CVS changes by file

review to branch (2010-05-11 to 2010-05-18) v231

• src/blat/version.doc
  • 1.77 lines changed: 1, context: html, text, full: html, text
    Dealing with primers that match but dangle off the ends of the chrom
• src/hg/archaeStuff/chooseorg/chooseorg.c
  • 1.4 lines changed: 20, context: html, text, full: html, text
    fix autocomplete problem for some species by Andrew H.
• src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
  • 1.5 lines changed: 39, context: html, text, full: html, text
    files, types, and checksums ooh my
  • 1.4 lines changed: 8, context: html, text, full: html, text
    more general characteristics system
  • 1.3 lines changed: 307, context: html, text, full: html, text
    more general characteristics system
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.239 lines changed: 1, context: html, text, full: html, text
    Flip mouse cell color to match human analog (k562)
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.224 lines changed: 17, context: html, text, full: html, text
    take out parallel BAM validation path that was broken
• src/hg/encode/utils/elandExtToSAM/elandExtToSAM.py
  • 1.5 lines changed: 3, context: html, text, full: html, text
    Added info that input can be bzip2/gzip/plain to usage - suggested by Galt
• src/hg/encode/utils/tagAlignToSAM/tagAlignToSAM.py
  • 1.1 lines changed: 134, context: html, text, full: html, text
    Initial checking of converter script for Philip @ Stanford for ENCODE. Converts from tagAlign to SAM format
• src/hg/hgGenome/import.c
  • 1.20 lines changed: 18, context: html, text, full: html, text
    Getting rid of some special cases no longer needed for mrna track.
• src/hg/hgTables/custom.c
  • 1.48 lines changed: 6, context: html, text, full: html, text
    Refactoring a bit so can pass a table string rather than a track struct to eliminate a track/table potential blending of things.
• src/hg/hgTables/hgTables.c
  • 1.196 lines changed: 8, context: html, text, full: html, text
    Refactoring a bit so can pass a table string rather than a track struct to eliminate a track/table potential blending of things.
  • 1.195 lines changed: 13, context: html, text, full: html, text
    Making show schema link work when track != table.
• src/hg/hgTables/hgTables.h
  • 1.145 lines changed: 1, context: html, text, full: html, text
    Refactoring a bit so can pass a table string rather than a track struct to eliminate a track/table potential blending of things.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.525 lines changed: 10, context: html, text, full: html, text
    More noodling getting multiWig UI page to work, mostly by pretending to be composite.
• src/hg/hgTracks/container.c
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Making click on multi-wig bring up trackUi page.
• src/hg/hgTracks/container.h
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Making click on multi-wig bring up trackUi page.
• src/hg/hgTracks/imageV2.c
  • 1.29 lines changed: 4, context: html, text, full: html, text
    improving layout of comment
  • 1.28 lines changed: 3, context: html, text, full: html, text
    Got rid of imgOrd hidden inputs. This is set by ajax now.
• src/hg/hgTracks/multiWig.c
  • 1.4 lines changed: 22, context: html, text, full: html, text
    Making click on multi-wig bring up trackUi page.
  • 1.3 lines changed: 74, context: html, text, full: html, text
    Making it so that multi-wigs can draw without overlay as well.
• src/hg/hgTracks/wigTrack.c
  • 1.109 lines changed: 0, context: html, text, full: html, text
    Making it so that multi-wigs can draw without overlay as well.
• src/hg/hgc/encodeClick.c
  • 1.16 lines changed: 52, context: html, text, full: html, text
    Working on details pages for DNase Clusters and Txn Factor ChIP tracks.
• src/hg/hgc/hgc.c
  • 1.1625 lines changed: 5, context: html, text, full: html, text
    Putting in page that shows all tracks that could contribute items to a cluster. Link to this page at the end of items in cluster table.
  • 1.1624 lines changed: 4, context: html, text, full: html, text
    Working on details pages for DNase Clusters and Txn Factor ChIP tracks.
  • 1.1623 lines changed: 4, context: html, text, full: html, text
    Adding handler for clustered-peaks like wgEncodeRegDnaseClustered
  • 1.1622 lines changed: 28, context: html, text, full: html, text
    Starting a generic click handler for containers. Not really useful now though since decided to just go straight to hgTrackUi for multiWigs.
  • 1.1621 lines changed: 1, context: html, text, full: html, text
    change how the two sequences are printed out for split aligns
• src/hg/hgc/hgc.h
  • 1.54 lines changed: 6, context: html, text, full: html, text
    Putting in page that shows all tracks that could contribute items to a cluster. Link to this page at the end of items in cluster table.
  • 1.53 lines changed: 7, context: html, text, full: html, text
    Working on details pages for DNase Clusters and Txn Factor ChIP tracks.
  • 1.52 lines changed: 3, context: html, text, full: html, text
    Adding handler for clustered-peaks like wgEncodeRegDnaseClustered
• src/hg/hgc/makefile
  • 1.67 lines changed: 4, context: html, text, full: html, text
    Adding handler for clustered-peaks like wgEncodeRegDnaseClustered
• src/hg/hgc/peakClusters.c
  • 1.3 lines changed: 119, context: html, text, full: html, text
    Putting in page that shows all tracks that could contribute items to a cluster. Link to this page at the end of items in cluster table.
  • 1.2 lines changed: 180, context: html, text, full: html, text
    Working on details pages for DNase Clusters and Txn Factor ChIP tracks.
  • 1.1 lines changed: 200, context: html, text, full: html, text
    Adding handler for clustered-peaks like wgEncodeRegDnaseClustered
• src/hg/inc/hui.h
  • 1.152 lines changed: 11, context: html, text, full: html, text
    implementing compositeGroupLabel and compositeGroupId functions, and exposing existing static function as compositeLabelWithVocabLink
  • 1.151 lines changed: 2, context: html, text, full: html, text
    Removing sum and product type aggregates from UI since they aren't implemented now, and may not be soon.
  • 1.150 lines changed: 6, context: html, text, full: html, text
    Adding stuff for aggregate/overlay dropdown.
• src/hg/inc/versionInfo.h
  • 1.172 lines changed: 1, context: html, text, full: html, text
    "New version number v231"
• src/hg/inc/wiggle.h
  • 1.91 lines changed: 1, context: html, text, full: html, text
    Adding stuff for aggregate/overlay dropdown.
• src/hg/instinct/bioInt2/populateDb.c
  • 1.14 lines changed: 10, context: html, text, full: html, text
    Added profile option for loading data, so we can use -profile=cancerPubDb
  • 1.13 lines changed: 15, context: html, text, full: html, text
    Removed sexCorrect and skipped X/Y on CNV only
• src/hg/js/ajax.js
  • 1.7 lines changed: 27, context: html, text, full: html, text
    Added setCartVars to set an array of names and values. Needed for inageV2 imgOrd
• src/hg/js/hgTracks.js
  • 1.68 lines changed: 11, context: html, text, full: html, text
    Got rid of imgOrd hidden inputs. This is set by ajax now.
• src/hg/js/hui.js
  • 1.53 lines changed: 104, context: html, text, full: html, text
    Supprt for new filterComposite
• src/hg/js/makefile
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Added ui.core and ui.dropdownchecklist to support composites with filter boxes
• src/hg/js/ui.core.js
  • 1.1 lines changed: 529, context: html, text, full: html, text
    Untouched from download. Needed for certain jquery plug-ins
• src/hg/js/ui.dropdownchecklist.js
  • 1.3 lines changed: 506, context: html, text, full: html, text
    Un-dos-ed this file
  • 1.2 lines changed: 14, context: html, text, full: html, text
    Added default message when no selection has been made is empty
  • 1.1 lines changed: 500, context: html, text, full: html, text
    Initial check-in of modified plug-in needed for filterComposite functionality
• src/hg/lib/gwasCatalog.as
  • 1.2 lines changed: 1, context: html, text, full: html, text
    replSample now needs to be lstring not just string.
• src/hg/lib/gwasCatalog.sql
  • 1.2 lines changed: 28, context: html, text, full: html, text
    replSample now needs to be lstring not just string.
• src/hg/lib/hdb.c
  • 1.427 lines changed: 1, context: html, text, full: html, text
    Fixing sprung-loose visibilities.
• src/hg/lib/hui.c
  • 1.288 lines changed: 39, context: html, text, full: html, text
    implementing compositeGroupLabel and compositeGroupId functions, and exposing existing static function as compositeLabelWithVocabLink
  • 1.287 lines changed: 718, context: html, text, full: html, text
    Support for new filterComosite. Rearranged and reworked the mebersForAll struct. Need to redo it as slLists.
  • 1.286 lines changed: 4, context: html, text, full: html, text
    Removing sum and product type aggregates from UI since they aren't implemented now, and may not be soon.
  • 1.285 lines changed: 35, context: html, text, full: html, text
    Adding stuff for aggregate/overlay dropdown.
• src/hg/lib/ntOoaHaplo.as
  • 1.1 lines changed: 19, context: html, text, full: html, text
    Candidate regions for gene flow from Neandertal to non-African modern humans (table 5 of Green et al. 2010).
• src/hg/lib/ntOoaHaplo.sql
  • 1.1 lines changed: 26, context: html, text, full: html, text
    Candidate regions for gene flow from Neandertal to non-African modern humans (table 5 of Green et al. 2010).
• src/hg/lib/trackDbCustom.c
  • 1.88 lines changed: 59, context: html, text, full: html, text
    Making overrides apply to settings rather than fields. Fields are recalculated from settings later by another routine.
• src/hg/makeDb/doc/calJac3.txt
  • 1.11 lines changed: 130, context: html, text, full: html, text
    Add gap annotation for multiz13way
  • 1.10 lines changed: 13, context: html, text, full: html, text
    adding fixes to dates to the makedoc
• src/hg/makeDb/doc/felCatV17e.txt
  • 1.14 lines changed: 267, context: html, text, full: html, text
    Conservation track
• src/hg/makeDb/doc/hg18.nt.txt
  • 1.1 lines changed: 472, context: html, text, full: html, text
    hg18.nt.txt
• src/hg/makeDb/doc/hg18.txt
  • 1.420 lines changed: 17, context: html, text, full: html, text
    Recreated Signal subtracks for Burge RNA-seq data. Used -bed12 option for bedItemOverlapCount to take the blocks into account.
  • 1.419 lines changed: 20, context: html, text, full: html, text
    hg18.nt.txt
  • 1.418 lines changed: 12, context: html, text, full: html, text
    Updated downloads for new CRG mapability data.
  • 1.417 lines changed: 12, context: html, text, full: html, text
    Updated gwasCatalog.
  • 1.416 lines changed: 84, context: html, text, full: html, text
    add retrogene track ucscRetroAli
• src/hg/makeDb/doc/hg19.txt
  • 1.112 lines changed: 13, context: html, text, full: html, text
    Recreated Signal subtracks for Burge RNA-seq data. Used -bed12 option for bedItemOverlapCount to take the blocks into account.
  • 1.111 lines changed: 1, context: html, text, full: html, text
    Minor edit.
  • 1.110 lines changed: 51, context: html, text, full: html, text
    Complete Affy_U95 track
  • 1.109 lines changed: 17, context: html, text, full: html, text
    Documented adding Mapability 24mer subtrack (CRG) to trackDb entry. Updated downloads for CRG Mapability subtracks.
  • 1.108 lines changed: 7, context: html, text, full: html, text
    Updated gwasCatalog.
  • 1.107 lines changed: 83, context: html, text, full: html, text
    add ucscRetroAli track for hg19
  • 1.106 lines changed: 58, context: html, text, full: html, text
    Add Affy_U133Plus2 track
  • 1.105 lines changed: 25, context: html, text, full: html, text
    Updated names of files and tables as all ENCODE tracks are to have wgEncode prefix.
• src/hg/makeDb/doc/mm9.txt
  • 1.137 lines changed: 82, context: html, text, full: html, text
    add retroGene track on mm9 ucscRetroAli
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.70 lines changed: 1, context: html, text, full: html, text
    Fixing a ->table that should be a ->track. Thanks Angie for spotting this.
  • 1.69 lines changed: 1, context: html, text, full: html, text
    Fixing composite tag search that should have been compositeTrack search.
  • 1.68 lines changed: 26, context: html, text, full: html, text
    Removing old code.
• src/hg/makeDb/schema/all.joiner
  • 1.801 lines changed: 5, context: html, text, full: html, text
    Adding bam% to tablesIgnored $gbd and Neandertal tracks to tablesIgnored $hg18.
  • 1.800 lines changed: 5, context: html, text, full: html, text
    rename ucscRetroAli4 to ucscRetroAli
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeAffyRnaChip.ra
  • 1.2 lines changed: 1873, context: html, text, full: html, text
    fixed problems with metadata
  • 1.1 lines changed: 0, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra
  • 1.1 lines changed: 11164, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBuOrchid.ra
  • 1.2 lines changed: 35, context: html, text, full: html, text
    fixed problems with metadata
  • 1.1 lines changed: 0, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • 1.2 lines changed: 4037, context: html, text, full: html, text
    add metadata from fileDb.ra in download dirs
  • 1.1 lines changed: 3043, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • 1.1 lines changed: 12139, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • 1.1 lines changed: 480, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • 1.1 lines changed: 982, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeDukeAffyExonArray.ra
  • 1.1 lines changed: 1045, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisDnaPet.ra
  • 1.1 lines changed: 579, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisPet.ra
  • 1.2 lines changed: 825, context: html, text, full: html, text
    add metadata from fileDb.ra in download dirs
  • 1.1 lines changed: 1484, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • 1.1 lines changed: 445, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHelicosRnaSeq.ra
  • 1.1 lines changed: 55, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Fix one inputType
  • 1.2 lines changed: 194, context: html, text, full: html, text
    Arrival of some missing fastqs for hg18
  • 1.1 lines changed: 16385, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaCnv.ra
  • 1.1 lines changed: 103, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethyl27.ra
  • 1.1 lines changed: 97, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra
  • 1.1 lines changed: 1611, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaRnaSeq.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    hopefully updating to the right value
  • 1.1 lines changed: 279, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeRikenCage.ra
  • 1.2 lines changed: 397, context: html, text, full: html, text
    add metadata from fileDb.ra in download dirs
  • 1.1 lines changed: 1044, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSangerGencode.ra
  • 1.2 lines changed: 55, context: html, text, full: html, text
    fixed problems with metadata
  • 1.1 lines changed: 0, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSunyalbanyRnaGeneChip.ra
  • 1.1 lines changed: 134, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • 1.1 lines changed: 12796, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDGF.ra
  • 1.1 lines changed: 469, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
  • 1.1 lines changed: 7608, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • 1.1 lines changed: 24601, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeBroadChipSeq.ra
  • 1.2 lines changed: 11164, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeChromatinMap.ra
  • 1.2 lines changed: 12139, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeHudsonalphaChipSeq.ra
  • 1.2 lines changed: 16385, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeHudsonalphaRnaSeq.ra
  • 1.3 lines changed: 279, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeUwChIPSeq.ra
  • 1.2 lines changed: 12796, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeUwDGF.ra
  • 1.2 lines changed: 469, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeUwDnaseSeq.ra
  • 1.2 lines changed: 7608, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeYaleChIPseq.ra
  • 1.2 lines changed: 24601, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/trackDb.cancer2.ra
  • 1.5 lines changed: 74, context: html, text, full: html, text
    remove ispy track from trackDb.cancer2.ra
• src/hg/makeDb/trackDb/human/hg18/trackDb.genome-cancer.ra
  • 1.13 lines changed: 23, context: html, text, full: html, text
    Removed broken tracks
  • 1.12 lines changed: 370, context: html, text, full: html, text
    Updated tracks and put in dbProfile to get working with the browser again
  • 1.11 lines changed: 26, context: html, text, full: html, text
    Changed from logicalDb to dbProfile flag
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.487 lines changed: 170, context: html, text, full: html, text
    Moving wgEncodeReg track and subtracks to hg18/trackDb.wgEncode.ra from hg18/trackDb.ra. Also starting on a couple of the html descriptions - just a bare start.
  • 1.486 lines changed: 3, context: html, text, full: html, text
    Adding inputTracks tags to wgEncodeReg DNAse component
  • 1.485 lines changed: 83, context: html, text, full: html, text
    More tinkering on encode regulation track.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.974 lines changed: 5, context: html, text, full: html, text
    Changed file names in beta release metadata for CRG Mapability subtracks.
  • 1.973 lines changed: 5, context: html, text, full: html, text
    Changed file names in alpha release metadata for CRG Mapability subtracks.
  • 1.972 lines changed: 21, context: html, text, full: html, text
    Removed release restrictions on UW DNase DGF track.
  • 1.971 lines changed: 3, context: html, text, full: html, text
    Adding inputTracks* tags to another wgEncodeReg track.
  • 1.970 lines changed: 172, context: html, text, full: html, text
    Moving wgEncodeReg track and subtracks to hg18/trackDb.wgEncode.ra from hg18/trackDb.ra. Also starting on a couple of the html descriptions - just a bare start.
  • 1.969 lines changed: 2, context: html, text, full: html, text
    move RikenCage includes to the new policy
  • 1.968 lines changed: 1336, context: html, text, full: html, text
    Removed metadata lines from Yale and HAIB. Added filterComposite to HAIB TFBS
  • 1.967 lines changed: 5, context: html, text, full: html, text
    add color to H1hesc for GIS RNA-seq
  • 1.966 lines changed: 5, context: html, text, full: html, text
    made cell line in some Yale TFBS shortLables more distinct; shorted a Yale TFBS shortLable
  • 1.965 lines changed: 5, context: html, text, full: html, text
    taking LongPolyA+ out of the sort order and dimensions since it is always set in the data for GIS RNA-seq
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • 1.11 lines changed: 2, context: html, text, full: html, text
    add information about the clustering process
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html
  • 1.8 lines changed: 6, context: html, text, full: html, text
    add some more text about the alignments to describe their color
  • 1.7 lines changed: 18, context: html, text, full: html, text
    Edits to method section, mainly punctuation and spacing
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegDnaseClustered.html
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Moving wgEncodeReg track and subtracks to hg18/trackDb.wgEncode.ra from hg18/trackDb.ra. Also starting on a couple of the html descriptions - just a bare start.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhancer.html
  • 1.1 lines changed: 3, context: html, text, full: html, text
    Moving wgEncodeReg track and subtracks to hg18/trackDb.wgEncode.ra from hg18/trackDb.ra. Also starting on a couple of the html descriptions - just a bare start.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
  • 1.18 lines changed: 2, context: html, text, full: html, text
    change Alignments view to be called Tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.new.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    change alignments view to Tags view
  • 1.1 lines changed: 721, context: html, text, full: html, text
    conform to the threeStateTrackDb naming scheme
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.ra
  • 1.1 lines changed: 699, context: html, text, full: html, text
    conform to the threeStateTrackDb naming scheme
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • 1.1 lines changed: 1399, context: html, text, full: html, text
    add these in the alpha dir
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • 1.1 lines changed: 467, context: html, text, full: html, text
    add these in the alpha dir
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • 1.1 lines changed: 2639, context: html, text, full: html, text
    add these in the alpha dir
• src/hg/makeDb/trackDb/human/hg19/metaDb/wgEncodeHaibTfbs.ra
  • 1.3 lines changed: 1399, context: html, text, full: html, text
    moving these down to the alpha directory
  • 1.2 lines changed: 231, context: html, text, full: html, text
    HAIB TFBS: Added Metadata for submission 1189 (Control's for cell lines)
• src/hg/makeDb/trackDb/human/hg19/metaDb/wgEncodeSydhHistone.ra
  • 1.2 lines changed: 467, context: html, text, full: html, text
    moving these down to the alpha directory
• src/hg/makeDb/trackDb/human/hg19/metaDb/wgEncodeSydhTfbs.ra
  • 1.3 lines changed: 2639, context: html, text, full: html, text
    moving these down to the alpha directory
  • 1.2 lines changed: 135, context: html, text, full: html, text
    SYDH TFBS: Updated MetaDb to include information from new submission 1190
• src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra
  • 1.21 lines changed: 1331, context: html, text, full: html, text
    moving this to trackDb.wgEncode.ra
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.118 lines changed: 1, context: html, text, full: html, text
    Changed include to new ENCODE trackDb filename.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • 1.8 lines changed: 75, context: html, text, full: html, text
    HAIB TFBS: Added 5 new tracks from submission 1189 (Control) experiments of cell lines. Updated Data Matrix to include new dimensions.
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Corrected filename.
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Changed data version for CRG Mapability 36mer track as it was produced in January.
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Changed file names back to gzipped version as these refer to downloads.
  • 1.4 lines changed: 18, context: html, text, full: html, text
    Added subtrack entry for CRG 24mers in Mapability track. Updated file names in metadata.
  • 1.3 lines changed: 21, context: html, text, full: html, text
    SYDH TFBS: Added Peak and Signal tracks to include new submission 1190
  • 1.2 lines changed: 16, context: html, text, full: html, text
    Updated Mapability track and subtrack names to have the wgEncode prefix instead of enc.
  • 1.1 lines changed: 1331, context: html, text, full: html, text
    moving trackDb.enc.ra to here
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.html
  • 1.1 lines changed: 49, context: html, text, full: html, text
    Changed name of the Mapability track, used to be encMapability.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.534 lines changed: 1, context: html, text, full: html, text
    Adjusting some visibilities
• src/hg/makeDb/trackDb/mouse/mm9/mdbSydhHistone.ra
  • 1.1 lines changed: 67, context: html, text, full: html, text
    Meta data information for Sydh Histone track.
• src/hg/makeDb/trackDb/mouse/mm9/mdbSydhTfbs.ra
  • 1.1 lines changed: 551, context: html, text, full: html, text
    The meta data tables for the Sydh Tfbs for mm9
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.enc.ra
  • 1.10 lines changed: 423, context: html, text, full: html, text
    moved to trackDb.wgEncode.ra
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.92 lines changed: 1, context: html, text, full: html, text
    moved trackDb.enc.ra to trackDb.wgEncode.ra
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • 1.1 lines changed: 423, context: html, text, full: html, text
    moved from trackDb.enc.ra
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.html
  • 1.1 lines changed: 49, context: html, text, full: html, text
    Track descriptions for mm9 SYDH Histones. This is our first draft.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
  • 1.1 lines changed: 160, context: html, text, full: html, text
    Track description first draft for mm9 TFBS.
• src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
  • 1.28 lines changed: 1, context: html, text, full: html, text
    changing shortLabel to be organism for monDom5
• src/hg/makeDb/trackDb/pig/susScr2/description.html
  • 1.4 lines changed: 4, context: html, text, full: html, text
    editing example to be more pig centric
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.23 lines changed: 3, context: html, text, full: html, text
    Adding factorSource to inputTracks*
  • 1.22 lines changed: 23, context: html, text, full: html, text
    Adding setting that are used by customTracks to reserve them, and hopefully avoid conflicts in the figure like we had with 'dataUrl' which had to be renamed at some cost to 'bigDataUrl'
  • 1.21 lines changed: 1, context: html, text, full: html, text
    Added dbProfile flag
  • 1.20 lines changed: 5, context: html, text, full: html, text
    Supprt for new filterComposite
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.631 lines changed: 1, context: html, text, full: html, text
    Adjusting some visibilities
• src/hg/regulate/regCluster/regCluster.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Putting in something so that multiple peaks in the same cluster from the same source don't get counted twice.
• src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
  • 1.4 lines changed: 3, context: html, text, full: html, text
    moving literal 6 to variable scoreColIx
• src/hg/wikiMods/README
  • 1.4 lines changed: 3, context: html, text, full: html, text
    add 1.13.0 URL
• src/inc/genoFind.h
  • 1.83 lines changed: 1, context: html, text, full: html, text
    Dealing with primers that match but dangle off the ends of the chrom
• src/inc/obscure.h
  • 1.37 lines changed: 1, context: html, text, full: html, text
    Fixed small typo in parameter name in function prototype.
• src/jkOwnLib/gfPcrLib.c
  • 1.13 lines changed: 38, context: html, text, full: html, text
    Dealing with primers that match but dangle off the ends of the chrom
• src/lib/cheapcgi.c
  • 1.135 lines changed: 6, context: html, text, full: html, text
    Got rid of unused CSS class that was causing errors.
• src/lib/pipeline.c
  • 1.25 lines changed: 1, context: html, text, full: html, text
    explictly ignore read status to keep certain version of GCC happy
• src/lib/sqlNum.c
  • 1.17 lines changed: 4, context: html, text, full: html, text
    invalid number is actually invalid integer
• src/product/ex.hg.conf
  • 1.26 lines changed: 1, context: html, text, full: html, text
    maybe is may be
  • 1.25 lines changed: 55, context: html, text, full: html, text
    added info on configuring dbProfiles
• src/utils/qa/retirePushQ.csh
  • 1.11 lines changed: 4, context: html, text, full: html, text
    dealing with tcsh number handling for leading zeros
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.113 lines changed: 3, context: html, text, full: html, text
    v231 final build
• src/utils/qa/weeklybld/buildHgCentralSql.csh
  • 1.21 lines changed: 21, context: html, text, full: html, text
    Updated the notes echoed at the end to reflect the automatic copy to hgdownload.

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• files changed: 125