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
- 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
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
- 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
- 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
- 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 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
- 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 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
- 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
- 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