All File Changes
v235_preview to v235_base (2010-06-29 to 2010-07-06) v235
- .gitignore
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Adding more common things for git to ignore.
- src/ameme/ameme.c
- src/ameme/makefile
- src/hg/encode/DAFs/2.0/caltechRnaSeq.daf
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New DAF's for the June 21st 2010 freeze
- src/hg/encode/DAFs/2.0/gisDnaPet.daf
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New DAF's for the June 21st 2010 freeze
- src/hg/encode/DAFs/2.0/haibMethylRrbs.daf
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New DAF's for the June 21st 2010 freeze
- src/hg/encode/DAFs/2.0/haibRnaSeq.daf
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New DAF's for the June 21st 2010 freeze
- src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf
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Added comments for aditional Lab Yale in both Dafs
- src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf
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Added comments for aditional Lab Yale in both Dafs
- src/hg/encode/encodeCharts/June2010-Freeze.html
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Updated URL to genecats server. Added changes requested by Kate
- src/hg/encode/encodeCharts/README
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Updated with new file info and build instructions
- src/hg/encode/encodeCharts/encodeDist.py
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Now uses new freeze label and color functions
- src/hg/encode/encodeCharts/encodeDistUnrelease.py
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Now uses new freeze label and color functions
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Added the "downloads" status
- src/hg/encode/encodeCharts/encodeReportFilter.py
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More robustly handle freeze labels with "post" keyword
- src/hg/encode/encodeCharts/encodeReportLib.py
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Changed URL to genecats server
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Improved report file finding function, added new function for dealing with colors and freeze labels with the keyword "post"
- src/hg/encode/encodeCharts/encodeStatus.py
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Now uses new freeze label and color functions
- lines changed 1, context: html, text, full: html, text
Added the "downloads" status
- src/hg/encode/encodeCharts/makefile
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Fixed incorrect make variables
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Initial checkin - places files in proper location
- src/hg/encode/encodeMergeReplicatesBatch/encodeMergeReplicatesBatch.c
- src/hg/encode/encodeValidate/config/cv.ra
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Changed nm to nM for 2 treatments Estradiol_10nm and Genistein_100nm to register them correctly.
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Added 7 treatments registered by the Hudson Alpha (Myers) lab
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Added document names for the validation documents provided for Antibodies
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Added 3 new antibodies, 2 with validation documents. Antibodies added: Pol2(phosphoS2),ETS1,MEF2A
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Remove special chars from tags. Minor tweaks for consistency (e.g. caps)
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Updated the sex of MEL (mouse) to U, unidentified as we do not know this sex at the moment.
- lines changed 299, context: html, text, full: html, text
Added new mouse cell types
- src/hg/encode/hgEncodeSubmit/go.sample
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swapping order so that background runs after foreground seems to work better
- src/hg/encode/validateFiles/validateFiles.c
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fix totally brain dead bug that my code buddy should have caught (take that anonymous buddy!). Also add option for testing
- src/hg/hgTracks/cds.c
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make 32-bit PNG the default, use painter's algorithm for mRNA track
- src/hg/hgTracks/hgTracks.c
- src/hg/hgTracks/simpleTracks.c
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prototype code to support 'remote' tracks
- src/hg/hgc/encodeClick.c
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Removing unused routine.
- src/hg/hgc/hgc.h
- src/hg/hgc/peakClusters.c
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Eliminating inputTracks and inputTrackSelGroup tags, which have been replaced with the inputTrackTable tag.
- src/hg/htdocs/ENCODE/controlledVocabulary.html
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removed this file because it will not be needed after all
- src/hg/htdocs/ENCODE/releaseLog.html
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"Encode release log update"
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"Encode release log update"
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"Encode release log update"
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"Encode release log update"
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"Encode release log update"
- lines changed 15, context: html, text, full: html, text
"Encode release log update"
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"Encode release log update"
- src/hg/htdocs/FAQ/FAQlicense.html
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rm obsolete sentence about 'cvs update' make stmt
- src/hg/htdocs/admin/403.html
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Added execute permission to html files that include the topbar.
- src/hg/htdocs/admin/404.html
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Added execute permission to html files that include the topbar.
- src/hg/htdocs/admin/500.html
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Added execute permission to html files that include the topbar.
- src/hg/htdocs/admin/cvs.html
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Added execute permission to html files that include the topbar.
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Fix left margin for the Obsolete message
- src/hg/htdocs/admin/git.html
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Added execute permission to html files that include the topbar.
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Fixing permissions on html files.
- src/hg/htdocs/admin/index.html
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Added execute permission to html files that include the topbar.
- src/hg/htdocs/admin/jk-install.html
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Added execute permission to html files that include the topbar.
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Fixing permissions on html files.
- src/hg/htdocs/admin/mirror.html
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Added execute permission to html files that include the topbar.
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Fixing permissions on html files.
- src/hg/htdocs/goldenPath/releaseLog.html
- src/hg/htdocs/makefile
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Moved gitFiles to a makefile variable in htdocs, to allow an override.
Builds off a tag must not reference the repository. This change allows
an override, e.g. make FIND=find, for such builds.
- src/hg/inc/mdb.h
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Rearranged code and comments as per Jims suggestion. Made selection by var=val pairs more full proof
- src/hg/inc/versionInfo.h
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"New version number v235"
- src/hg/js/hgTracks.js
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fix off-by-one error when setting end during selection; more remote renderer work (dead code in non-dev trees)
- src/hg/js/utils.js
- src/hg/lib/mdb.c
- lines changed 242, context: html, text, full: html, text
Rearranged code and comments as per Jims suggestion. Made selection by var=val pairs more full proof
- src/hg/lib/web.c
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Removed ifdefs which were past their expiration date
- src/hg/makeDb/doc/ailMel1.txt
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complete LASTZ Panda Swap
- src/hg/makeDb/doc/danRer6.txt
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adding changes for danRer6 makedoc relating to downloads
- src/hg/makeDb/doc/encodeDccHg19/gencodeV4.txt
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download new gtf files from FelixK. Need to re-load and change release notes
- src/hg/makeDb/doc/felCat4.txt
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complete LASTZ Panda Swap
- lines changed 32, context: html, text, full: html, text
complete LASTZ Panda Swap
- src/hg/makeDb/doc/hg18.txt
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Updating comment that had grown stale.
- lines changed 620, context: html, text, full: html, text
Restoring about 600 lines deleted mysteriously in 3 different places. I sure don't remember doing this and wander what sort of editor typo I could have made. Any way the code review caught it at least!
- src/hg/makeDb/doc/hg19.txt
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adding haplotypeLocations track on hg19
- src/hg/makeDb/mdbUpdate/mdbPrint.c
- lines changed 184, context: html, text, full: html, text
Rearranged code and comments as per Jims suggestion. Made selection by var=val pairs more full proof
- src/hg/makeDb/mdbUpdate/mdbUpdate.c
- lines changed 3, context: html, text, full: html, text
Rearranged code and comments as per Jims suggestion. Made selection by var=val pairs more full proof
- src/hg/makeDb/schema/all.joiner
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correct comment on retroRefGene
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adding refGene name to ucscRetroInfo refSeq relation and inverse
- src/hg/makeDb/trackDb/README
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Eliminating inputTracks and inputTrackSelGroup tags, which have been replaced with the inputTrackTable tag.
- src/hg/makeDb/trackDb/cat/felCat4/description.html
- src/hg/makeDb/trackDb/cat/felCat4/gap.html
- src/hg/makeDb/trackDb/cat/felCat4/gold.html
- src/hg/makeDb/trackDb/cat/felCat4/trackDb.ra
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra
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UCSF Brain Methyl: take out Brain from individual tracks long and short labels, change RNAseq to RNA-seq
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change some stuff that Mary wanted
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Added the temporary rfamHuman table
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Adding the RfamExactMatch track
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adding release alpha blocks for polyA tracks
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- lines changed 4, context: html, text, full: html, text
Eliminating inputTracks and inputTrackSelGroup tags, which have been replaced with the inputTrackTable tag.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLoRnaSeq.html
- lines changed 113, context: html, text, full: html, text
CSHL Long RNA Track improvements in the display
- src/hg/makeDb/trackDb/human/hg18/wgEncodeReg.html
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Doing another pass at the integrated regulatory track .html pages.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeRegDnaseClustered.html
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Improving grammar in description.
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Doing another pass at the integrated regulatory track .html pages.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhH3k27ac.html
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Doing another pass at the integrated regulatory track .html pages.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhH3k4me1.html
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Doing another pass at the integrated regulatory track .html pages.
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Renaming .html file to correspond to track name.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhH3k4me3.html
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Doing another pass at the integrated regulatory track .html pages.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhancer.html
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Renaming .html file to correspond to track name.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeRegTfbsClustered.html
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Doing another pass at the integrated regulatory track .html pages.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeRegTxn.html
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Doing another pass at the integrated regulatory track .html pages.
- src/hg/makeDb/trackDb/human/hg19/haplotypeLocations.html
- lines changed 7, context: html, text, full: html, text
adding haplotypeLocations track on hg19
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
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add wgEncodeHaibMethylSeq.ra
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add some ra files to the makefile
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
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Improvements on meta data and on display for CaltechRNA seq
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 337, context: html, text, full: html, text
The meta data for CHSL Long RNA Seq
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
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metadata for CSHL Small RNA-seq
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
- lines changed 829, context: html, text, full: html, text
add Haib MethylSeq to hg19
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 14, context: html, text, full: html, text
Added the temporary rfamHuman table
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limit haplotypeLocations to the three chromosomes it is on
- lines changed 10, context: html, text, full: html, text
adding haplotypeLocations track on hg19
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
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add Haib MethylSeq to hg19
- lines changed 1, context: html, text, full: html, text
first pass at CSHL short RNA
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeCaltechRnaSeq.ra
- lines changed 32, context: html, text, full: html, text
Added a super track and removed bad subtrack GM12878 2x75
- lines changed 30, context: html, text, full: html, text
Improvements on meta data and on display for CaltechRNA seq
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeCshlLongRnaSeq.ra
- lines changed 2, context: html, text, full: html, text
CSHL Long RNA Track improvements in the display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
- lines changed 393, context: html, text, full: html, text
first pass at CSHL short RNA
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
- lines changed 16, context: html, text, full: html, text
add Haib MethylSeq to hg19
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
- lines changed 1, context: html, text, full: html, text
add to RNA-seq supertrack
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
- src/hg/makeDb/trackDb/tagTypes.tab
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Eliminating inputTracks and inputTrackSelGroup tags, which have been replaced with the inputTrackTable tag.
- src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
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little minor edit to book chapter reference
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small edit plus references
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some html edits - fairly minor
- src/hg/makeDb/trackDb/zebrafish/danRer6/trackDb.ra
- lines changed 1, context: html, text, full: html, text
fixing order of species in danRer6
- src/hg/phyloGif/phyloGif.c
- lines changed 12, context: html, text, full: html, text
set up HTML to have the right file type
- lines changed 7, context: html, text, full: html, text
fix phyloGif to write out PNG, and make sure no one can write out GIF if USE_PNG is set
- src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c
- lines changed 3, context: html, text, full: html, text
Improving usage statement and a comment.
- src/hg/utils/automation/doBlastzChainNet.pl
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no need to copy README.txt when symlink is good
- src/hg/utils/automation/makeDownloads.pl
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Change download url from http://hgwdev.cse.ucsc.edu/goldenPath/ to http://hgdownload-test.cse.ucsc.edu/goldenPath/
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correcly symlink 2bit file for chrom based assembly
- src/hg/utils/mutationClassifier/mutationClassifier.c
- lines changed 62, context: html, text, full: html, text
adding changes to tmp branch for merge
- lines changed 11, context: html, text, full: html, text
fix bug which was causing us to miss exonica mutations in SNPs in N:NN>NN format; use existing dnaMotifBitScore library routine
- lines changed 5, context: html, text, full: html, text
start adding mapability support
- lines changed 293, context: html, text, full: html, text
-lazyLoading; support regulatory classification
- src/inc/common.mk
- lines changed 5, context: html, text, full: html, text
make 32-bit PNG the default, use painter's algorithm for mRNA track
- src/inc/htmshell.h
- lines changed 3, context: html, text, full: html, text
Removed ifdefs which were past their expiration date
- src/lib/gifLabel.c
- lines changed 7, context: html, text, full: html, text
use png instead of gif if USE_PNG is set
- src/lib/gifwrite.c
- lines changed 2, context: html, text, full: html, text
fix phyloGif to write out PNG, and make sure no one can write out GIF if USE_PNG is set
- src/lib/htmshell.c
- lines changed 16, context: html, text, full: html, text
Removed ifdefs which were past their expiration date
- src/lib/net.c
- lines changed 3, context: html, text, full: html, text
create paraFetchStatus right away for monitoring programs
- lines changed 5, context: html, text, full: html, text
only want to check FD_ISSET for real open descriptors >= 0
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return FALSE instead of errAbort; if downloaded size not equal to fileSize, return FALSE
- lines changed 36, context: html, text, full: html, text
fixed bug in doubly-freeing hash when size not returned from server. cleaned up verbose messages. fixed minor sign-related numeric issues
- lines changed 3, context: html, text, full: html, text
explain to user if requests too many connections
- src/lib/pngwrite.c
- lines changed 2, context: html, text, full: html, text
don't fiddle with palette transparency if we're 32-bit
- src/lib/rqlParse.c
- lines changed 3, context: html, text, full: html, text
Making it so that a missing 'from' clause in a rql select statement triggers an error message instead of just causing empty output.
- src/tracks/tracks.c
- src/utils/git-reports/git-reports.c
- lines changed 2, context: html, text, full: html, text
removing automatic-merges from the commit-list, by request
- src/utils/gitTools/gilt
- lines changed 1, context: html, text, full: html, text
backing off on the pathspec limitation of staged stuff, since it is fast for git to generate and it is important to know what would get committed
- lines changed 12, context: html, text, full: html, text
handling plurals for gilt
- lines changed 51, context: html, text, full: html, text
initial commit of gilt git status tool
- src/utils/gitTools/makefile
- lines changed 4, context: html, text, full: html, text
handling programs versus scripts better in gitTools makefile
- lines changed 1, context: html, text, full: html, text
initial commit of gilt git status tool
- src/utils/makefile
- lines changed 2, context: html, text, full: html, text
added git-reports and gitTools to makefile
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/qa/weeklybld/doNewReview.csh
- lines changed 3, context: html, text, full: html, text
oops should say git not cvs in error messages
- src/weblet/counter/counter.c
- src/weblet/counter/makefile
- lines changed: 13760
- files changed: 188