All File Changes

v240_base to v241_preview (2010-09-14 to 2010-09-21) v241

• src/hg/checkTableCoords/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    Fixing csh syntax that snuck into makefile -- Ubuntu bash complained.
• src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf
  • lines changed 11, context: html, text, full: html, text
    bringing the DAFs up to the most recent submissions
  • lines changed 15, context: html, text, full: html, text
    adding labProtocolId for Transcriptome Labs
  • lines changed 2, context: html, text, full: html, text
    unretiring order from fields.ra as it causes doEncodeValidate to fail, add comment on line where I think it needs to be fixed
• src/hg/encode/DAFs/2.0/rikenCageSolexa.daf
  • lines changed 3, context: html, text, full: html, text
    bringing the DAFs up to the most recent submissions
  • lines changed 21, context: html, text, full: html, text
    unretiring order from fields.ra as it causes doEncodeValidate to fail, add comment on line where I think it needs to be fixed
• src/hg/encode/DAFs/2.0/stanfordChipSeq.daf
  • lines changed 1, context: html, text, full: html, text
    retiring the term dataAgreementSuffix from all DAFs and fields.ra
• src/hg/encode/DAFs/2.0/stanfordHg19HistInput.daf
  • lines changed 1, context: html, text, full: html, text
    retiring the term dataAgreementSuffix from all DAFs and fields.ra
• src/hg/encode/DAFs/2.0/stanfordHg19Tfbs.daf
  • lines changed 1, context: html, text, full: html, text
    retiring the term dataAgreementSuffix from all DAFs and fields.ra
• src/hg/encode/DAFs/2.0/stanfordHg19TfbsInput.daf
  • lines changed 1, context: html, text, full: html, text
    retiring the term dataAgreementSuffix from all DAFs and fields.ra
• src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf
  • lines changed 1, context: html, text, full: html, text
    retiring the term dataAgreementSuffix from all DAFs and fields.ra
• src/hg/encode/DAFs/2.0/stanfordMm9TfbsInput.daf
  • lines changed 1, context: html, text, full: html, text
    retiring the term dataAgreementSuffix from all DAFs and fields.ra
• src/hg/encode/DAFs/2.0/stanfordNucleosome.daf
  • lines changed 1, context: html, text, full: html, text
    retiring the term dataAgreementSuffix from all DAFs and fields.ra
• src/hg/encode/DAFs/2.0/ucDHg19Hist.daf
  • lines changed 1, context: html, text, full: html, text
    retiring the term dataAgreementSuffix from all DAFs and fields.ra
• src/hg/encode/encodeMdbToDdf/makefile
  • lines changed 1, context: html, text, full: html, text
    fixed path for make
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    added some more datatypes for Caltech data
• src/hg/encode/encodeMkGeoPkg/README.txt
  • lines changed 33, context: html, text, full: html, text
    Process documentation started for GEO packager
• src/hg/encode/encodeMkGeoPkg/encodeAddAccessions
  • lines changed 114, context: html, text, full: html, text
    first draft of script to import GEO accession numbers into the metaDb table
  • lines changed 114, context: html, text, full: html, text
    added Geo to script name
• src/hg/encode/encodeMkGeoPkg/encodeAddGeoAccessions
  • lines changed 114, context: html, text, full: html, text
    added Geo to script name
• src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
  • lines changed 104, context: html, text, full: html, text
    added another spelling of ChIP-seq
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 3, context: html, text, full: html, text
    Minor tweaks to labels for NHGRI reporting
  • lines changed 5, context: html, text, full: html, text
    Renamed the term G1E_ER4+E2 to G1E-ER4+E2
  • lines changed 15, context: html, text, full: html, text
    remove the rnaExtract terms that were not used at Carrie Davis request
  • lines changed 29, context: html, text, full: html, text
    Added new Hardison lab antibodies and validation documents
  • lines changed 63, context: html, text, full: html, text
    Redid type dataType: draft 2
  • lines changed 3, context: html, text, full: html, text
    changed DGF to DNaseDgf
• src/hg/encode/encodeValidate/config/expVars.ra
  • lines changed 10, context: html, text, full: html, text
    added exp. vars. for wgEncodeUwChIPSeq
• src/hg/encode/encodeValidate/config/fields.ra
  • lines changed 52, context: html, text, full: html, text
    Retiring fields that are not being used anymore, they are commented out for now for wrangler retraining purposes
  • lines changed 5, context: html, text, full: html, text
    retiring the term dataAgreementSuffix from all DAFs and fields.ra
  • lines changed 8, context: html, text, full: html, text
    adding labProtocolId for Transcriptome Labs
  • lines changed 5, context: html, text, full: html, text
    unretiring order from fields.ra as it causes doEncodeValidate to fail, add comment on line where I think it needs to be fixed
  • lines changed 13, context: html, text, full: html, text
    Added medianFragLength and fragLengthRange such that HAIB lab will be able to continue to submit data.
  • lines changed 5, context: html, text, full: html, text
    Unretireing noAutoCreate, it was hard coded in doEncodeValidate
  • lines changed 11, context: html, text, full: html, text
    added geoSample and geoSeries to store accession numbers from GEO
  • lines changed 6, context: html, text, full: html, text
    added term for experiment defining variables for composites
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    unretiring order from fields.ra as it causes doEncodeValidate to fail, add comment on line where I think it needs to be fixed
  • lines changed 1, context: html, text, full: html, text
    Changed the if statement about noAutoCreate as we are not auto creating any longer
  • lines changed 1, context: html, text, full: html, text
    Changing the if statement to check existance of noAutoCreate variable first
• src/hg/encode/encodeValidate/manual.all.txt
  • lines changed 4, context: html, text, full: html, text
    update Gencode
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCaltechRnaSeq.soft
  • lines changed 1712, context: html, text, full: html, text
    added first two SOFT files
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeUwChIPSeq.soft
  • lines changed 4436, context: html, text, full: html, text
    added first two SOFT files
• src/hg/hgTables/great.c
  • lines changed 1, context: html, text, full: html, text
    Fixing warning messages from gcc Ubuntu 4.4.1-4ubuntu9.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 17, context: html, text, full: html, text
    Fixed tdbVisLimitedByAncestry which caused supertrack contained and visibble tracks to appear hidden in findTracks. Added composite/view vis reshaping based upon subtrack specific vis.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    Fixing warning messages from gcc Ubuntu 4.4.1-4ubuntu9.
  • lines changed 45, context: html, text, full: html, text
    SuperTracks may have superpowers, but still should avoiding cloning kids.
  • lines changed 2, context: html, text, full: html, text
    Fixed problem with uncalled static function.
• src/hg/hgTracks/imageV2.c
  • lines changed 1, context: html, text, full: html, text
    add a NULL test to fix a problem when hitting "hide all"
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    fix problem with hitting Enter in IE and Safari
• src/hg/hgTracks/searchTracks.c
  • lines changed 28, context: html, text, full: html, text
    add help links; code cleanup
  • lines changed 2, context: html, text, full: html, text
    fix problem with hitting Enter in IE and Safari
  • lines changed 1, context: html, text, full: html, text
    Fixing warning messages from gcc Ubuntu 4.4.1-4ubuntu9.
  • lines changed 1, context: html, text, full: html, text
    Added hgsid hidden var because I think the lack of it was causing problems
  • lines changed 9, context: html, text, full: html, text
    Fixed tdbVisLimitedByAncestry which caused supertrack contained and visibble tracks to appear hidden in findTracks. Added composite/view vis reshaping based upon subtrack specific vis.
  • lines changed 4, context: html, text, full: html, text
    superTrack children also need the _sel button
  • lines changed 1, context: html, text, full: html, text
    fix wonky metadata select when the user deleted the second from last metadata item
  • lines changed 1, context: html, text, full: html, text
    missed a cloneString in last checkin
• src/hg/hgc/encodeClick.c
  • lines changed 2, context: html, text, full: html, text
    Fixing warning messages from gcc Ubuntu 4.4.1-4ubuntu9.
• src/hg/hgc/hgc.c
  • lines changed 9, context: html, text, full: html, text
    add transcriptType to Gencode hgc page
  • lines changed 14, context: html, text, full: html, text
    use safecpy, safecat and chopSuffixAt
  • lines changed 86, context: html, text, full: html, text
    move the pal link for refGene down into "links to sequence"
• src/hg/hgc/peakClusters.c
  • lines changed 6, context: html, text, full: html, text
    Fixing warning messages from gcc Ubuntu 4.4.1-4ubuntu9.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 7, context: html, text, full: html, text
    added hg19 Gencode Genes
• src/hg/htdocs/ENCODE/index.html
  • lines changed 101, context: html, text, full: html, text
    adding Genome Browser link to hg19 on ENCODE portal; adding News item for release of first couple ENCODE tracks on hg19; added older news items to news archives
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 96, context: html, text, full: html, text
    adding Genome Browser link to hg19 on ENCODE portal; adding News item for release of first couple ENCODE tracks on hg19; added older news items to news archives
• src/hg/htdocs/admin/mirror.html
  • lines changed 9, context: html, text, full: html, text
    Add license information
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 7, context: html, text, full: html, text
    Fixed a few links.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 50, context: html, text, full: html, text
    Adding drag reorder announcement to news page, minimizing most recent post and removing last post
• src/hg/htdocs/indexNews.html
  • lines changed 52, context: html, text, full: html, text
    Adding drag reorder announcement to news page, minimizing most recent post and removing last post
• src/hg/htdocs/mirror.html
  • lines changed 7, context: html, text, full: html, text
    Add license information
• src/hg/inc/cart.h
  • lines changed 17, context: html, text, full: html, text
    Fixed tdbVisLimitedByAncestry which caused supertrack contained and visibble tracks to appear hidden in findTracks. Added composite/view vis reshaping based upon subtrack specific vis.
• src/hg/inc/hui.h
  • lines changed 5, context: html, text, full: html, text
    Fixed tdbVisLimitedByAncestry which caused supertrack contained and visibble tracks to appear hidden in findTracks. Added composite/view vis reshaping based upon subtrack specific vis.
• src/hg/inc/trackDb.h
  • lines changed 14, context: html, text, full: html, text
    Composite views needed to be distinguished from subtracks
  • lines changed 4, context: html, text, full: html, text
    Fixed tdbVisLimitedByAncestry which caused supertrack contained and visibble tracks to appear hidden in findTracks. Added composite/view vis reshaping based upon subtrack specific vis.
  • lines changed 2, context: html, text, full: html, text
    SuperTracks may have superpowers, but still should avoiding cloning kids.
• src/hg/js/hgTracks.js
  • lines changed 7, context: html, text, full: html, text
    fix problem with hitting Enter in IE and Safari
  • lines changed 26, context: html, text, full: html, text
    Added back in findTracksChangeVis() which never should have been dropped
  • lines changed 6, context: html, text, full: html, text
    check for null trackDbJson in makeMapItem to fix errors in console logs when CONTEXT_MENU is turned off
  • lines changed 25, context: html, text, full: html, text
    superTrack children also need the _sel button
  • lines changed 10, context: html, text, full: html, text
    special case "Click to alter" map items
  • lines changed 1, context: html, text, full: html, text
    Minus all didn't work correctly on non-subtracks
• src/hg/js/hui.js
  • lines changed 2, context: html, text, full: html, text
    Larry suggested where my history bug might be. Now subtrack cfg popups in hgTrackUi does not affect history.
• src/hg/lib/cart.c
  • lines changed 286, context: html, text, full: html, text
    Fixed tdbVisLimitedByAncestry which caused supertrack contained and visibble tracks to appear hidden in findTracks. Added composite/view vis reshaping based upon subtrack specific vis.
  • lines changed 79, context: html, text, full: html, text
    SuperTracks may have superpowers, but still should avoiding cloning kids.
• src/hg/lib/hdb.c
  • lines changed 4, context: html, text, full: html, text
    Composite views needed to be distinguished from subtracks
• src/hg/lib/hui.c
  • lines changed 33, context: html, text, full: html, text
    Fixed tdbVisLimitedByAncestry which caused supertrack contained and visibble tracks to appear hidden in findTracks. Added composite/view vis reshaping based upon subtrack specific vis.
• src/hg/lib/mafGene.c
  • lines changed 1, context: html, text, full: html, text
    take out wayward space
• src/hg/lib/trackDbCustom.c
  • lines changed 39, context: html, text, full: html, text
    Fixed tdbVisLimitedByAncestry which caused supertrack contained and visibble tracks to appear hidden in findTracks. Added composite/view vis reshaping based upon subtrack specific vis.
  • lines changed 24, context: html, text, full: html, text
    SuperTracks may have superpowers, but still should avoiding cloning kids.
• src/hg/makeDb/doc/bruMal1.txt
  • lines changed 49, context: html, text, full: html, text
    initial Brugia malayi browser build
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 94, context: html, text, full: html, text
    finished download files
• src/hg/makeDb/doc/ce9.txt
  • lines changed 75, context: html, text, full: html, text
    added sanger RNA and Pseudo gene tracks
  • lines changed 457, context: html, text, full: html, text
    coming to a close on sangerGene and geneSorter construction
  • lines changed 190, context: html, text, full: html, text
    have sanger gene tables with names fixed
  • lines changed 2, context: html, text, full: html, text
    have sanger gene tables with names fixed
  • lines changed 81, context: html, text, full: html, text
    adding sangerGeneToWBGeneID table
  • lines changed 37, context: html, text, full: html, text
    donw with chainSelf
• src/hg/makeDb/doc/dm2.txt
  • lines changed 5, context: html, text, full: html, text
    Redmine Track #671 (BDTNP for dm2): Loading up corrected data file emailed from Mark Biggin. Hopefully this completes the track update.
• src/hg/makeDb/doc/dm3.txt
  • lines changed 2, context: html, text, full: html, text
    Redmine Track #671 (BDTNP for dm2): Loading up corrected data file emailed from Mark Biggin. Hopefully this completes the track update.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 104, context: html, text, full: html, text
    Redmine Track #1079 (1000 Genomes Coverage Masks)
  • lines changed 45, context: html, text, full: html, text
    Redmine Track #1100 (HGDP: correct for strand or fix hgdpGeo.as) / MLQ #1097 (HGDP SNP data). It was actually pretty easy to normalize items to + strand using the SNP reference allele, and remap to snp130 at the same time.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 53, context: html, text, full: html, text
    Redmine Track #1092 (HGDP Allele Freq on hg19): used hg19.snp131 to map hgdpGeo RS IDs, and used script tweak from #1100.
• src/hg/makeDb/doc/melHap1.txt
  • lines changed 52, context: html, text, full: html, text
    initial sequence for Meloidogyne hapla - Root Knot nematode
• src/hg/makeDb/doc/melInc1.txt
  • lines changed 49, context: html, text, full: html, text
    initial sequence for Meloidogyne incognita WS210
• src/hg/makeDb/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    add a few relationships for Gencode V4
  • lines changed 3, context: html, text, full: html, text
    adding ce9
  • lines changed 2, context: html, text, full: html, text
    some exceptions for ce9
  • lines changed 1, context: html, text, full: html, text
    incorrect character on a ce9 definition
  • lines changed 2, context: html, text, full: html, text
    Updated $mm to $hg for hg19 hgIkmc track.
  • lines changed 4, context: html, text, full: html, text
    Corrected wrong update to all.joiner
• src/hg/makeDb/trackDb/human/covMask1kGPilotLowCov.html
  • lines changed 71, context: html, text, full: html, text
    Redmine Track #1079 (1000 Genomes Coverage Masks)
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 540, context: html, text, full: html, text
    added GEO samples and series accessions to CAltech RNA-seq
  • lines changed 1, context: html, text, full: html, text
    added exp vars for wgEncodeCaltechRnaSeq
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 50, context: html, text, full: html, text
    change SKN-SH-RA to HTB-11
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 3507, context: html, text, full: html, text
    Changed the Yale metaDB to remove relaoded, chromstart, errors in dates, etc
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    new HudsonAlpha ChIP-seq
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
  • lines changed 386, context: html, text, full: html, text
    changing SK-N-SHRA to HTB-11
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 362, context: html, text, full: html, text
    added release beta,public
• src/hg/makeDb/trackDb/human/hg18/wgEncodeReg.html
  • lines changed 1, context: html, text, full: html, text
    fixed incorrect reference to Restricted Until column
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 734, context: html, text, full: html, text
    standardize the RNA-seq references
  • lines changed 346, context: html, text, full: html, text
    changing dataType to be consistent
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 44, context: html, text, full: html, text
    changing dataType to be consistent
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 193, context: html, text, full: html, text
    fix up some table and file names
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 60, context: html, text, full: html, text
    changing dataType to be consistent
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 37, context: html, text, full: html, text
    removing Chipseq
  • lines changed 127, context: html, text, full: html, text
    consolidated UCD names from UCDavis UC Davis UCD to UCD(Farnham)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 3, context: html, text, full: html, text
    staged wgEncodeGisRnaSeq metaDb on beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaSeq.ra
  • lines changed 257, context: html, text, full: html, text
    staged wgEncodeGisRnaSeq metaDb on beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    getting metaDb on public in preparation for release of Gencode Genes
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGencode.ra
  • lines changed 99, context: html, text, full: html, text
    getting metaDb on public in preparation for release of Gencode Genes
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisDnaPet.ra
  • lines changed 121, context: html, text, full: html, text
    copied file over for release to the RR
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.html
  • lines changed 7, context: html, text, full: html, text
    fixed katrinas requests in redmine ticket 44
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
  • lines changed 5, context: html, text, full: html, text
    fixed katrinas requests in redmine ticket 44
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.ra
  • lines changed 8, context: html, text, full: html, text
    add search method for 2wayConsPseudo track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 68, context: html, text, full: html, text
    staging on beta
  • lines changed 68, context: html, text, full: html, text
    removed the release alpha,beta tags accidentally changed it on the wrong track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 12, context: html, text, full: html, text
    staging on hgwbeta
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 6, context: html, text, full: html, text
    change table names for different metadata
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
  • lines changed 186, context: html, text, full: html, text
    Updated track description page.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 91, context: html, text, full: html, text
    Redmine Track #1079 (1000 Genomes Coverage Masks)
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding bruMal1 to the build
  • lines changed 1, context: html, text, full: html, text
    initial sequence for Meloidogyne hapla - Root Knot nematode
  • lines changed 1, context: html, text, full: html, text
    initial sequence for Meloidogyne incognita WS210
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 20, context: html, text, full: html, text
    Changed conservation and most conserved tracks to use views on release beta . . . the addition of the phyloP track means there are too many tracks to work without views.
• src/hg/makeDb/trackDb/worm/bruMal1/description.html
  • lines changed 129, context: html, text, full: html, text
    initial Brugia malayi browser build
• src/hg/makeDb/trackDb/worm/bruMal1/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial Brugia malayi browser build
• src/hg/makeDb/trackDb/worm/bruMal1/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial Brugia malayi browser build
• src/hg/makeDb/trackDb/worm/bruMal1/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    initial Brugia malayi browser build
• src/hg/makeDb/trackDb/worm/ce9/trackDb.ra
  • lines changed 21, context: html, text, full: html, text
    adding sangerRnaGene and sangerPseudoGene
  • lines changed 11, context: html, text, full: html, text
    adding chainSelf
• src/hg/makeDb/trackDb/worm/melHap1/description.html
  • lines changed 129, context: html, text, full: html, text
    initial sequence for Meloidogyne hapla - Root Knot nematode
• src/hg/makeDb/trackDb/worm/melHap1/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial sequence for Meloidogyne hapla - Root Knot nematode
• src/hg/makeDb/trackDb/worm/melHap1/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial sequence for Meloidogyne hapla - Root Knot nematode
• src/hg/makeDb/trackDb/worm/melHap1/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    initial sequence for Meloidogyne hapla - Root Knot nematode
• src/hg/makeDb/trackDb/worm/melInc1/description.html
  • lines changed 129, context: html, text, full: html, text
    initial sequence for Meloidogyne incognita WS210
• src/hg/makeDb/trackDb/worm/melInc1/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial sequence for Meloidogyne incognita WS210
• src/hg/makeDb/trackDb/worm/melInc1/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial sequence for Meloidogyne incognita WS210
• src/hg/makeDb/trackDb/worm/melInc1/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    initial sequence for Meloidogyne incognita WS210
• src/hg/orthoMap/orthoPickIntron.c
  • lines changed 1, context: html, text, full: html, text
    Fixing warning messages from gcc Ubuntu 4.4.1-4ubuntu9.
• src/hg/protein/pbCalResStdGlobal/pbCalResStdGlobal.c
  • lines changed 8, context: html, text, full: html, text
    Fixing warning messages from gcc Ubuntu 4.4.1-4ubuntu9.
• src/hg/utils/automation/Encode.pm
  • lines changed 1, context: html, text, full: html, text
    unretiring order from fields.ra as it causes doEncodeValidate to fail, add comment on line where I think it needs to be fixed
• src/hg/utils/mutationClassifier/mutationClassifier.c
  • lines changed 18, context: html, text, full: html, text
    switch to using nibTwoCache per markd's suggestion
  • lines changed 141, context: html, text, full: html, text
    support additional geneModels (refGene and ensGene); modify intersectBeds to use binKeeper; this fixes a problem when using gene models with overlapping items
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    Typo fix: KNETFILE_HOOKS needs an S at the end.
• src/lib/bwgCreate.c
  • lines changed 1, context: html, text, full: html, text
    allow start = chromSize boundary condition
• src/product/README.install
  • lines changed 2, context: html, text, full: html, text
    trash symlink not needed in cgi-bin
• src/product/scripts/browserEnvironment.txt
  • lines changed 2, context: html, text, full: html, text
    samtools is on version 0.1.8 now
• src/product/scripts/loadDb.sh
  • lines changed 2, context: html, text, full: html, text
    fixups to be more neutral for Mac utilities
  • lines changed 0, context: html, text, full: html, text
    fixups to be more neutral for Mac utilities
• src/product/scripts/updateHtml.sh
  • lines changed 5, context: html, text, full: html, text
    better exclude statements
• src/utils/git-reports/git-reports.c
  • lines changed 1, context: html, text, full: html, text
    Fixing warning messages from gcc Ubuntu 4.4.1-4ubuntu9.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v241 preview
• src/weblet/counter/makefile
  • lines changed 1, context: html, text, full: html, text
    properly use EXE extension

• lines changed: 17793
• files changed: 173