All File Changes
v311_base to v312_preview (2015-01-26 to 2015-02-02) v312
- src/browserbox/makefile
- lines changed 6, context: html, text, full: html, text
adding possibility to force auto updates to off in gbib, refs #14602
- src/browserbox/root/updateBrowser.sh
- lines changed 26, context: html, text, full: html, text
adding possibility to force auto updates to off in gbib, refs #14602
- src/hg/hgAi/hgAi.c
- lines changed 6, context: html, text, full: html, text
Add yet another special case for all_* tables.
- src/hg/hgTables/schema.c
- lines changed 2, context: html, text, full: html, text
Fixed a bug that caused split tables to crash in the browser
- src/hg/hgTracks/config.c
- lines changed 6, context: html, text, full: html, text
Fixes #7474 - mouseover now shows exon and intron numbers for linkedFeatures tracks.
- src/hg/hgTracks/hgTracks.c
- lines changed 1, context: html, text, full: html, text
Fixes #7474 - mouseover now shows exon and intron numbers for linkedFeatures tracks.
- src/hg/hgTracks/hgTracks.h
- lines changed 1, context: html, text, full: html, text
Fixes #7474 - mouseover now shows exon and intron numbers for linkedFeatures tracks.
- src/hg/hgTracks/retroGene.c
- lines changed 9, context: html, text, full: html, text
update hard-coded list of retrogene tracks to register
- src/hg/hgTracks/simpleTracks.c
- lines changed 227, context: html, text, full: html, text
Fixes #7474 - mouseover now shows exon and intron numbers for linkedFeatures tracks.
- src/hg/hgc/retroClick.c
- lines changed 1, context: html, text, full: html, text
Removed description line which would only appear on the details page and merged it with the existing Description section in the HTML description page.
- src/hg/htdocs/goldenPath/help/gbib.html
- lines changed 3, context: html, text, full: html, text
Adding link in GBiB help doc to Assembly Hub step-by-step example
- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
- lines changed 39, context: html, text, full: html, text
Adding notes to Track Hub User Guide about new Assembly QuickStart Guide, and updating Hub Connection process
- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
- lines changed 259, context: html, text, full: html, text
Adding quick start guide to assembly hubs with blat documentation
- lines changed 28, context: html, text, full: html, text
Adding notes to Track Hub User Guide about new Assembly QuickStart Guide, and updating Hub Connection process
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
- lines changed 3, context: html, text, full: html, text
Documents new trackDb setting exonNumbers 7474
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
- lines changed 3, context: html, text, full: html, text
Documents new trackDb setting exonNumbers 7474
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 12, context: html, text, full: html, text
Documents new trackDb setting exonNumbers 7474
- lines changed 1, context: html, text, full: html, text
adding type psl to list of allowed types for new exonNumbers setting
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 16, context: html, text, full: html, text
Staging entries for relaunch of training intake survey. refs #14714
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 6, context: html, text, full: html, text
Adding Ebola paper to pubs.
- src/hg/htdocs/images/training/vidTitle06.jpg
- lines changed 0, context: html, text, full: html, text
adding title slides for vids 06, 07. refs #13969
- src/hg/htdocs/images/training/vidTitle07.jpg
- lines changed 0, context: html, text, full: html, text
adding title slides for vids 06, 07. refs #13969
- src/hg/htdocs/indexNews.html
- lines changed 35, context: html, text, full: html, text
Abridged entries were missing for last 3 announcements. Prepping for survey relaunch. refs #14714
- lines changed 22, context: html, text, full: html, text
Staging entries for relaunch of training intake survey. refs #14714
- src/hg/js/hgTracks.js
- lines changed 17, context: html, text, full: html, text
Fixes #7474 - mouseover now shows exon and intron numbers for linkedFeatures tracks.
- src/hg/js/react/hgAi/hgAi.jsx
- lines changed 32, context: html, text, full: html, text
Minor refactoring: instead of passing a schema link object into AddDataSource,
make it locally.
- src/hg/lib/cartJson.c
- lines changed 14, context: html, text, full: html, text
All Tracks / All Tables groups are not yet working in hgAi; I have a
plan to fix it right, but for now, just omit those groups.
refs #14579
- src/hg/makeDb/doc/bosTau8.txt
- lines changed 79, context: html, text, full: html, text
lastz chain net liftOver files for user request refs #14625
- src/hg/makeDb/doc/danRer10/initialBuild.txt
- lines changed 105, context: html, text, full: html, text
now running genbank refs #14017
- lines changed 19, context: html, text, full: html, text
liftOver to danRer7 refs #14017
- src/hg/makeDb/doc/danRer7.txt
- lines changed 15, context: html, text, full: html, text
liftOver to danRer10 refs #14017
- src/hg/makeDb/doc/eboVir3/gbkToGp.pl
- lines changed 1, context: html, text, full: html, text
update 2015-01-06 refs #14278
- src/hg/makeDb/doc/eboVir3/newSequences.txt
- lines changed 49, context: html, text, full: html, text
update 2015-01-06 refs #14278
- lines changed 6, context: html, text, full: html, text
update added KP658432v1 KP342330v1 refs #14278
- src/hg/makeDb/doc/equCab2.txt
- lines changed 79, context: html, text, full: html, text
lastz chain net liftOver files for user request refs #14625
- src/hg/makeDb/doc/felCat8/initialBuild.txt
- lines changed 8, context: html, text, full: html, text
felCat8 in the pushQ refs #14412
- src/hg/makeDb/doc/felCat8/lastzRuns.txt
- lines changed 73, context: html, text, full: html, text
felCat8 in the pushQ refs #14412
- src/hg/makeDb/doc/hg19.txt
- lines changed 18, context: html, text, full: html, text
Jonathan found that snp*ExceptionDesc's NonIntegerChromCount was more
than twice the number of rows in the snp table with that exception.
Turns out it was incremented in a loop on alleles. Rebuilt w/corrected
counts. Note: ExceptionDesc counts can still be slightly higher than
snp table counts because several exceptions are logged before the point
at which we decide whether to keep or discard a variant.
refs #14189
- lines changed 0, context: html, text, full: html, text
lastz chain net liftOver files for user request refs #14625
- src/hg/makeDb/doc/hg38/reg.txt
- lines changed 11, context: html, text, full: html, text
Add tool to check links in a table (based on columnName 'url')
- src/hg/makeDb/doc/hg38/variation.txt
- lines changed 18, context: html, text, full: html, text
Jonathan found that snp*ExceptionDesc's NonIntegerChromCount was more
than twice the number of rows in the snp table with that exception.
Turns out it was incremented in a loop on alleles. Rebuilt w/corrected
counts. Note: ExceptionDesc counts can still be slightly higher than
snp table counts because several exceptions are logged before the point
at which we decide whether to keep or discard a variant.
refs #14189
- src/hg/makeDb/doc/macFas5/initialBuild.txt
- lines changed 20, context: html, text, full: html, text
in the pushQ refs #11174
- src/hg/makeDb/doc/macFas5/lastzRuns.txt
- lines changed 151, context: html, text, full: html, text
in the pushQ refs #11174
- src/hg/makeDb/doc/mm10.txt
- lines changed 0, context: html, text, full: html, text
lastz chain net liftOver files for user request refs #14625
- src/hg/makeDb/doc/oviAri3.txt
- lines changed 49, context: html, text, full: html, text
lastz chain net liftOver files for user request refs #14625
- src/hg/makeDb/genbank/etc/align.dbs
- lines changed 1, context: html, text, full: html, text
Added danRer10 - Zebrafish refs #14017
- src/hg/makeDb/genbank/etc/euronode-copy
- lines changed 1, context: html, text, full: html, text
some moving around of data on the euronode
- src/hg/makeDb/genbank/etc/euronode-dbload
- lines changed 2, context: html, text, full: html, text
some moving around of data on the euronode
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 19, context: html, text, full: html, text
Added danRer10; refs #14017
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- lines changed 1, context: html, text, full: html, text
Added danRer10 - Zebrafish refs #14017
- src/hg/makeDb/genbank/etc/ignore.idx
- lines changed 13, context: html, text, full: html, text
new things for the genbank pipeline to ignore
- lines changed 1, context: html, text, full: html, text
another thing for genbank to ignore
- lines changed 1, context: html, text, full: html, text
another thing to ignore from genbank
- src/hg/makeDb/schema/all.joiner
- lines changed 9, context: html, text, full: html, text
Removing merge conflict caught by Kate. refs #14740
- lines changed 11, context: html, text, full: html, text
adding danRer10 rules refs #14017
- src/hg/makeDb/trackDb/ebola/eboVir3/newSeqs.html
- lines changed 2, context: html, text, full: html, text
adding KP342330.1 KP658432.1 refs #14278
- src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.newSequences.ra
- lines changed 1, context: html, text, full: html, text
adding KP342330.1 KP658432.1 refs #14278
- lines changed 1, context: html, text, full: html, text
correct ordering KP342330.1 KP658432.1 refs #14278
- src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
- lines changed 65, context: html, text, full: html, text
Clean up hg19 ENCODE Regulation track defaults on genome-test
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Removed the nextItemButton setting for Retroposed Genes V9.
- lines changed 2, context: html, text, full: html, text
Changing shortLabel and turning off mouseover exon numbering for Retroposed genes track on mm10,hg38. refs #14719 #14720
- src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
Added wgEncodeReg.ra to the file
- src/hg/makeDb/trackDb/human/hg38/ucscRetroAli9.html
- lines changed 6, context: html, text, full: html, text
Merged a track description hard-coded in retroClick.c (hgc) into the Description section in the HTML description page.
- src/hg/makeDb/trackDb/human/hg38/uwDnase.ra
- lines changed 421, context: html, text, full: html, text
Polish track labels. Change defaults to be cell types in ENCODE Reg Txn track. refs #14353
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
- lines changed 384, context: html, text, full: html, text
Created a .ra file describing the ENCODE Regulatory basic tracks
- src/hg/makeDb/trackDb/human/snp142.shared.html
- lines changed 16, context: html, text, full: html, text
Correcting the names of the dbSNP download files since they now tweak the paths for human.
refs #14189
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Removed the nextItemButton setting for Retroposed Genes V6.
- lines changed 2, context: html, text, full: html, text
Changing shortLabel and turning off mouseover exon numbering for Retroposed genes track on mm10,hg38. refs #14719 #14720
- src/hg/makeDb/trackDb/mouse/mm10/ucscRetroAli6.html
- lines changed 6, context: html, text, full: html, text
Merged a track description hard-coded in retroClick.c (hgc) into the Description section in the HTML description page.
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 1, context: html, text, full: html, text
Fixes #7474 - mouseover now shows exon and intron numbers for linkedFeatures tracks.
- lines changed 1, context: html, text, full: html, text
adding type psl to list of allowed types for new exonNumbers setting
- src/hg/snp/snpLoad/snpNcbiToUcsc.c
- lines changed 4, context: html, text, full: html, text
Jonathan found that snp*ExceptionDesc's NonIntegerChromCount was more
than twice the number of rows in the snp table with that exception.
Turns out it was incremented in a loop on alleles. Rebuilt w/corrected
counts. Note: ExceptionDesc counts can still be slightly higher than
snp table counts because several exceptions are logged before the point
at which we decide whether to keep or discard a variant.
refs #14189
- src/hg/utils/checkUrlsInTable/checkUrlsInTable.c
- lines changed 76, context: html, text, full: html, text
Tool for checking metadata term tables (and any others having a column with urls
- src/hg/utils/checkUrlsInTable/makefile
- lines changed 4, context: html, text, full: html, text
Makefile for table checker
- src/hg/utils/makefile
- lines changed 13, context: html, text, full: html, text
Add tool to check links in a table (based on columnName 'url')
- lines changed 1, context: html, text, full: html, text
fixed plurality typo - script is checkUrlsInTable, not Tables
- src/lib/common.c
- lines changed 1, context: html, text, full: html, text
don't flush stdin magic handle on close
- src/utils/bedToBigBed/bedToBigBed.c
- lines changed 2, context: html, text, full: html, text
incremented bedToBigBed version to 2.7
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
v312 preview1 refs #14768
- lines changed: 2564
- files changed: 81