All File Changes
v277_base to v278_preview (2012-12-18 to 2013-01-08) v278
- python/lib/ucscGb/encode/cv.py
- lines changed 21, context: html, text, full: html, text
updated libraries and some tools to make some things clearer, as per code review v276 final
- python/lib/ucscGb/encode/encodeUtils.py
- lines changed 10, context: html, text, full: html, text
updated libraries and some tools to make some things clearer, as per code review v276 final
- python/lib/ucscGb/encode/track.py
- lines changed 8, context: html, text, full: html, text
updated libraries and some tools to make some things clearer, as per code review v276 final
- python/lib/ucscGb/externalData/geo/soft.py
- lines changed 4, context: html, text, full: html, text
updated libraries and some tools to make some things clearer, as per code review v276 final
- python/programs/mkGeoPkg/mkGeoPkg
- lines changed 491, context: html, text, full: html, text
updated libraries and some tools to make some things clearer, as per code review v276 final
- python/programs/trackInfo/trackInfo
- lines changed 22, context: html, text, full: html, text
updated libraries and some tools to make some things clearer, as per code review v276 final
- python/programs/viewTrack/viewTrack
- lines changed 55, context: html, text, full: html, text
updated libraries and some tools to make some things clearer, as per code review v276 final
- src/hg/cartDump/cartDump.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/cartReset/cartReset.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/encode/hgEncodeApi/hgEncodeApi.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/hgApi/hgApi.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/hgBlat/hgBlat.c
- lines changed 3, context: html, text, full: html, text
single stderr message at exit to indicate total run time in apache error_log
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/hgConvert/hgConvert.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/hgCustom/hgCustom.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/hgFileSearch/hgFileSearch.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/hgFileUi/hgFileUi.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/hgGateway/hgGateway.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/hgGene/hgGene.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/hgGenome/hgGenome.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/hgLiftOver/hgLiftOver.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/hgLogin/hgLogin.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/hgPal/hgPal.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/hgPcr/hgPcr.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/hgSession/hgSession.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/hgSuggest/hgSuggest.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/hgTables/bigBed.c
- lines changed 41, context: html, text, full: html, text
Bug #9860 (Table Browser paste identifiers button not working for 1000 genomes ph1 Accessible Regions):getExamples() was unaware of bigBed, so an illegal mysql query was constructed.
Fix: added randomBigBedIds(). While in there, enhanced ramdomVcfIds() to ignore
runs of identical IDs because those are placeholders, and might otherwise crowd
out a few meaningful IDs (#8886 note 28).
- src/hg/hgTables/hgTables.c
- lines changed 3, context: html, text, full: html, text
stderr print at exit to report total time in apache error_og
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/hgTables/hgTables.h
- lines changed 3, context: html, text, full: html, text
Bug #9860 (Table Browser paste identifiers button not working for 1000 genomes ph1 Accessible Regions):getExamples() was unaware of bigBed, so an illegal mysql query was constructed.
Fix: added randomBigBedIds(). While in there, enhanced ramdomVcfIds() to ignore
runs of identical IDs because those are placeholders, and might otherwise crowd
out a few meaningful IDs (#8886 note 28).
- src/hg/hgTables/identifiers.c
- lines changed 13, context: html, text, full: html, text
Bug #9860 (Table Browser paste identifiers button not working for 1000 genomes ph1 Accessible Regions):getExamples() was unaware of bigBed, so an illegal mysql query was constructed.
Fix: added randomBigBedIds(). While in there, enhanced ramdomVcfIds() to ignore
runs of identical IDs because those are placeholders, and might otherwise crowd
out a few meaningful IDs (#8886 note 28).
- src/hg/hgTables/vcf.c
- lines changed 9, context: html, text, full: html, text
Bug #9860 (Table Browser paste identifiers button not working for 1000 genomes ph1 Accessible Regions):getExamples() was unaware of bigBed, so an illegal mysql query was constructed.
Fix: added randomBigBedIds(). While in there, enhanced ramdomVcfIds() to ignore
runs of identical IDs because those are placeholders, and might otherwise crowd
out a few meaningful IDs (#8886 note 28).
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/hgTracks/hgTracks.c
- lines changed 6, context: html, text, full: html, text
adding measureTiming outputs for png trash file write and cart write close at end plus a single stderr output for overall total time to apache error_log
- src/hg/hgTracks/mainMain.c
- lines changed 4, context: html, text, full: html, text
adding measureTiming outputs for png trash file write and cart write close at end plus a single stderr output for overall total time to apache error_log
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/hgTracks/renderMain.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/hg/hgc/hgc.c
- lines changed 27, context: html, text, full: html, text
Finished redmine track #9629 ExonJunction Primers (qPCR Primers) track.
- lines changed 3, context: html, text, full: html, text
single stderr message at exit to indicate total run time in apache error_log
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/htdocs/ENCODE/index.html
- lines changed 1, context: html, text, full: html, text
Remove Updated notice on ENCODE portal
- src/hg/htdocs/FAQ/FAQreleases.html
- lines changed 1, context: html, text, full: html, text
Fixed a typo in release table.
- src/hg/htdocs/bestlinks.html
- lines changed 495, context: html, text, full: html, text
removing bestlinks.html
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 2, context: html, text, full: html, text
grammar edits from Donna's code review
- lines changed 312, context: html, text, full: html, text
Added news announcement for 28 new assemblies.
- lines changed 61, context: html, text, full: html, text
Fixed a few formatting things, added a link.
- lines changed 8, context: html, text, full: html, text
Moved tree shrew info in news item.
- lines changed 3, context: html, text, full: html, text
Fixed a few last typos noted by Steve.
- lines changed 1, context: html, text, full: html, text
Removed extraneous 'boliviensis' from saiBol1 Latin name
- lines changed 1, context: html, text, full: html, text
Removed extraneous 'boliviensis' from saiBol1
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 67, context: html, text, full: html, text
Updated 3 NAR DB pubs with final links + citation info.
- src/hg/htdocs/indexNews.html
- lines changed 2, context: html, text, full: html, text
grammar edits from Donna's code review
- lines changed 196, context: html, text, full: html, text
Added news announcement for 28 new assemblies.
- lines changed 7, context: html, text, full: html, text
Fixed a few formatting things, added a link.
- lines changed 10, context: html, text, full: html, text
Moved tree shrew info in news item.
- lines changed 2, context: html, text, full: html, text
Fixed a few last typos noted by Steve.
- lines changed 1, context: html, text, full: html, text
Removed extraneous 'boliviensis' from saiBol1 Latin name
- lines changed 1, context: html, text, full: html, text
Removed extraneous 'boliviensis' from saiBol1
- lines changed 1, context: html, text, full: html, text
changed link from direct link to genome list to a link to the contact us page (that way, folks might actually see that their post will live on forever)
- src/hg/inc/cart.h
- lines changed 4, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/lib/cart.c
- lines changed 8, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/lib/coriellDelDup.as
- lines changed 17, context: html, text, full: html, text
initial table definitions for coriellDelDup
- src/hg/lib/coriellDelDup.sql
- lines changed 17, context: html, text, full: html, text
initial table definitions for coriellDelDup
- src/hg/lib/encode/unused/README
- src/hg/lib/exonJunctionPrimers.as
- lines changed 18, context: html, text, full: html, text
redmine 9269: use bedDetail.as for exonJunctionPrimers track.
- src/hg/lib/exonJunctionPrimers.c
- lines changed 218, context: html, text, full: html, text
redmine 9269: use bedDetail.as for exonJunctionPrimers track.
- src/hg/lib/exonJunctionPrimers.sql
- lines changed 24, context: html, text, full: html, text
redmine 9269: use bedDetail.as for exonJunctionPrimers track.
- src/hg/lib/hdb.c
- lines changed 38, context: html, text, full: html, text
clean up error handling a little in support of #3130. Made failure to open seq file equivalent to other errors finding sequence in the database. This should change nothing if the seq is found, and should only change the error message if the file mentioned in extFile is not found, in which case the error will be something like "can't find sequence blatDeBlah" instead of "External file /gbdb/genbank/./data/processed/refseq.46/full/mrna.fa cannot be opened or has wrong size." Codon and base translation in hgTracks will fail silently and default to the standard display if the sequence is not available.
- src/hg/lib/makefile
- lines changed 1, context: html, text, full: html, text
redmine 9269: use bedDetail.as for exonJunctionPrimers track.
- src/hg/lib/tests/expected/spDbTest
- lines changed 170, context: html, text, full: html, text
add back spDbTest with database that exists
- src/hg/lib/tests/makefile
- lines changed 1, context: html, text, full: html, text
temporarily disabling spDbTest until I figure out how it should work with the most recent uniProt database.
- lines changed 3, context: html, text, full: html, text
add back spDbTest with database that exists
- src/hg/makeDb/doc/encodeAwgHg19/.awg.txt.swp
- lines changed 0, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- src/hg/makeDb/doc/encodeAwgHg19/awg.txt
- lines changed 142, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- src/hg/makeDb/doc/encodeAwgHg19/make.txt
- lines changed 13, context: html, text, full: html, text
New make doc for ENCODE analysis tracks
- src/hg/makeDb/doc/hg19.txt
- lines changed 24, context: html, text, full: html, text
redmine 9269: use bedDetail.as for exonJunctionPrimers track.
- lines changed 26, context: html, text, full: html, text
COSMIC v62 update script run
- lines changed 21, context: html, text, full: html, text
trackDb stuff for qPCR Primers tracks for mm10 and hg19 (redmine #9269)
- lines changed 38, context: html, text, full: html, text
redmine 6530 adding Coriell del/dup cell line track
- lines changed 3, context: html, text, full: html, text
redmine 9269 Rename exonJunction Primer to qPCR Primers.
- src/hg/makeDb/doc/mm10.txt
- lines changed 8, context: html, text, full: html, text
redmine 9269: use bedDetail.as for exonJunctionPrimers track.
- lines changed 213, context: html, text, full: html, text
Track #7043 (SNPs for mm10): build snp137* for mouse.
- lines changed 1, context: html, text, full: html, text
redmine 9269 Rename exonJunction Primer to qPCR Primers.
- src/hg/makeDb/doc/mm9.txt
- lines changed 28, context: html, text, full: html, text
trackDb stuff for qPCR Primers tracks for mm10 and hg19 (redmine #9269)
- src/hg/makeDb/genbank/etc/hgwbeta.dbs
- lines changed 1, context: html, text, full: html, text
Added petMar2 to hgwbeta.dbs; fixed ordering in hgwdev.dbs (redmine #9153)
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- lines changed 2, context: html, text, full: html, text
Added petMar2 to hgwbeta.dbs; fixed ordering in hgwdev.dbs (redmine #9153)
- src/hg/makeDb/genbank/etc/rr.dbs
- lines changed 1, context: html, text, full: html, text
Added petMar2 (redmine #9153)
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
Changed 'cpgIsland%' to 'cpgIslandExt' - cpgIslandExt was not being recognized in the tables ignored list
- lines changed 8, context: html, text, full: html, text
adding hg19Patch10 definitions
- src/hg/makeDb/trackDb/affyAllExonProbes.html
- src/hg/makeDb/trackDb/apis/apiMel1/description.html
- src/hg/makeDb/trackDb/apis/apiMel2/description.html
- src/hg/makeDb/trackDb/chicken/galGal2/description.html
- src/hg/makeDb/trackDb/chicken/galGal3/description.html
- src/hg/makeDb/trackDb/chicken/galGal4/description.html
- src/hg/makeDb/trackDb/cow/bosTau1/description.html
- src/hg/makeDb/trackDb/cow/bosTau2/description.html
- src/hg/makeDb/trackDb/cow/bosTau3/description.html
- src/hg/makeDb/trackDb/cow/bosTau4/description.html
- src/hg/makeDb/trackDb/cow/bosTau5/description.html
- src/hg/makeDb/trackDb/cow/bosTau6/description.html
- src/hg/makeDb/trackDb/cow/bosTau7/description.html
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 15, context: html, text, full: html, text
Adding the Snyder Heart sample
- lines changed 1, context: html, text, full: html, text
Correcting maligned website address for CELF1 catalogue page
- lines changed 5, context: html, text, full: html, text
Adding snyderlab to missing orderUrl and correcting EBF1 valdiation information to include IP-MassSpec and removing Western from MEF2A validation doc pointer
- lines changed 1, context: html, text, full: html, text
Adding URL to our protocl where line exists about ordering MRT_TTC549 from Dr. Timothy Triche
- lines changed 1, context: html, text, full: html, text
Removing redundancy of Snyder HEK293b protocols
- lines changed 12, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- lines changed 2, context: html, text, full: html, text
Fixing 8 typos in a couple of treatments
- lines changed 1, context: html, text, full: html, text
Fixing serum_stimulated_media description with details from Greg Crawford
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 203, context: html, text, full: html, text
beta review this is mostly antibody information being added from the pdfs or corrected pdfs being added
- src/hg/makeDb/trackDb/drosophila/geneMapper.html
- lines changed 2, context: html, text, full: html, text
Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
- src/hg/makeDb/trackDb/est.new.html
- lines changed 133, context: html, text, full: html, text
est.new.html should have been added months (years?) ago.
- src/hg/makeDb/trackDb/firstEF.html
- src/hg/makeDb/trackDb/human/coriellDelDup.html
- lines changed 18, context: html, text, full: html, text
adding new style of coriellDelDup track
- lines changed 58, context: html, text, full: html, text
updated coriell track description
- lines changed 1, context: html, text, full: html, text
found a better word to use
- src/hg/makeDb/trackDb/human/hg17/encodeMavidAlign.html
- lines changed 3, context: html, text, full: html, text
Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
- src/hg/makeDb/trackDb/human/hg17/encodeMavidCons.html
- lines changed 1, context: html, text, full: html, text
Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
- src/hg/makeDb/trackDb/human/hg17/encodeMsaElements.html
- lines changed 3, context: html, text, full: html, text
Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
- src/hg/makeDb/trackDb/human/hg19/cosmic.html
- lines changed 11, context: html, text, full: html, text
Updated links; fixed so links would open in a new window
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- lines changed 1, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnase.ra
- lines changed 1854, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- src/hg/makeDb/trackDb/human/hg19/snp137.html
- lines changed 1, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- src/hg/makeDb/trackDb/human/hg19/snp137.shared.html
- lines changed 1, context: html, text, full: html, text
html tag typo fix (found by hgTablesTest).
- lines changed 462, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- src/hg/makeDb/trackDb/human/hg19/snp137Common.html
- lines changed 28, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- src/hg/makeDb/trackDb/human/hg19/snp137Flagged.html
- lines changed 1, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- src/hg/makeDb/trackDb/human/hg19/snp137FlaggedMention.html
- lines changed 4, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- src/hg/makeDb/trackDb/human/hg19/snp137Mult.html
- lines changed 25, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 47, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- lines changed 8, context: html, text, full: html, text
trackDb stuff for qPCR Primers tracks for mm10 and hg19 (redmine #9269)
- lines changed 2, context: html, text, full: html, text
Finished redmine track #9629 ExonJunction Primers (qPCR Primers) track.
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 3, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnase.ra
- lines changed 910, context: html, text, full: html, text
First cut trackDb and HTML for AWG Dnase track
- lines changed 128, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- lines changed 4, context: html, text, full: html, text
Adjust ENCODE DNase track ordering
- src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniPk.html
- lines changed 59, context: html, text, full: html, text
First cut trackDb and HTML for AWG Dnase track
- src/hg/makeDb/trackDb/human/hg19/wgEncodeDNAseSuper.html
- lines changed 4, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
- lines changed 1, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release3.ra
- lines changed 1, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- lines changed 1, context: html, text, full: html, text
Adjust ENCODE DNase track ordering
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.ra
- lines changed 2, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- lines changed 1, context: html, text, full: html, text
Adjust ENCODE DNase track ordering
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra
- lines changed 2, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- lines changed 3, context: html, text, full: html, text
Adjust ENCODE DNase track ordering
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.ra
- lines changed 2, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- lines changed 1, context: html, text, full: html, text
Adjust ENCODE DNase track ordering
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release6.ra
- lines changed 2, context: html, text, full: html, text
ENCODE Analysis DNase I HS from uniform pipeline. Track #9850
- lines changed 1, context: html, text, full: html, text
Adjust ENCODE DNase track ordering
- lines changed 1, context: html, text, full: html, text
It had the wrong view limits
- src/hg/makeDb/trackDb/human/slamMouse.html
- lines changed 1, context: html, text, full: html, text
Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
- src/hg/makeDb/trackDb/human/slamNonCodingMouse.html
- lines changed 1, context: html, text, full: html, text
Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
- src/hg/makeDb/trackDb/human/slamNonCodingRat.html
- lines changed 1, context: html, text, full: html, text
Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
- src/hg/makeDb/trackDb/human/slamRat.html
- lines changed 1, context: html, text, full: html, text
Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
- src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
Added priority section for petMar2 to various trackDb.chainNet.ra files; adjusted release tags for petMar1/2 chainNet.ra files in the main trackDb.chainNet.ra file (redmine #9153)
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 12, context: html, text, full: html, text
adding new style of coriellDelDup track
- lines changed 1, context: html, text, full: html, text
moving coriell track to phenotype/disease group. these variants are all disease-asociated
- src/hg/makeDb/trackDb/human/vistaEnhancers.html
- src/hg/makeDb/trackDb/lamprey/petMar1/description.html
- lines changed 1, context: html, text, full: html, text
Updated photo link (redmine #9153)
- src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
- lines changed 64, context: html, text, full: html, text
Updated links in References section; made other minor corrections (redmine #9153)
- lines changed 2, context: html, text, full: html, text
Fixed entries in the 'Gene tracks used for codon translation' table (redmine #9153)
- src/hg/makeDb/trackDb/lamprey/petMar2/description.html
- lines changed 1, context: html, text, full: html, text
Updated photo link (redmine #9153)
- lines changed 1, context: html, text, full: html, text
Made minor corrections (redmine #9153)
- src/hg/makeDb/trackDb/lamprey/petMar2/gap.html
- lines changed 3, context: html, text, full: html, text
Made minor corrections (redmine #9153)
- src/hg/makeDb/trackDb/lamprey/petMar2/gold.html
- lines changed 4, context: html, text, full: html, text
Made minor corrections (redmine #9153)
- src/hg/makeDb/trackDb/lamprey/petMar2/trackDb.ra
- lines changed 8, context: html, text, full: html, text
add perfect search rule for the gold table to find all frags
- src/hg/makeDb/trackDb/lancelet/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
Added priority section for petMar2 to various trackDb.chainNet.ra files; adjusted release tags for petMar1/2 chainNet.ra files in the main trackDb.chainNet.ra file (redmine #9153)
- src/hg/makeDb/trackDb/mouse/igtc.html
- lines changed 6, context: html, text, full: html, text
IGTC member link corrections from Steve.
- src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
- lines changed 30, context: html, text, full: html, text
Changed data-download-only links to hgGateway links now that all assemblies in the 60-way have been released to the RR.
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
- lines changed 10, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- lines changed 8, context: html, text, full: html, text
trackDb stuff for qPCR Primers tracks for mm10 and hg19 (redmine #9269)
- lines changed 2, context: html, text, full: html, text
Finished redmine track #9629 ExonJunction Primers (qPCR Primers) track.
- src/hg/makeDb/trackDb/mouse/slamHuman.html
- lines changed 2, context: html, text, full: html, text
Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
- src/hg/makeDb/trackDb/mouse/slamNonCodingHuman.html
- lines changed 3, context: html, text, full: html, text
Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
- src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
Added priority section for petMar2 to various trackDb.chainNet.ra files; adjusted release tags for petMar1/2 chainNet.ra files in the main trackDb.chainNet.ra file (redmine #9153)
- src/hg/makeDb/trackDb/opossum/monDom1/description.html
- src/hg/makeDb/trackDb/opossum/monDom2/description.html
- src/hg/makeDb/trackDb/opossum/monDom4/description.html
- src/hg/makeDb/trackDb/opossum/monDom5/description.html
- src/hg/makeDb/trackDb/pig/susScr2/description.html
- src/hg/makeDb/trackDb/qpcrPrimers.html
- lines changed 85, context: html, text, full: html, text
Use qpcrPrimers.html to describe qpcrPrimers track. Redmine 9269.
- lines changed 16, context: html, text, full: html, text
Finished redmine track #9629 ExonJunction Primers (qPCR Primers) track.
- lines changed 21, context: html, text, full: html, text
redmine 9269 qPCR Primers track: Make exonJunctionPrimers table exact search-able, and polishing the descrition html per feedback from data provider.
- src/hg/makeDb/trackDb/rat/rn1/description.html
- src/hg/makeDb/trackDb/rat/rn2/description.html
- src/hg/makeDb/trackDb/rat/rn3/description.html
- src/hg/makeDb/trackDb/rat/rn4/description.html
- src/hg/makeDb/trackDb/rat/rn5/description.html
- src/hg/makeDb/trackDb/rat/slamHuman.html
- lines changed 2, context: html, text, full: html, text
Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
- src/hg/makeDb/trackDb/rat/slamNonCodingHuman.html
- lines changed 6, context: html, text, full: html, text
Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
- src/hg/makeDb/trackDb/snp137.html
- lines changed 31, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- src/hg/makeDb/trackDb/snp137.shared.html
- lines changed 460, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- src/hg/makeDb/trackDb/snp137Common.html
- lines changed 28, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- src/hg/makeDb/trackDb/snp137Mult.html
- lines changed 25, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- src/hg/makeDb/trackDb/trackDb.chainNet.ra
- lines changed 2, context: html, text, full: html, text
Added priority section for petMar2 to various trackDb.chainNet.ra files; adjusted release tags for petMar1/2 chainNet.ra files in the main trackDb.chainNet.ra file (redmine #9153)
- lines changed 2, context: html, text, full: html, text
Adjusted release tags for petMar1/2 (redmine #9153)
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 50, context: html, text, full: html, text
Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
with mouse. Leave Flagged SNPs in human/hg19 because that track is
human-only, and mention Flagged SNPs only in human description.
- lines changed 12, context: html, text, full: html, text
trackDb stuff for qPCR Primers tracks for mm10 and hg19 (redmine #9269)
- lines changed 1, context: html, text, full: html, text
Use qpcrPrimers.html to describe qpcrPrimers track. Redmine 9269.
- lines changed 3, context: html, text, full: html, text
Finished redmine track #9629 ExonJunction Primers (qPCR Primers) track.
- lines changed 4, context: html, text, full: html, text
redmine 9269 qPCR Primers track: Make exonJunctionPrimers table exact search-able, and polishing the descrition html per feedback from data provider.
- src/hg/makeDb/trackDb/zebrafish/danRer1/description.html
- src/hg/makeDb/trackDb/zebrafish/danRer2/description.html
- src/hg/makeDb/trackDb/zebrafish/danRer3/description.html
- src/hg/makeDb/trackDb/zebrafish/danRer4/description.html
- src/hg/makeDb/trackDb/zebrafish/danRer5/description.html
- src/hg/makeDb/trackDb/zebrafish/danRer6/description.html
- src/hg/makeDb/trackDb/zebrafish/danRer7/description.html
- src/hg/near/hgNear/hgNear.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime printout to a number of CGI binaries
- src/hg/snp/snpLoad/snpNcbiToUcsc.c
- lines changed 2, context: html, text, full: html, text
Track #7043 (SNPs for mm10): bump up MAX_SNP_ID.
- src/hg/utils/automation/doDbSnp.pl
- lines changed 28, context: html, text, full: html, text
Track #7043 (SNPs for mm10): added ignoreDbSnpContigsFile config.ra option (see -help output).
- src/hg/utils/automation/makeGenomeDb.pl
- lines changed 5, context: html, text, full: html, text
fixup URL links to NCBI for description pages redmine 9153
- src/hg/visiGene/hgVisiGene/hgVisiGene.c
- lines changed 2, context: html, text, full: html, text
adding cgiExitTime stderr printout to CGI binaries for apache error_log information
- src/inc/localmem.h
- lines changed 5, context: html, text, full: html, text
Code Review #9844 - Hiram pointed out that localmem.h is not protectedagainst multiple inclusion; fixed. Also cleaned up some redundant
inclusions of localmem.h in files that already include bbiFile.h.
- src/kehayden/alphaAsm/alphaAsm.c
- lines changed 130, context: html, text, full: html, text
Starting work on a second pass of processing to put in monomers that did not get omitted by main pass.
- lines changed 29, context: html, text, full: html, text
Adding a new check on input.
- lines changed 13, context: html, text, full: html, text
More progress towards substituting in missing monomers.
- lines changed 158, context: html, text, full: html, text
Fixing end condition in matchExceptCenter. Rearranging debugging code.
- lines changed 61, context: html, text, full: html, text
Adding fall back logic to place unused monomers by type if they can't be placed by context.
- lines changed 32, context: html, text, full: html, text
Making subCenterInNeighborhood routine work on a wider variety of input and putting in some additional logging/debugging options.
- src/lib/bbiRead.c
- lines changed 1, context: html, text, full: html, text
Code Review #9844 - Hiram pointed out that localmem.h is not protectedagainst multiple inclusion; fixed. Also cleaned up some redundant
inclusions of localmem.h in files that already include bbiFile.h.
- src/lib/bbiWrite.c
- lines changed 1, context: html, text, full: html, text
Code Review #9844 - Hiram pointed out that localmem.h is not protectedagainst multiple inclusion; fixed. Also cleaned up some redundant
inclusions of localmem.h in files that already include bbiFile.h.
- src/lib/bigBed.c
- lines changed 1, context: html, text, full: html, text
Code Review #9844 - Hiram pointed out that localmem.h is not protectedagainst multiple inclusion; fixed. Also cleaned up some redundant
inclusions of localmem.h in files that already include bbiFile.h.
- src/lib/bwgCreate.c
- lines changed 1, context: html, text, full: html, text
Code Review #9844 - Hiram pointed out that localmem.h is not protectedagainst multiple inclusion; fixed. Also cleaned up some redundant
inclusions of localmem.h in files that already include bbiFile.h.
- src/lib/bwgQuery.c
- lines changed 1, context: html, text, full: html, text
Code Review #9844 - Hiram pointed out that localmem.h is not protectedagainst multiple inclusion; fixed. Also cleaned up some redundant
inclusions of localmem.h in files that already include bbiFile.h.
- src/lib/bwgValsOnChrom.c
- lines changed 1, context: html, text, full: html, text
Code Review #9844 - Hiram pointed out that localmem.h is not protectedagainst multiple inclusion; fixed. Also cleaned up some redundant
inclusions of localmem.h in files that already include bbiFile.h.
- src/utils/qa/checkAllStaticLinks.csh
- lines changed 6, context: html, text, full: html, text
changed the usgae statement a bit
- src/utils/qa/checkStaticLinks.csh
- lines changed 55, context: html, text, full: html, text
added process-specific filenaming using 32392 where possible. made tmp filenames less clobberish via more obscure names where not. improved usage statement. all in response to feedback from brooke
- src/utils/qa/linkCheckExclude
- lines changed 1, context: html, text, full: html, text
adding releaseLog.html to list of files not to check. 500+ errors being found.
- src/utils/qa/showLastGit.csh
- lines changed 2, context: html, text, full: html, text
mods per brooke's suggestions. fixes bug when the word 'commit' is in the commit comment and changes old name for script in usage statement to current name
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/qa/whoMadeIt.csh
- lines changed 33, context: html, text, full: html, text
made filewriting less clobber-prone by adding 32393 to filenames where convenient, renaming tmp-dollar-i to tmp001-dollar-i because not convenient to add 32393. added cleanup. all per suggestions from brooke
- lines changed: 8624
- files changed: 240