
    all tetraodon xenTro1 and xenTro2 chain net tracks are now composite
  • 1.61 lines changed: 1, context: html, text, full: html, text
    all mouse chain net tracks are now composites
  • 1.60 lines changed: 6, context: html, text, full: html, text
    all hg18 hg19 chain net tracks are now composites
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    all monDom chain nets are now composites
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    fixed termRegex of search block for gold so that searching on danRer6 works and so all danRer assemblies now pick up the chrM contig (they were not before)
• src/hg/makeDb/trackDbPatch/trackDbPatch.c
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    Merging viewInTheMiddle branch.
• src/hg/mouseStuff/axtToPsl/makefile
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• src/hg/mouseStuff/mafFetch/makefile
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• src/hg/mouseStuff/mafRanges/makefile
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• src/hg/mouseStuff/mafToAxt/makefile
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• src/hg/mouseStuff/mafToPsl/makefile
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• src/hg/mouseStuff/subsetAxt/makefile
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• src/hg/oneShot/freen/freen.c
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• src/hg/oneShot/makeTrackDbTagVals/makeTrackDbTagVals.c
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• src/hg/oneShot/tdbRewriteReduceReplaces/tdbRewriteReduceReplaces.c
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• src/hg/oneShot/tdbRewriteRemoveUnused/makefile
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    file makefile was initially added on branch viewInTheMiddle.
• src/hg/oneShot/tdbRewriteRemoveUnused/tdbRewriteRemoveUnused.c
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    file tdbRewriteRemoveUnused.c was initially added on branch viewInTheMiddle.
• src/hg/oneShot/tdbRewriteSortTags/tdbRewriteSortTags.c
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• src/hg/oneShot/tdbRewriteViewsToSubtracks/tdbRewriteViewsToSubtracks.c
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• src/hg/pslCrudeCmp/makefile
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• src/hg/ratStuff/mafFrags/makefile
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• src/hg/ratStuff/mafOrtholog/makefile
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• src/hg/spideyToPsl/makefile
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• src/hg/tcga/pBamBam/bamBamCNV.c
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• src/hg/tcga/pBamBam/bam_helper.c
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• src/hg/tcga/pBamBam/bam_helper.h
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• src/hg/tcga/pBamBam/makefile
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    added bambam variants code
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    initial commit
• src/hg/tcga/pBamBam/pBamBam.c
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    updated
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    added bambam variants code
• src/hg/tcga/pBamBam/pBamBamCNV.c
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• src/hg/trfBig/trfBig.c
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    forgot check for fork failure
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    integrated change from stanford to no print out a error message when trf actually succeeded
• src/hg/utils/automation/Encode.pm
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    Add subroutines for dealing with pipeline statuses
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    Add access for CV rags (used by reporting)
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    Plug up a runtime warning warning
• src/hg/utils/phyloTrees/findScores.pl
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    Look for older styles, do the reverse lookup automatically if not found and show defaults when not specified
• src/hg/utils/tdbQuery/tdbQuery.c
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• src/hg/zoo/pslToFa/makefile
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• src/inc/common.h
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    correctly check return status of system; removed confusing function that is no longer used
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    Added must{Open,Read,Write,Close}Fd and mustLseek to common.c, for operations on file descriptors. Some were already in lib/tests/pipelineTester.c - replaced those.
• src/lib/bigBed.c
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• src/lib/cheapcgi.c
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• src/lib/common.c
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    correctly check return status of system; removed confusing function that is no longer used
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    Added must{Open,Read,Write,Close}Fd and mustLseek to common.c, for operations on file descriptors. Some were already in lib/tests/pipelineTester.c - replaced those.
• src/lib/errCatch.c
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    need a cast on a pointer to (int) for compile on MAC
• src/lib/net.c
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    Fixed comparison edge condition (not a huge problem, it just set tv_{sec,usec} to {0,1000000} not {1,0}) and more importantly, added a missing EOF check that was allowing unexpected EOF from FTP to result in inf. loop.
• src/lib/tests/pipelineTester.c
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    Added must{Open,Read,Write,Close}Fd and mustLseek to common.c, for operations on file descriptors. Some were already in lib/tests/pipelineTester.c - replaced those.
• src/lib/tests/udcTest.c
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    Added options -fork (true concurrent access: actually gets no errors unlike the same-process/interleaved-access test!), -seed (try 1261180550 for big failure on empty cache files without -fork), and -protocol (default ftp, can do http instead, boring/no errors).
• src/lib/udc.c
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    Changed all FILE * vars and operations (fopen etc) to integer file descriptors and 'man 2' operations (open etc), for unbuffered I/O which should make it harder for the bitmap file to get out of sync with the sparseData file when there are multiple udcFile*'s accessing the same part of a URL and those files. Unfortunately this doesn't completely prevent udcTest failures (try seed=1261180550), just reduces frequency a bit. Also added a speed optimization: to avoid heavy reconnect penalty when we need to skip a few udc blocks because they have already been cached, just read and discard those blocks' data.
• src/parasol/para/para.c
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    fix minor timing bug
• src/utils/est2genomeToPsl/makefile
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• src/utils/faFlyBaseToUcsc/makefile
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• src/utils/faSimplify/makefile
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• src/utils/gffPeek/makefile
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• src/utils/qa/weeklybld/buildEnv.csh
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    v222 preview
• src/utils/qa/weeklybld/cvs-reports-d
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    changes to support diff of what happend on a branch
• src/utils/spacedToTab/makefile
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• src/weblet/bottleneck/makefile
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• lines changed: 38541
• files changed: 292