All File Changes
v339_preview to v339_preview2 (2016-09-12 to 2016-09-19) v339
Show details
- src/hg/cirm/cdw/lib/cdwValid.c
- lines changed 6, context: html, text, full: html, text
3de1b67bd1fd8a4aa09a2cccd5d567974170280a Thu Sep 15 13:32:10 2016 -0700
Added prostate cancer to disease CV and RRBS to assay.
- src/hg/hgTables/identifiers.c
- lines changed 4, context: html, text, full: html, text
c2e328a602e37d5f2852483ab52b0955fa8917a1 Wed Sep 14 10:59:01 2016 -0700
fix a problem with paste identifiers in hgTables and knownGene
- lines changed 1, context: html, text, full: html, text
396071902267c1654f7eafaf60962aad935a9558 Thu Sep 15 17:08:36 2016 -0700
Changing htmlSafef to use %s|none| instead of %-s because %-s has some legitimate uses in html output which means left-justifying the text. Jim uses it in hgBlat. This will make it more general, although it is longer to read and write. For sqlSafef, there was no legitimate expected need to have left-justified output in the production of a SQL statement.
- src/hg/hgTracks/mafTrack.h
- lines changed 2, context: html, text, full: html, text
ce26615a6b46918c97156a4a4dea119f5b552538 Sun Sep 18 07:41:37 2016 -0700
make the switch to MAF summary mode be settable by a conf or cart
variable
- src/hg/hgc/bigBedClick.c
- lines changed 17, context: html, text, full: html, text
2a17d0be037117b42ee7c740fd98fadf0e58aff2 Mon Sep 12 16:58:05 2016 -0700
changes after code review, refs #18067
- lines changed 7, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/hgc/hgc.c
- lines changed 3, context: html, text, full: html, text
c7fdc1805832f663571ace22ba66a39efc420dc3 Thu Sep 15 12:14:04 2016 -0700
abort on bigBedItem not being found rather than core dump (this is happening because of other errors in the browser)
- lines changed 8, context: html, text, full: html, text
3fbd5278d976e75ab044723b2356bea81ab4aa26 Thu Sep 15 13:04:15 2016 -0700
Always encode item names when generating URLs in hgcAnchorSomewhere. This prevents item names with CGI-unsafe characters from being incorrectly encode. This was happening with PSLs, but could happen in other structures
- src/hg/htdocs/goldenPath/help/bigBed.html
- lines changed 14, context: html, text, full: html, text
2a17d0be037117b42ee7c740fd98fadf0e58aff2 Mon Sep 12 16:58:05 2016 -0700
changes after code review, refs #18067
- src/hg/htdocs/images/crisprFig_effScores.png
- lines changed 0, context: html, text, full: html, text
2a17d0be037117b42ee7c740fd98fadf0e58aff2 Mon Sep 12 16:58:05 2016 -0700
changes after code review, refs #18067
- lines changed 0, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- lines changed 0, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/htdocs/images/crisprFig_mitScore.png
- lines changed 0, context: html, text, full: html, text
2a17d0be037117b42ee7c740fd98fadf0e58aff2 Mon Sep 12 16:58:05 2016 -0700
changes after code review, refs #18067
- lines changed 0, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/js/ajax.js
- lines changed 0, context: html, text, full: html, text
73f3cdf57c975b34070a5c6a93c82565aa3b8c6f Wed Sep 14 14:35:48 2016 -0700
fixing tabs
- src/hg/js/autocomplete.js
- lines changed 0, context: html, text, full: html, text
73f3cdf57c975b34070a5c6a93c82565aa3b8c6f Wed Sep 14 14:35:48 2016 -0700
fixing tabs
- src/hg/js/hgTracks.js
- lines changed 2, context: html, text, full: html, text
37b585ad1c4f5bfa5598fa987485d56120ef6d9e Wed Sep 14 14:18:05 2016 -0700
Fixes #18702. Uses async=false flag with cart.setVarsObj to prevent network error in Firefox and Safari while saving the state of the hidden highlight popup. It needs to wait for the ajax update to finish before submitting the form.
- lines changed 0, context: html, text, full: html, text
73f3cdf57c975b34070a5c6a93c82565aa3b8c6f Wed Sep 14 14:35:48 2016 -0700
fixing tabs
- src/hg/js/utils.js
- lines changed 0, context: html, text, full: html, text
73f3cdf57c975b34070a5c6a93c82565aa3b8c6f Wed Sep 14 14:35:48 2016 -0700
fixing tabs
- src/hg/lib/chromAlias.as
- lines changed 7, context: html, text, full: html, text
cfb63bd22072217bc504665d8abeb5f81587c8d7 Thu Sep 15 18:09:14 2016 -0700
better to call chromXref as chromAlias and now is a three column table with primary key refs #18027
- src/hg/lib/chromAlias.c
- lines changed 164, context: html, text, full: html, text
cfb63bd22072217bc504665d8abeb5f81587c8d7 Thu Sep 15 18:09:14 2016 -0700
better to call chromXref as chromAlias and now is a three column table with primary key refs #18027
- src/hg/lib/chromAlias.h
- lines changed 68, context: html, text, full: html, text
cfb63bd22072217bc504665d8abeb5f81587c8d7 Thu Sep 15 18:09:14 2016 -0700
better to call chromXref as chromAlias and now is a three column table with primary key refs #18027
- src/hg/lib/chromAlias.sql
- lines changed 15, context: html, text, full: html, text
cfb63bd22072217bc504665d8abeb5f81587c8d7 Thu Sep 15 18:09:14 2016 -0700
better to call chromXref as chromAlias and now is a three column table with primary key refs #18027
- src/hg/lib/chromXref.as
- lines changed 8, context: html, text, full: html, text
afa4cc7f36a1d3d5c2e4dc4f20fbf6332a4258a3 Thu Sep 15 11:28:56 2016 -0700
allow chrom name lookup to use the new chromXref table refs #18027
- lines changed 8, context: html, text, full: html, text
cfb63bd22072217bc504665d8abeb5f81587c8d7 Thu Sep 15 18:09:14 2016 -0700
better to call chromXref as chromAlias and now is a three column table with primary key refs #18027
- src/hg/lib/chromXref.c
- lines changed 180, context: html, text, full: html, text
afa4cc7f36a1d3d5c2e4dc4f20fbf6332a4258a3 Thu Sep 15 11:28:56 2016 -0700
allow chrom name lookup to use the new chromXref table refs #18027
- lines changed 180, context: html, text, full: html, text
cfb63bd22072217bc504665d8abeb5f81587c8d7 Thu Sep 15 18:09:14 2016 -0700
better to call chromXref as chromAlias and now is a three column table with primary key refs #18027
- src/hg/lib/chromXref.h
- lines changed 69, context: html, text, full: html, text
afa4cc7f36a1d3d5c2e4dc4f20fbf6332a4258a3 Thu Sep 15 11:28:56 2016 -0700
allow chrom name lookup to use the new chromXref table refs #18027
- lines changed 69, context: html, text, full: html, text
cfb63bd22072217bc504665d8abeb5f81587c8d7 Thu Sep 15 18:09:14 2016 -0700
better to call chromXref as chromAlias and now is a three column table with primary key refs #18027
- src/hg/lib/chromXref.sql
- lines changed 17, context: html, text, full: html, text
afa4cc7f36a1d3d5c2e4dc4f20fbf6332a4258a3 Thu Sep 15 11:28:56 2016 -0700
allow chrom name lookup to use the new chromXref table refs #18027
- lines changed 17, context: html, text, full: html, text
cfb63bd22072217bc504665d8abeb5f81587c8d7 Thu Sep 15 18:09:14 2016 -0700
better to call chromXref as chromAlias and now is a three column table with primary key refs #18027
- src/hg/lib/hdb.c
- lines changed 15, context: html, text, full: html, text
938f87d8ba8f5b68f03d807bec70521363de8a48 Thu Sep 15 10:45:05 2016 -0700
allow chrom name lookup to use the new chromXref table refs #18027
- lines changed 7, context: html, text, full: html, text
797801aaef4865bebc8a7c79dfb3d642f34d229d Thu Sep 15 18:09:41 2016 -0700
better to call chromXref as chromAlias and now is a three column table with primary key refs #18027
- src/hg/lib/jksql.c
- lines changed 1, context: html, text, full: html, text
8d22a576e16342266ce80501318803e7b0fa466b Fri Sep 16 11:48:02 2016 -0700
redundant va_end called is not needed. now it follows the standard. va_end was getting called twice incorrectly even though we saw no errors from it.
- src/hg/lib/makefile
- lines changed 1, context: html, text, full: html, text
2edf7f2a5c920c48a1dcef8a6a4b898cdf6bbd81 Thu Sep 15 11:29:10 2016 -0700
allow chrom name lookup to use the new chromXref table refs #18027
- lines changed 1, context: html, text, full: html, text
cfb63bd22072217bc504665d8abeb5f81587c8d7 Thu Sep 15 18:09:14 2016 -0700
better to call chromXref as chromAlias and now is a three column table with primary key refs #18027
- src/hg/makeDb/crisprTrack/README.txt
- lines changed 20, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- src/hg/makeDb/crisprTrack/convOffs.py
- lines changed 218, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- lines changed 2, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/crisprTrack/createBigBed.py
- lines changed 269, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- lines changed 29, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/crisprTrack/crispr.as
- lines changed 24, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- lines changed 2, context: html, text, full: html, text
6a6601af833d56ea447e086ceffc061c5c7054e9 Thu Sep 15 10:50:11 2016 -0700
fixing .as file for crispr track, refs #17235
- lines changed 2, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/crisprTrack/crisprScanRanks.tab
- lines changed 175, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- src/hg/makeDb/crisprTrack/doCrispr.sh
- lines changed 143, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/crisprTrack/findGuides.py
- lines changed 203, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- src/hg/makeDb/crisprTrack/fusiRanks.tab
- lines changed 111, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- src/hg/makeDb/crisprTrack/jobCalcEffScores.py
- lines changed 64, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- src/hg/makeDb/crisprTrack/lib/twobitreader/__init__.py
- lines changed 698, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- src/hg/makeDb/crisprTrack/lib/twobitreader/__main__.py
- lines changed 3, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- src/hg/makeDb/crisprTrack/lib/twobitreader/download.py
- lines changed 50, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- src/hg/makeDb/crisprTrack/makeSpecJoblist.py
- lines changed 26, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- src/hg/makeDb/crisprTrack/makefile
- lines changed 3, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- lines changed 7, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/crisprTrack/splitGuidesEffScore.py
- lines changed 79, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- src/hg/makeDb/crisprTrack/splitGuidesSpecScore.py
- lines changed 94, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- src/hg/makeDb/doc/ce10.txt
- lines changed 3, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/doc/ci2.txt
- lines changed 3, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/doc/danRer7.txt
- lines changed 3, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/doc/dm6.txt
- lines changed 3, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- lines changed 81, context: html, text, full: html, text
236f60e04690010ceaa4f617413f59b6b5ddace1 Sat Sep 17 18:44:23 2016 -0700
refGenePfam for dm6
- src/hg/makeDb/doc/hg19.txt
- lines changed 3, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/doc/hg38/crispr.txt
- lines changed 2, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/doc/mm10.txt
- lines changed 3, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/doc/rn5.txt
- lines changed 3, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/doc/sacCer3.txt
- lines changed 3, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
788a0c75d33b15155e69eb89b72506aa0c463099 Mon Sep 12 14:20:03 2016 -0700
Adding dupeOk to lrgTranscriptAli rule, refs #13359
- src/hg/makeDb/trackDb/crispr.html
- lines changed 163, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/hg/makeDb/trackDb/human/hg19/exac.html
- lines changed 17, context: html, text, full: html, text
6ab1064d063308d205d8bf728c0cebd91b45293f Mon Sep 12 10:08:52 2016 -0700
Adding a publication to ExAC track and removing a broken link, and adding an email referenced on their gitHub account for questions about the Fort Lauderdale Agreement.
- src/hg/makeDb/trackDb/human/hgIkmc.html
- lines changed 1, context: html, text, full: html, text
5230f98c19ad8146ee8403754ef3393c09bbd30f Thu Sep 15 16:21:35 2016 -0700
Fixing bad url for ikmc pages, no refs
- src/hg/makeDb/trackDb/mouse/ikmc.html
- lines changed 1, context: html, text, full: html, text
5230f98c19ad8146ee8403754ef3393c09bbd30f Thu Sep 15 16:21:35 2016 -0700
Fixing bad url for ikmc pages, no refs
- src/hg/makeDb/trackDb/mouse/komp.html
- lines changed 1, context: html, text, full: html, text
5230f98c19ad8146ee8403754ef3393c09bbd30f Thu Sep 15 16:21:35 2016 -0700
Fixing bad url for ikmc pages, no refs
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 4, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- lines changed 67, context: html, text, full: html, text
2ab1d0e97c6166a86f047eeef1492750267bde3f Fri Sep 16 10:34:32 2016 -0700
small changes to trackDb after feedback from Matt, refs #17235
- lines changed 12, context: html, text, full: html, text
236f60e04690010ceaa4f617413f59b6b5ddace1 Sat Sep 17 18:44:23 2016 -0700
refGenePfam for dm6
- src/hg/makeDb/trackDb/worm/ce11/cons26way.html
- lines changed 1, context: html, text, full: html, text
00323180dc4e75f5be5794c0e882dfcdf23460c4 Fri Sep 16 13:51:04 2016 -0700
fixed minor typo refs #17802
- src/hg/utils/hubCheck/hubCheck.c
- lines changed 1, context: html, text, full: html, text
ec595ab048d47ee3d75de1f1c25160575339626e Wed Sep 14 22:09:54 2016 -0700
enable hubCheck on bigPsl files [you can have my PSL when you pry it out of cold, crashed emacs]
- src/inc/cheapcgi.h
- lines changed 2, context: html, text, full: html, text
b8023f3df3e17b6f60875f88935e60c232d64d16 Fri Sep 16 22:40:13 2016 -0700
refs #177282. fixes textarea xss vulnerability in cheapcgi.c visible in hgVai. Added functions to allow outputs of large but indeterminate size such as dyString and file streams like fprintf.
- src/inc/htmshell.h
- lines changed 39, context: html, text, full: html, text
b8023f3df3e17b6f60875f88935e60c232d64d16 Fri Sep 16 22:40:13 2016 -0700
refs #177282. fixes textarea xss vulnerability in cheapcgi.c visible in hgVai. Added functions to allow outputs of large but indeterminate size such as dyString and file streams like fprintf.
- src/lib/cheapcgi.c
- lines changed 1, context: html, text, full: html, text
c8202d99df0aa4ac3b592b5557822a65253214a4 Mon Sep 12 14:13:31 2016 -0700
fixed typo
- lines changed 2, context: html, text, full: html, text
b8023f3df3e17b6f60875f88935e60c232d64d16 Fri Sep 16 22:40:13 2016 -0700
refs #177282. fixes textarea xss vulnerability in cheapcgi.c visible in hgVai. Added functions to allow outputs of large but indeterminate size such as dyString and file streams like fprintf.
- src/lib/htmshell.c
- lines changed 15, context: html, text, full: html, text
396071902267c1654f7eafaf60962aad935a9558 Thu Sep 15 17:08:36 2016 -0700
Changing htmlSafef to use %s|none| instead of %-s because %-s has some legitimate uses in html output which means left-justifying the text. Jim uses it in hgBlat. This will make it more general, although it is longer to read and write. For sqlSafef, there was no legitimate expected need to have left-justified output in the production of a SQL statement.
- lines changed 97, context: html, text, full: html, text
b8023f3df3e17b6f60875f88935e60c232d64d16 Fri Sep 16 22:40:13 2016 -0700
refs #177282. fixes textarea xss vulnerability in cheapcgi.c visible in hgVai. Added functions to allow outputs of large but indeterminate size such as dyString and file streams like fprintf.
- src/utils/doCrispr.sh
- lines changed 5, context: html, text, full: html, text
a21f21b13b09a794b09e89168a51d4c8a1da85af Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235
- lines changed 133, context: html, text, full: html, text
9037401af48af40c7df11285b7d3bb713e6c75d8 Thu Sep 15 16:45:06 2016 -0700
a bunch of small fixes to the crispr track, hopefully last round before
the pushq. refs #17235
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
12dd655aeea30d04babf079fb277f6421c4a0299 Mon Sep 19 09:58:50 2016 -0700
v339 preview2 refs #18077
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