All File Changes

v245_preview to v245_preview2 (2010-12-14 to 2010-12-21) v245

• src/ameme/ameme.c
  • lines changed 9, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/hg/checkTableCoords/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    add -noHistory option to hgLoadPsl for use in tests (#25)
• src/hg/dbTrash/dbTrash.c
  • lines changed 1, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/encode/DAFs/2.0/cshlSupportDocs.daf
  • lines changed 37, context: html, text, full: html, text
    Added a new DAF for all of CSHL support documentation
• src/hg/encode/DAFs/2.0/uChicagoTfbs.daf
  • lines changed 63, context: html, text, full: html, text
    First cut DAF for White lab ARRA grant (TFBS by epitope-tag chIP-seq)
• src/hg/encode/DAFs/2.0/ydhrRnaSeq.daf
  • lines changed 10, context: html, text, full: html, text
    changed DAF to have .bigWig not bedgraph
• src/hg/encode/docId/docIdView/docIdView.c
  • lines changed 2, context: html, text, full: html, text
    don't try to validate metadata
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • lines changed 172, context: html, text, full: html, text
    Added sort option. However, the hgFileUi CGI should really be used if a sortable downloads page is desired.
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 2, context: html, text, full: html, text
    change RR path for C' and D sections as per #2100
• src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
  • lines changed 17, context: html, text, full: html, text
    added support DGF (treated as DNase) and made provider optional (gives warning)
• src/hg/encode/encodeMkGeoPkg/makefile
  • lines changed 2, context: html, text, full: html, text
    fixed makefile
• src/hg/encode/encodeValidate/config/expVars.ra
  • lines changed 3, context: html, text, full: html, text
    added vars for wgEncodeHudsonalphaMethylSeq
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 87, context: html, text, full: html, text
    validate narrowPeak and broadPeak files with chromInfo files set by sex
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlShortRnaSeq.hg19.soft
  • lines changed 407, context: html, text, full: html, text
    added SOFT file for hg19.wgEncodeCshlShortRnaSeq
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 4, context: html, text, full: html, text
    add routine to let validateFiles check for the signature at the beginning and end of bigWigs
  • lines changed 6, context: html, text, full: html, text
    support -1 for peak value in narrowPeak file
• src/hg/fastaToPsl/fastaToPsl.c
  • lines changed 86, context: html, text, full: html, text
    first draft of FASTA pair alignment to PSL converter
  • lines changed 86, context: html, text, full: html, text
    fixed size bugs and makefile bug
• src/hg/fastaToPsl/makefile
  • lines changed 24, context: html, text, full: html, text
    first draft of FASTA pair alignment to PSL converter
  • lines changed 24, context: html, text, full: html, text
    fixed size bugs and makefile bug
• src/hg/fastaToPsl/tests/input/fa_seq_align.fa
  • lines changed 4, context: html, text, full: html, text
    test file for fastaToPsl
  • lines changed 4, context: html, text, full: html, text
    fixed size bugs and makefile bug
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 140, context: html, text, full: html, text
    New CFI 'hgFileUi' for composites with downloadable files
• src/hg/hgFileUi/makefile
  • lines changed 15, context: html, text, full: html, text
    New CFI 'hgFileUi' for composites with downloadable files
• src/hg/hgGene/altSplice.c
  • lines changed 5, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/hg/hgGenome/mainPage.c
  • lines changed 5, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/hg/hgTables/correlatePlot.c
  • lines changed 16, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    Fixed some sort issure and minor styling for metadata '...'
  • lines changed 35, context: html, text, full: html, text
    Make use of fileUi.h macros and support hgFileUi CGI
  • lines changed 7, context: html, text, full: html, text
    move if(ajax) return b/c hidden form doesn't work in modal dialog
• src/hg/hgTracks/bamTrack.c
  • lines changed 43, context: html, text, full: html, text
    BAM tracks that have too many items to map now draw one big map box with a message telling the user to zoom in if they want to click on an item. #1279
• src/hg/hgTracks/cds.c
  • lines changed 2, context: html, text, full: html, text
    BAM tracks that have too many items to map now draw one big map box with a message telling the user to zoom in if they want to click on an item. #1279
• src/hg/hgTracks/cds.h
  • lines changed 2, context: html, text, full: html, text
    BAM tracks that have too many items to map now draw one big map box with a message telling the user to zoom in if they want to click on an item. #1279
• src/hg/hgTracks/hgTracks.c
  • lines changed 23, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/hg/hgTracks/hgTracks.h
  • lines changed 5, context: html, text, full: html, text
    BAM tracks that have too many items to map now draw one big map box with a message telling the user to zoom in if they want to click on an item. #1279
• src/hg/hgTracks/searchTracks.c
  • lines changed 1, context: html, text, full: html, text
    Track search should post selected tracks before sorting or going to a configuration page
• src/hg/hgc/hgc.c
  • lines changed 8, context: html, text, full: html, text
    indicate database on Get DNA screen for information
  • lines changed 5, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
  • lines changed 3, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
  • lines changed 4, context: html, text, full: html, text
    change Get DNA wording (see redmin 1333)
  • lines changed 2, context: html, text, full: html, text
    add database/organism to the View DNA sentence
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 5, context: html, text, full: html, text
    releasing UW Dnase HS I hg19, redmine issue #66
  • lines changed 15, context: html, text, full: html, text
    adding the just released HAIB Methyl RRBS hg19 track and the previously released Mapability track (which was missing from the page) to the ENCODE downloads page
  • lines changed 1, context: html, text, full: html, text
    fixing typo
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 3, context: html, text, full: html, text
    Removed lines about pgSnp needing to have track type specified. Belinda added automatic detection of the track type.
• src/hg/htdocs/images/denisovaCave.jpg
  • lines changed 0, context: html, text, full: html, text
    Denisova cave entrance, copyright (C) 2010 Johanes Krause
• src/hg/htdocs/images/phylo/felCat4_6way.gif
  • lines changed 0, context: html, text, full: html, text
    Annotate 6-way multiple alignment
• src/hg/htdocs/images/phylo/felCatV17e_6way.gif
  • lines changed 0, context: html, text, full: html, text
    retire felCatV17e
• src/hg/htdocs/mirror.html
  • lines changed 12, context: html, text, full: html, text
    changed location of Danish mirror
  • lines changed 4, context: html, text, full: html, text
    changed location of Danish mirror
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    Katrina doesn' like 3D sort column headers
  • lines changed 2, context: html, text, full: html, text
    Solved problem of subtrack table occasionally text wrapping to 2 lines per subtrack. Used the power of CSS.
  • lines changed 3, context: html, text, full: html, text
    Makes invisible border around subtrack list which helps with page sizing
• src/hg/inc/fileUi.h
  • lines changed 1, context: html, text, full: html, text
    Fixed some sort issure and minor styling for metadata '...'
  • lines changed 10, context: html, text, full: html, text
    New CFI 'hgFileUi' for composites with downloadable files
• src/hg/inc/hCommon.h
  • lines changed 3, context: html, text, full: html, text
    New CFI 'hgFileUi' for composites with downloadable files
• src/hg/inc/hgRelate.h
  • lines changed 19, context: html, text, full: html, text
    assign ids in seq and extFile tables locally rather than globally (RM #26)
• src/hg/inc/hvGfx.h
  • lines changed 9, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/hg/inc/snp132Ext.h
  • lines changed 81, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
• src/hg/js/ajax.js
  • lines changed 11, context: html, text, full: html, text
    Fixed the mdb '...' table so that it can overflow the longLable table cell.
  • lines changed 1, context: html, text, full: html, text
    Background color for '...' metadata table should be added always, since there can be more than 3 shades to the table rows.
• src/hg/js/hgTracks.js
  • lines changed 5, context: html, text, full: html, text
    Allow rightClick to configure superTracks when aaviable
  • lines changed 1, context: html, text, full: html, text
    Fixed rightClick hide when track is a superTrack child
  • lines changed 25, context: html, text, full: html, text
    Track search should post selected tracks before sorting or going to a configuration page
• src/hg/js/hui.js
  • lines changed 21, context: html, text, full: html, text
    Move drag and drop registration to utils because this needs to be reregistered after a sort.
• src/hg/js/utils.js
  • lines changed 166, context: html, text, full: html, text
    Fixed some sort issues.
  • lines changed 4, context: html, text, full: html, text
    Fixed the mdb '...' table so that it can overflow the longLable table cell.
  • lines changed 32, context: html, text, full: html, text
    Move drag and drop registration to utils because this needs to be reregistered after a sort.
  • lines changed 9, context: html, text, full: html, text
    Add row highlighting on sortable tables. Make sure that initialize of sort table turns off greying when done.
• src/hg/lib/cart.c
  • lines changed 46, context: html, text, full: html, text
    Hopefully top-down and bottom-up clean-up of composite cart vars now works. Top-down first, but does not remove new subtrack-level vis
• src/hg/lib/fileUi.c
  • lines changed 188, context: html, text, full: html, text
    Fixed some sort issure and minor styling for metadata '...'
  • lines changed 31, context: html, text, full: html, text
    Make use of fileUi.h macros and support hgFileUi CGI
  • lines changed 1, context: html, text, full: html, text
    Minor css change
• src/hg/lib/hCommon.c
  • lines changed 7, context: html, text, full: html, text
    New CFI 'hgFileUi' for composites with downloadable files
• src/hg/lib/hgExp.c
  • lines changed 5, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/hg/lib/hgRelate.c
  • lines changed 105, context: html, text, full: html, text
    assign ids in seq and extFile tables locally rather than globally (RM #26)
• src/hg/lib/hui.c
  • lines changed 21, context: html, text, full: html, text
    Fixed some sort issure and minor styling for metadata '...'
  • lines changed 6, context: html, text, full: html, text
    Fixed the mdb '...' table so that it can overflow the longLable table cell.
  • lines changed 11, context: html, text, full: html, text
    Had to add back in the 'windowSize' table or else things like top light blue bar start breaking
  • lines changed 7, context: html, text, full: html, text
    Solved problem of subtrack table occasionally text wrapping to 2 lines per subtrack. Used the power of CSS.
  • lines changed 130, context: html, text, full: html, text
    Made Track Name and Restricted Until sortable columns in the subtrack list of hgTrackUi.
  • lines changed 15, context: html, text, full: html, text
    Make use of fileUi.h macros and support hgFileUi CGI
  • lines changed 36, context: html, text, full: html, text
    Subtrack list needed to exclude the view all/visible radio buttons when it is sortable.
• src/hg/lib/hvGfx.c
  • lines changed 10, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/hg/lib/liftOver.c
  • lines changed 6, context: html, text, full: html, text
    bedOverSmall had a limit of 20 words per line, while other functionshad a limit of 64. The new snp132Ext has >20 columns and lines were truncated due to the 20-word limit. Changed limit to 64 everywhere.
  • lines changed 1, context: html, text, full: html, text
    follow-on to 4963dda: Fixed one more spot with a hardcoded lower wordcount limit.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
• src/hg/lib/snp132Ext.as
  • lines changed 30, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
• src/hg/lib/snp132Ext.c
  • lines changed 345, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
• src/hg/lib/tests/pslReaderTests.mk
  • lines changed 2, context: html, text, full: html, text
    add -noHistory option to hgLoadPsl for use in tests (#25)
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 240, context: html, text, full: html, text
    setting priorities for danRer7 chain and net tracks
  • lines changed 32, context: html, text, full: html, text
    completed chain nets with danRer7
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeUwDnaseSeq.release4.notes.txt
  • lines changed 752, context: html, text, full: html, text
    Removed 3 experiments and updated release 4 notes.
  • lines changed 370, context: html, text, full: html, text
    Fixed known files paths to be pointing towards release4
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 44, context: html, text, full: html, text
    Added two more controls.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release1.notes
  • lines changed 1542, context: html, text, full: html, text
    Added release notes for Histone and Tfbs tracks.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release1.notes
  • lines changed 988, context: html, text, full: html, text
    Added release notes for Histone and Tfbs tracks.
• src/hg/makeDb/doc/equCab2.txt
  • lines changed 10, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): work-in-progress: getting the new doDbSnp.pl to work on hg19 snp132.
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 39, context: html, text, full: html, text
    Annotate 6-way multiple alignment
  • lines changed 4, context: html, text, full: html, text
    Annotate 6-way multiple alignment with gene annotations
• src/hg/makeDb/doc/gasAcu1.txt
  • lines changed 18, context: html, text, full: html, text
    setting priorities for danRer7 chain and net tracks
• src/hg/makeDb/doc/hg18.nt.txt
  • lines changed 133, context: html, text, full: html, text
    indicate lift to hg19 procedure
• src/hg/makeDb/doc/hg19.txt
  • lines changed 45, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): work-in-progress: getting the new doDbSnp.pl to work on hg19 snp132.
  • lines changed 12, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): doDbSnp.pl now runs successfullyon hg19 snp132 and loads the additional tables into hg19snp132 (Allele, Batch, SNPAlleleFreq, SNPSubSNPLink, SNP_bitfield, SubSNP). Next, make use of that new info to add some columns to snp132...
  • lines changed 27, context: html, text, full: html, text
    fixup loading procedure for Neandertal sequence reads
  • lines changed 1, context: html, text, full: html, text
    fixing vistaEnhancers link
  • lines changed 24, context: html, text, full: html, text
    cgapSage track lifted to hg19
  • lines changed 7, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
  • lines changed 63, context: html, text, full: html, text
    running danRer7 lastz
  • lines changed 105, context: html, text, full: html, text
    Brain Histone H3K4me3 track from UMass Medical School (Zhiping Weng and Shachram Akbarian)
  • lines changed 14, context: html, text, full: html, text
    completed chain nets with danRer7
  • lines changed 52, context: html, text, full: html, text
    adding hg19 switch gear TSS track lift
  • lines changed 28, context: html, text, full: html, text
    Make instructions for hg19 Fosmid End Pairs track plus trakDb
  • lines changed 3, context: html, text, full: html, text
    small addition to the make instructions of the GAD track
  • lines changed 2, context: html, text, full: html, text
    small addition for instructions to rgdQtl track
• src/hg/makeDb/doc/mm9.txt
  • lines changed 58, context: html, text, full: html, text
    completed danRer7 lastz run and swap
• src/hg/makeDb/doc/oryLat2.txt
  • lines changed 20, context: html, text, full: html, text
    setting priorities for danRer7 chain and net tracks
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 20, context: html, text, full: html, text
    Debugged some unix commands on the Rfam stuff. Replaced the erroneous hgsql -E with hgsql -e. In one place, added the hgsql database where it was missing
• src/hg/makeDb/doc/xenTro2.txt
  • lines changed 19, context: html, text, full: html, text
    completed chain nets with danRer7
• src/hg/makeDb/genbank/etc/build.crontab
  • lines changed 5, context: html, text, full: html, text
    push to hgdownload rather than pulling, removing need for nfs mount on hgdownload (#2099)
  • lines changed 1, context: html, text, full: html, text
    added push to hgdownload-sd
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    yank and put mention of multiz maf that doesn't yet for danRer7
• src/hg/makeDb/genbank/etc/hgdownload-copy
  • lines changed 17, context: html, text, full: html, text
    push to hgdownload rather than pulling, removing need for nfs mount on hgdownload (#2099)
• src/hg/makeDb/genbank/etc/hgdownload.crontab
  • lines changed 9, context: html, text, full: html, text
    push to hgdownload rather than pulling, removing need for nfs mount on hgdownload (#2099)
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    adding danRer7 to hgwbeta.dbs to start genbank updates on beta
• src/hg/makeDb/genbank/makefile
  • lines changed 6, context: html, text, full: html, text
    push to hgdownload rather than pulling, removing need for nfs mount on hgdownload (#2099)
  • lines changed 2, context: html, text, full: html, text
    ensure gitFiles is in path to avoid generates a really bogus rsync
• src/hg/makeDb/genbank/src/copy/gbCopyDownload
  • lines changed 24, context: html, text, full: html, text
    push to hgdownload rather than pulling, removing need for nfs mount on hgdownload (#2099)
• src/hg/makeDb/hgKgMrna/hgKgMrna.c
  • lines changed 9, context: html, text, full: html, text
    assign ids in seq and extFile tables locally rather than globally (RM #26)
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • lines changed 7, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgLoadBlastTab/hgLoadBlastTab.c
  • lines changed 4, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgLoadChain/hgLoadChain.c
  • lines changed 4, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgLoadMaf/hgLoadMaf.c
  • lines changed 1, context: html, text, full: html, text
    assign ids in seq and extFile tables locally rather than globally (RM #26)
• src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
  • lines changed 1, context: html, text, full: html, text
    assign ids in seq and extFile tables locally rather than globally (RM #26)
• src/hg/makeDb/hgLoadNet/hgLoadNet.c
  • lines changed 4, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgLoadPsl/hgLoadPsl.c
  • lines changed 7, context: html, text, full: html, text
    add -noHistory option to hgLoadPsl for use in tests (#25)
  • lines changed 5, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgLoadSeq/hgLoadSeq.c
  • lines changed 15, context: html, text, full: html, text
    assign ids in seq and extFile tables locally rather than globally (RM #26)
• src/hg/makeDb/hgLoadSqlTab/hgLoadSqlTab.c
  • lines changed 6, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
  • lines changed 1, context: html, text, full: html, text
    Resolved compilation warnings from gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9),mostly by folding unnecessary safef's into hgHistoryComment which takes varargs (pragma recently added by MarkD meant newly detected lack of format strings).
• src/hg/makeDb/hgStanfordMicroarray/hgStanfordMicroarray.c
  • lines changed 1, context: html, text, full: html, text
    assign ids in seq and extFile tables locally rather than globally (RM #26)
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    cgapSage track lifted to hg19
  • lines changed 4, context: html, text, full: html, text
    removing all mention of felCatV17e from all.joiner http://redmine.soe.ucsc.edu/issues/791
• src/hg/makeDb/trackDb/cat/felCat4/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Annotate 6-way multiple alignment
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 3, context: html, text, full: html, text
    Accepted a provisional stanza that defines a new Switchgear dataType
  • lines changed 1, context: html, text, full: html, text
    Had to shorten dateUnrestricted's typeOfTerm label, to fit '...' metadata table.
  • lines changed 21, context: html, text, full: html, text
    In many cases where a substrate is produced by a specific individual rather than purchased from a vendor, added a link to that person's home page (or a reasonable proxy) as order URL
  • lines changed 4, context: html, text, full: html, text
    Checking in change log for cv.ra that was resuscitated from October 11, 2010. A fall-back to use when reconstructing history, as the actual revision history was lost when the file was moved.
  • lines changed 16, context: html, text, full: html, text
    Added the antibody GATA1_(SC-266)
  • lines changed 1, context: html, text, full: html, text
    Fixed a typo in the registration of GATA1_SC266
  • lines changed 1, context: html, text, full: html, text
    fixed one more typo in the validation filename
  • lines changed 51, context: html, text, full: html, text
    Resolving a conflicted merge. (1) Removed the Provisional keyword from the new Switchgear data type (2) in cases where a person's email address had served as the order URL, removed the email address and provided a link to the person's home page (or best reasonable proxy) instead
  • lines changed 18, context: html, text, full: html, text
    Added the antibody SETDB_(SC-66884) for the Farnham lab
  • lines changed 8, context: html, text, full: html, text
    Added a comment on where to place the keyword 'Provisional' when modifying this file
  • lines changed 2, context: html, text, full: html, text
    cleaned up the new stanza for Setdb
• src/hg/makeDb/trackDb/cv/alpha/v242_cv.ra.blame
  • lines changed 6849, context: html, text, full: html, text
    Checking in change log for cv.ra that was resuscitated from October 11, 2010. A fall-back to use when reconstructing history, as the actual revision history was lost when the file was moved.
• src/hg/makeDb/trackDb/cv/alpha/v242_cv.ra.log
  • lines changed 2290, context: html, text, full: html, text
    Checking in change log for cv.ra that was resuscitated from October 11, 2010. A fall-back to use when reconstructing history, as the actual revision history was lost when the file was moved.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 77, context: html, text, full: html, text
    Copying one batch of commits from alpha to beta
• src/hg/makeDb/trackDb/human/altSeqComposite.html
  • lines changed 74, context: html, text, full: html, text
    major revisions to description page for GRC Patch Release. http://redmine.soe.ucsc.edu/issues/1892
• src/hg/makeDb/trackDb/human/bamSLDenisova.html
  • lines changed 70, context: html, text, full: html, text
    separate Methods section for each denisova track
• src/hg/makeDb/trackDb/human/denisova.html
  • lines changed 28, context: html, text, full: html, text
    updated methods and including cave photograph
  • lines changed 66, context: html, text, full: html, text
    obsolete html removed
• src/hg/makeDb/trackDb/human/denisovaModernHumans.html
  • lines changed 66, context: html, text, full: html, text
    separate Methods section for each denisova track
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 3, context: html, text, full: html, text
    Removed Accession from meta-data terms. Moved information into new field dccNotes which will keep this information that is not of use to the DCC, but information the lab provided.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
  • lines changed 175, context: html, text, full: html, text
    Removed reference in trackDb and metaDb for the Jurkat G1 and HIPEpiC Experiments.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 27, context: html, text, full: html, text
    Removed Accession from meta-data terms. Moved information into new field dccNotes which will keep this information that is not of use to the DCC, but information the lab provided.
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeAffyRnaChip.ra
  • lines changed 1873, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeCshlShortRnaSeq.ra
  • lines changed 1018, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeDukeAffyExonArray.ra
  • lines changed 1045, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeGisDnaPet.ra
  • lines changed 551, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeGisRnaSeq.ra
  • lines changed 439, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHelicosRnaSeq.ra
  • lines changed 54, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaCnv.ra
  • lines changed 103, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Short labels were backward.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2541, context: html, text, full: html, text
    Trying to fix the RR not having any metadata
  • lines changed 287, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
  • lines changed 1, context: html, text, full: html, text
    Updated new.ra to have release alpha tags.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.new.ra
  • lines changed 1002, context: html, text, full: html, text
    Trying to fix the RR not having any metadata
  • lines changed 109, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.ra
  • lines changed 1106, context: html, text, full: html, text
    Trying to fix the RR not having any metadata
  • lines changed 109, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.ra
  • lines changed 282, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 538, context: html, text, full: html, text
    Trying to fix the RR not having any metadata
  • lines changed 48, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.ra
  • lines changed 582, context: html, text, full: html, text
    Trying to fix the RR not having any metadata
  • lines changed 49, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.new.ra
  • lines changed 448, context: html, text, full: html, text
    a few more files for the fixing the missing metaData on the RR issue
  • lines changed 58, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.ra
  • lines changed 507, context: html, text, full: html, text
    Trying to fix the RR not having any metadata
  • lines changed 59, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.new.ra
  • lines changed 109, context: html, text, full: html, text
    a few more files for the fixing the missing metaData on the RR issue
  • lines changed 7, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.ra
  • lines changed 116, context: html, text, full: html, text
    Trying to fix the RR not having any metadata
  • lines changed 8, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.new.ra
  • lines changed 324, context: html, text, full: html, text
    a few more files for the fixing the missing metaData on the RR issue
  • lines changed 0, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra
  • lines changed 342, context: html, text, full: html, text
    Trying to fix the RR not having any metadata
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.new.ra
  • lines changed 64, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.ra
  • lines changed 64, context: html, text, full: html, text
    Trying to fix the RR not having any metadata
  • lines changed 5, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.new.ra
  • lines changed 91, context: html, text, full: html, text
    Trying to fix the RR not having any metadata
  • lines changed 8, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.ra
  • lines changed 97, context: html, text, full: html, text
    Trying to fix the RR not having any metadata
  • lines changed 9, context: html, text, full: html, text
    changing these tracks to get their data from the mdb not the trackDB. A .new file for each with alpha tags and no metaData lines and a .ra file for each with beta,public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.ra
  • lines changed 242, context: html, text, full: html, text
    Updated new.ra to have release alpha tags.
  • lines changed 235, context: html, text, full: html, text
    Fixed mistake about having release alpha for .ra and beta,public as .new.ra
  • lines changed 64, context: html, text, full: html, text
    Removed reference in trackDb and metaDb for the Jurkat G1 and HIPEpiC Experiments.
  • lines changed 186, context: html, text, full: html, text
    Removed 3 experiments and updated release 4 notes.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.ra
  • lines changed 231, context: html, text, full: html, text
    Added back release tags in data inorder to facilitate the removal of 3 experiments.
  • lines changed 235, context: html, text, full: html, text
    Updated new.ra to have release alpha tags.
  • lines changed 235, context: html, text, full: html, text
    Fixed mistake about having release alpha for .ra and beta,public as .new.ra
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 3, context: html, text, full: html, text
    added DukeAffyExon and Suny Switchgear
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 316, context: html, text, full: html, text
    added the new metaData for DukeAffyExon
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 1457, context: html, text, full: html, text
    Added 10 submissions Fixed bam files.
  • lines changed 1170, context: html, text, full: html, text
    Added 5 ChIP-seq experiments on SK-N-SH_RA cells.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 34, context: html, text, full: html, text
    Removed Rank from meta-data
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 220, context: html, text, full: html, text
    Removed Rank from meta-data
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    staging UW Dnase HS I metaDb for release, redmine issue #66
  • lines changed 1, context: html, text, full: html, text
    preparing metadata for HAIB Methyl RRBS release
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibMethylRrbs.ra
  • lines changed 2672, context: html, text, full: html, text
    preparing metadata for HAIB Methyl RRBS release
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDnase.ra
  • lines changed 9463, context: html, text, full: html, text
    staging UW Dnase HS I metaDb for release, redmine issue #66
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    fixup type bigWig min/max limits and adding lifted Sel Swp Scan (S) to hg19
  • lines changed 19, context: html, text, full: html, text
    proper pennantIcon for neandertal track overrides
  • lines changed 4, context: html, text, full: html, text
    adding url link for fetch alt sequence hg19Patch2
  • lines changed 2, context: html, text, full: html, text
    generic url for hgc click in altSeqComposite
  • lines changed 1, context: html, text, full: html, text
    ntSeqContigs is actually ntSeqReads
  • lines changed 1, context: html, text, full: html, text
    fixing vistaEnhancers link
  • lines changed 4, context: html, text, full: html, text
    cgapSage track lifted to hg19
  • lines changed 1, context: html, text, full: html, text
    Brain Histone H3K4me3 track from UMass Medical School (Zhiping Weng and Shachram Akbarian)
  • lines changed 2, context: html, text, full: html, text
    adding clarification of which alternate squence the GRC Patch Release track is refering to http://redmine.soe.ucsc.edu/issues/1892
  • lines changed 4, context: html, text, full: html, text
    Make instructions for hg19 Fosmid End Pairs track plus trakDb
  • lines changed 1, context: html, text, full: html, text
    Removed "release alpha" from the hg19 override entry for rgdQtl
• src/hg/makeDb/trackDb/human/hg19/uMassBrainHistone.html
  • lines changed 65, context: html, text, full: html, text
    Brain Histone H3K4me3 track from UMass Medical School (Zhiping Weng and Shachram Akbarian)
• src/hg/makeDb/trackDb/human/hg19/uMassBrainHistone.ra
  • lines changed 166, context: html, text, full: html, text
    Brain Histone H3K4me3 track from UMass Medical School (Zhiping Weng and Shachram Akbarian)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
  • lines changed 13, context: html, text, full: html, text
    Added fileSortOrder to broad as first test case of hgFileUi CGI
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html
  • lines changed 18, context: html, text, full: html, text
    fixed issues that Katrina found in my code review, redmine issue #2084, for Caltech RNA-seq redmine issue #35
  • lines changed 1, context: html, text, full: html, text
    code review fix redmine issue #2081, fixed one remaining typo
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDnaMethylSuper.html
  • lines changed 15, context: html, text, full: html, text
    fixed a typo and fixed up the references
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.ra
  • lines changed 8, context: html, text, full: html, text
    update the matrix
  • lines changed 2, context: html, text, full: html, text
    sorted the treatments
  • lines changed 161, context: html, text, full: html, text
    Changed long and short labels, set the defaults
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
  • lines changed 44, context: html, text, full: html, text
    added View section, contact information, comment about the references, and data release policy
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html
  • lines changed 3, context: html, text, full: html, text
    Fixed hardcoded link to be relative link to downloads page.
  • lines changed 3, context: html, text, full: html, text
    Revoked changes of previous commit. Didn't correctly remove hardcoded-links.
  • lines changed 1, context: html, text, full: html, text
    changing hard-coded link in desc to hgdownload-test to hgdownload
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed labeling spacing problems that existed.
  • lines changed 6, context: html, text, full: html, text
    Updated Default Views to be Tier 1 and Tier 2 cell lines for Replicate 1.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 179, context: html, text, full: html, text
    Added 10 submissions Fixed bam files.
  • lines changed 154, context: html, text, full: html, text
    Added 5 ChIP-seq experiments on SK-N-SH_RA cells.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
  • lines changed 1, context: html, text, full: html, text
    moved into the SuperTrack
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html
  • lines changed 1, context: html, text, full: html, text
    making change suggested by Krish/Venkat (http://redmine.soe.ucsc.edu/issues/65#note-53)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed typo in track long label. Change Fingerprinting to Footprinting.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 336, context: html, text, full: html, text
    releasing ENCODE UW Dnase HS I hg19 track, redmine issue #66
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    setting priorities for danRer7 chain and net tracks
• src/hg/makeDb/trackDb/human/trackDb.denisova.ra
  • lines changed 2, context: html, text, full: html, text
    separate Methods section for each denisova track
• src/hg/makeDb/trackDb/human/trackDb.encode.ra
  • lines changed 15, context: html, text, full: html, text
    take out some spurious release alpha. Good catch rhead!!
• src/hg/makeDb/trackDb/human/trackDb.nt.ra
  • lines changed 1, context: html, text, full: html, text
    fixup type bigWig min/max limits and adding lifted Sel Swp Scan (S) to hg19
• src/hg/makeDb/trackDb/makefile
  • lines changed 5, context: html, text, full: html, text
    require that the beta and public targets be built on hgwbeta
• src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    setting priorities for danRer7 chain and net tracks
• src/hg/makeDb/trackDb/mouse/agilentCghAlpha.html
  • lines changed 8, context: html, text, full: html, text
    little grammar edits, changing the Biological Features column so that it matches the actual count(*) from the tables, adding bit about how the track was colored. For rn4 and mm9 only.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 149, context: html, text, full: html, text
    Added 2 submission for TFBS. In addition updated the lab from LICR to LICR-m
  • lines changed 45, context: html, text, full: html, text
    Updated errant mistake in lab variable for Stanford and Ren lab tracks.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 195, context: html, text, full: html, text
    Added 2 submission for TFBS. In addition updated the lab from LICR to LICR-m
  • lines changed 45, context: html, text, full: html, text
    Updated errant mistake in lab variable for Stanford and Ren lab tracks.
  • lines changed 105, context: html, text, full: html, text
    Added submission 2788, fastq and bam meta-data.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 305, context: html, text, full: html, text
    Added 2 new submissions. Updated the meta-data to have lab as Stanford-m instead of Stanford.
  • lines changed 49, context: html, text, full: html, text
    Updated errant mistake in lab variable for Stanford and Ren lab tracks.
• src/hg/makeDb/trackDb/mouse/mm9/targetScanS.html
  • lines changed 1, context: html, text, full: html, text
    oops fix mm9 targetScanS methods section
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Reverting workaround Brian added that fixed problem with the visibility code that was causing a crash on the RR.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Made new trackDb for release 2 with alpha tags that include all data. The original wgEncodeSydhTfbs.ra will only include data that will be released and now has release beta tags.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra
  • lines changed 6, context: html, text, full: html, text
    Removed metadata lines from trackDb.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
  • lines changed 702, context: html, text, full: html, text
    Made new trackDb for release 2 with alpha tags that include all data. The original wgEncodeSydhTfbs.ra will only include data that will be released and now has release beta tags.
  • lines changed 30, context: html, text, full: html, text
    Removed metadata lines from trackDb.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.ra
  • lines changed 41, context: html, text, full: html, text
    Added 2 new submissions. Updated the meta-data to have lab as Stanford-m instead of Stanford.
  • lines changed 481, context: html, text, full: html, text
    Made new trackDb for release 2 with alpha tags that include all data. The original wgEncodeSydhTfbs.ra will only include data that will be released and now has release beta tags.
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    setting priorities for danRer7 chain and net tracks
• src/hg/makeDb/trackDb/rat/agilentCghAlpha.html
  • lines changed 5, context: html, text, full: html, text
    little grammar edits, changing the Biological Features column so that it matches the actual count(*) from the tables, adding bit about how the track was colored. For rn4 and mm9 only.
• src/hg/makeDb/trackDb/sacCer/sacCer1/description.html
  • lines changed 1, context: html, text, full: html, text
    corrected bad link for photo credit. he's now at the Uni in Bremen, not Stuttgart.
• src/hg/makeDb/trackDb/sacCer/sacCer2/description.html
  • lines changed 1, context: html, text, full: html, text
    fixed link for photo credit. He moved to the Uni in Bremen
• src/hg/makeDb/trackDb/stickleback/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    setting priorities for danRer7 chain and net tracks
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder for downloads page via CGI
  • lines changed 1, context: html, text, full: html, text
    Since the tagType rules will apply to subtracks of a composite, then fileSortOrder must be for all
• src/hg/makeDb/trackDb/tetraodon/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    setting priorities for danRer7 chain and net tracks
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 56, context: html, text, full: html, text
    removing felCatV17e chainNet information from trackDb http://redmine.soe.ucsc.edu/issues/791
  • lines changed 51, context: html, text, full: html, text
    completed danRer7 chain and net
• src/hg/makeDb/trackDb/xenTro/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    setting priorities for danRer7 chain and net tracks
• src/hg/makeDb/trackDb/zebrafish/affyZonWildType.html
  • lines changed 6, context: html, text, full: html, text
    Corrected link to Affy. Adjusted text for one link to not be over 100 characters wide.
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra
  • lines changed 32, context: html, text, full: html, text
    eliminate duplicate EST and MRNA definitions
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    Added hgFileUi CGI
• src/hg/near/hgMapToGene/hgMapToGene.c
  • lines changed 8, context: html, text, full: html, text
    After learning that the function bedLength duplicates the pre-existing function bedTotalBlockSize, removed bedLength and replaced calls to bedLength with calls to bedTotalBlockSize
  • lines changed 19, context: html, text, full: html, text
    Removed some extraneous merge information
• src/hg/oneShot/bed15To3Col/bed15To3Col.c
  • lines changed 76, context: html, text, full: html, text
    Created a oneShot program to convert becd15 table to 3 col file.
• src/hg/oneShot/bed15To3Col/makefile
  • lines changed 18, context: html, text, full: html, text
    Created a oneShot program to convert becd15 table to 3 col file.
• src/hg/phyloGif/phyloGif.c
  • lines changed 14, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/hg/protein/lib/doTracks.c
  • lines changed 5, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/hg/protein/pbGlobal/pbGlobal.c
  • lines changed 5, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/hg/protein/pbTracks/pbTracks.c
  • lines changed 5, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/hg/qaPushQ/qaPushQ.c
  • lines changed 1, context: html, text, full: html, text
    increasing page size for qaPushQ
  • lines changed 2, context: html, text, full: html, text
    support longer file and table lists
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 2, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): tweaks to get doDbSnp.pl to runsuccessfully on hg19 snp132.
  • lines changed 473, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 31, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): work-in-progress: getting the new doDbSnp.pl to work on hg19 snp132.
  • lines changed 204, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): tweaks to get doDbSnp.pl to runsuccessfully on hg19 snp132.
  • lines changed 152, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): doDbSnp.pl now runs successfullyon hg19 snp132 and loads the additional tables into hg19snp132 (Allele, Batch, SNPAlleleFreq, SNPSubSNPLink, SNP_bitfield, SubSNP). Next, make use of that new info to add some columns to snp132...
  • lines changed 117, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added new columns to SNP table(snp132Ext.as) in doDbSnp.pl and snpNcbiToUcsc. It now runs successfully on hg19 snp132; I have verified that the first 17 columns match the old snp132.bed and that the pre-existing exceptions match the old snp132Exceptions.bed. The snp125 code in hgTracks/hgTrackUi/hgc works find on the new snp132 -- new columns are ignored. There is still some polishing to do before doDbSnp.pl is ready for general use -- more consistency checks, and much more info for the developer about what they need to follow through on. But next I plan to enhance the CGIs to make use of the new columns so we can get snp132 out the door.
• src/hg/utils/refreshNamedSessionCustomTracks/beta.trashCleanMonitor.sh
  • lines changed 1, context: html, text, full: html, text
    eliminate hiram email address
• src/hg/utils/refreshNamedSessionCustomTracks/rr.trashCleanMonitor.sh
  • lines changed 1, context: html, text, full: html, text
    eliminate hiram email address
• src/inc/bbiFile.h
  • lines changed 3, context: html, text, full: html, text
    add routine to let validateFiles check for the signature at the beginning and end of bigWigs
• src/inc/bigBed.h
  • lines changed 2, context: html, text, full: html, text
    add routine to let validateFiles check for the signature at the beginning and end of bigWigs
• src/inc/bigWig.h
  • lines changed 2, context: html, text, full: html, text
    add routine to let validateFiles check for the signature at the beginning and end of bigWigs
• src/inc/common.mk
  • lines changed 27, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/inc/memgfx.h
  • lines changed 27, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/inc/vGfx.h
  • lines changed 8, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/lib/bbiRead.c
  • lines changed 37, context: html, text, full: html, text
    add routine to let validateFiles check for the signature at the beginning and end of bigWigs
• src/lib/bigBed.c
  • lines changed 6, context: html, text, full: html, text
    add routine to let validateFiles check for the signature at the beginning and end of bigWigs
• src/lib/bwgQuery.c
  • lines changed 6, context: html, text, full: html, text
    add routine to let validateFiles check for the signature at the beginning and end of bigWigs
• src/lib/gifLabel.c
  • lines changed 13, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/lib/makefile
  • lines changed 3, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/lib/pngwrite.c
  • lines changed 3, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/lib/vPng.c
  • lines changed 2, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/product/README.building.source
  • lines changed 4, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/product/scripts/browserEnvironment.txt
  • lines changed 3, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/tracks/tracks.c
  • lines changed 5, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/utils/fastaToPsl/fastaToPsl.c
  • lines changed 95, context: html, text, full: html, text
    fixed size bugs and makefile bug
  • lines changed 36, context: html, text, full: html, text
    better logging and now iterates over targets
• src/utils/fastaToPsl/makefile
  • lines changed 24, context: html, text, full: html, text
    fixed size bugs and makefile bug
• src/utils/fastaToPsl/tests/input/fa_seq_align.fa
  • lines changed 4, context: html, text, full: html, text
    fixed size bugs and makefile bug
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v245 preview2
• src/utils/qa/weeklybld/defaultBuildSettings.mk
  • lines changed 1, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/utils/qa/weeklybld/downloadBuildSettings.mk
  • lines changed 1, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323
• src/weblet/counter/counter.c
  • lines changed 5, context: html, text, full: html, text
    remove USE_PNG and GIF support #1323

• lines changed: 53346
• files changed: 331