All File Changes
v341_preview2 to v341_base (2016-10-31 to 2016-11-07) v341
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- src/browserbox/root/updateBrowser.sh
- lines changed 3, context: html, text, full: html, text
1ebe979040195c2060ca0c1332638dd254430892 Thu Nov 3 14:07:30 2016 -0700
fixing 0-byte stuck html file in gbib update, refs #18337
- src/hg/cirm/cdw/cdwGetMetadataAsFile/cdwGetMetadataAsFile.c
- lines changed 96, context: html, text, full: html, text
fde95b41e4ce0f67bc81151e71805a9a32d0d509 Fri Nov 4 10:21:54 2016 -0700
Adding in the download meta data option to the analysis query tab, refs #17870
- src/hg/cirm/cdw/cdwGetMetadataAsFile/makefile
- lines changed 16, context: html, text, full: html, text
fde95b41e4ce0f67bc81151e71805a9a32d0d509 Fri Nov 4 10:21:54 2016 -0700
Adding in the download meta data option to the analysis query tab, refs #17870
- src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
- lines changed 1, context: html, text, full: html, text
ca112199cb040b7df91678144fb9ab6cc4290f77 Mon Oct 31 15:16:49 2016 -0700
Expanding buffer for large tag values.
- lines changed 98, context: html, text, full: html, text
fde95b41e4ce0f67bc81151e71805a9a32d0d509 Fri Nov 4 10:21:54 2016 -0700
Adding in the download meta data option to the analysis query tab, refs #17870
- src/hg/cirm/cdw/lib/cdwLib.c
- lines changed 122, context: html, text, full: html, text
fde95b41e4ce0f67bc81151e71805a9a32d0d509 Fri Nov 4 10:21:54 2016 -0700
Adding in the download meta data option to the analysis query tab, refs #17870
- src/hg/cirm/cdw/lib/cdwValid.c
- lines changed 138, context: html, text, full: html, text
a7255af50076812432601cb7d5f81dfd55d5ec05 Wed Nov 2 12:58:04 2016 -0700
Updating the accepted tags to include the MISCE terms that Clay and JCVI have been working on, refs #17334
- lines changed 193, context: html, text, full: html, text
83ff9557037715521b9cb3714ec7989763b92aa7 Wed Nov 2 16:17:40 2016 -0700
Updating cv checks for MISCE terms, and fixing a few typos in MISCE tags and removing old tag list and alphabetizing new tags list.
- src/hg/hgc/hgc.c
- lines changed 3, context: html, text, full: html, text
0684c7b8dc207944939299c15c37aa8356a90fbb Tue Nov 1 12:52:03 2016 -0700
no Gene Tree link on non-coding genes refs #18240
- src/hg/hgc/vcfClick.c
- lines changed 17, context: html, text, full: html, text
90f7a592103554129bc969299a356439ae02336c Thu Nov 3 10:56:04 2016 -0700
VCF details: don't show name if empty or placeholder. Show ExAC link before dbSNP link and make ExAC link label more consistent with ExAC display. refs #18284
- src/hg/htdocs/FAQ/FAQformat.html
- lines changed 1, context: html, text, full: html, text
8a0897c2c6eaa58fc358344d199b6b6d28da49c6 Fri Nov 4 09:33:46 2016 -0700
adding . as a possible letter for strand to bed documentation, no refseq
- lines changed 1, context: html, text, full: html, text
a357ce2e9b407564bc35e54b0ea0b4c6d5e79848 Fri Nov 4 09:40:27 2016 -0700
fixing bed docs some more, no redmine
- src/hg/htdocs/goldenPath/credits.html
- lines changed 16, context: html, text, full: html, text
87cb00b115a19d5642c7e31db84644e75edbf18d Mon Oct 31 11:24:11 2016 -0700
editing credits for panTro5 refs #17817
- lines changed 2, context: html, text, full: html, text
dd0a103495388a3b1b52d7dc61479165dea89ece Mon Oct 31 14:53:27 2016 -0700
updating Credits.html for Chimp refs #17817
- src/hg/htdocs/goldenPath/help/query.html
- lines changed 12, context: html, text, full: html, text
a9776d812aca78c00e47a513f40d0b29a345f6f3 Wed Nov 2 09:42:52 2016 -0700
added HGVS terms, refs #18079
- src/hg/htdocs/goldenPath/help/trackDb/README.txt
- lines changed 1, context: html, text, full: html, text
bf33b30d0b9c6988a61ba72ba347ad20b1f90dbb Wed Nov 2 14:49:42 2016 -0700
Changing readme
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 13, context: html, text, full: html, text
799e5c2048fab6f0beaf9cb733c15cb4c98fee9b Wed Nov 2 14:13:43 2016 -0700
Added an announcement about the new chromAlias table for hg38, refs #18250
- lines changed 2, context: html, text, full: html, text
9161c64d63829b54852ff00e9c700e3e3dd4d529 Wed Nov 2 14:30:25 2016 -0700
Putting the correct date, refs#18250
- lines changed 12, context: html, text, full: html, text
344bd499b559359b38e0f8988ac9e20e2deff7c0 Thu Nov 3 09:49:45 2016 -0700
Changing the date and formatting for the chromAlias announcement, ref #18250
- src/hg/htdocs/images/Drosophila_simulans.jpg
- lines changed 0, context: html, text, full: html, text
edba1b0991019bb90d73debfc028fcdc28f4e5b4 Tue Nov 1 14:06:34 2016 -0700
for droSim2 browser wikimedia commons Dr Andrew Weeks https://commons.wikimedia.org/wiki/File:Drosophila_simulans-female.jpg refs #18269
- src/hg/htdocs/indexNews.html
- lines changed 12, context: html, text, full: html, text
967b5384a5eca550af10177654cf924937dabf22 Wed Nov 2 14:25:18 2016 -0700
Adding a short headline for the new chromAlias table, refs# 18250
- lines changed 1, context: html, text, full: html, text
9161c64d63829b54852ff00e9c700e3e3dd4d529 Wed Nov 2 14:30:25 2016 -0700
Putting the correct date, refs#18250
- lines changed 1, context: html, text, full: html, text
8b71d6889ca58bfa8bff17469aeab3532befe245 Wed Nov 2 14:31:53 2016 -0700
Forgot to change the link to the newsarch.html page, refs #18250
- lines changed 2, context: html, text, full: html, text
344bd499b559359b38e0f8988ac9e20e2deff7c0 Thu Nov 3 09:49:45 2016 -0700
Changing the date and formatting for the chromAlias announcement, ref #18250
- src/hg/inc/versionInfo.h
- lines changed 1, context: html, text, full: html, text
a1494fec288ca82de0a42c1f6315412fba7a154a Mon Nov 7 10:06:28 2016 -0800
New version number v341
- src/hg/lib/trackHub.c
- lines changed 4, context: html, text, full: html, text
8cc61900672e957331a5ae02cea5b7cc53f8e5f9 Mon Oct 31 14:32:12 2016 -0700
check to see if tracks have duplicated names .
- src/hg/makeDb/crisprTrack/createBigBed.py
- lines changed 2, context: html, text, full: html, text
a46dc06c474d2bddcfe5743138e256ae35387459 Tue Nov 1 13:28:00 2016 -0700
tiny change to crispr bigBed creator, refs #17235
- src/hg/makeDb/doc/dm3.txt
- lines changed 69, context: html, text, full: html, text
aa99224331a34949e02ff3cc8942da2fd161ef3b Wed Nov 2 10:59:38 2016 -0700
liftOver to droSim2 per user request refs #18269
- src/hg/makeDb/doc/droSim1.txt
- lines changed 15, context: html, text, full: html, text
826af23bad85f06440c75d2f226160f0f21eaab2 Wed Nov 2 11:05:39 2016 -0700
liftOver to droSim2 refs #18269
- src/hg/makeDb/doc/droSim2/initialBuild.txt
- lines changed 564, context: html, text, full: html, text
653888d85818c108e9505c4d0ec4f801c459128b Wed Nov 2 11:06:51 2016 -0700
to construct dm3 to droSim2 liftOver refs #18269
- src/hg/makeDb/doc/mouseStrains/groups.txt
- lines changed 39, context: html, text, full: html, text
5c72520bca3d8ba7f0fe49ed1f1b8b473142a3ed Mon Nov 7 09:44:49 2016 -0800
the groups.txt file for the mouse strains refs #13553
- src/hg/makeDb/doc/mouseStrains/mouseStrains.genomes.txt
- lines changed 160, context: html, text, full: html, text
82cec746b350c7a69784e7f66959b36351c2ce14 Mon Nov 7 09:36:27 2016 -0800
the genomes.txt file refs #13553
- lines changed 33, context: html, text, full: html, text
43fd5b317fb16c32cf2895b70051c82fc4088e50 Mon Nov 7 09:53:41 2016 -0800
adding blat servers refs #13553
- lines changed 1, context: html, text, full: html, text
a08ce839f61a97d23b493640d7510ad13341990f Mon Nov 7 09:54:38 2016 -0800
adding blat servers refs #13553
- src/hg/makeDb/doc/mouseStrains/mouseStrainsBuildNotes.txt
- lines changed 84, context: html, text, full: html, text
47802304b1952dbda253f7b3c9d17cf0f8bf2d2e Sat Nov 5 14:14:30 2016 -0700
adding build notes refs #13553
- src/hg/makeDb/doc/mouseStrains/rnaSeqStar.html
- lines changed 190, context: html, text, full: html, text
910034e3ec1547b950e6434a7a98486ddb4cb5d9 Tue Nov 1 11:21:52 2016 -0700
description page for RNA Seq Star tracks, a copy of this file is in each species html directory refs #13553
- src/hg/makeDb/schema/all.joiner
- lines changed 85, context: html, text, full: html, text
dcd380328b878973aec7a29389391dbb03dd784c Tue Nov 1 16:56:47 2016 -0700
added forgotten VM11 join check
- src/hg/makeDb/trackDb/drosophila/droSim2/description.html
- lines changed 64, context: html, text, full: html, text
a500c95137dd448e2d073e240ff1e02a323cfdb5 Tue Nov 1 14:35:12 2016 -0700
adding droSim2 to the build refs #18269
- src/hg/makeDb/trackDb/drosophila/droSim2/gap.html
- lines changed 29, context: html, text, full: html, text
a500c95137dd448e2d073e240ff1e02a323cfdb5 Tue Nov 1 14:35:12 2016 -0700
adding droSim2 to the build refs #18269
- src/hg/makeDb/trackDb/drosophila/droSim2/gold.html
- lines changed 34, context: html, text, full: html, text
a500c95137dd448e2d073e240ff1e02a323cfdb5 Tue Nov 1 14:35:12 2016 -0700
adding droSim2 to the build refs #18269
- src/hg/makeDb/trackDb/drosophila/droSim2/trackDb.ra
- lines changed 8, context: html, text, full: html, text
a500c95137dd448e2d073e240ff1e02a323cfdb5 Tue Nov 1 14:35:12 2016 -0700
adding droSim2 to the build refs #18269
- src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV25.ra
- lines changed 1, context: html, text, full: html, text
f7d15a2fd90040351e6b92c4e1dac320ac68e63b Tue Nov 1 15:29:40 2016 -0700
updated hgFindSpec to match naming convention change on GENCODE 2-way pseudogene track
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
a500c95137dd448e2d073e240ff1e02a323cfdb5 Tue Nov 1 14:35:12 2016 -0700
adding droSim2 to the build refs #18269
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeCredits1.shared.html
- lines changed 110, context: html, text, full: html, text
7ba9ed84cc188859e75622549292ff3a5c7ff2bd Tue Nov 1 16:51:40 2016 -0700
updated GENCODE credits section
- lines changed 2, context: html, text, full: html, text
60a8742482f1c4cb169a020d4ff6980936e87e2c Wed Nov 2 08:34:54 2016 -0700
Fixing broken td tag, removing extra comma, making APPRIS link open in new tab, and making APPRIS lines fit within our less 100 char limits, refs #18295
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeDisplay1.shared.html
- lines changed 235, context: html, text, full: html, text
7ba9ed84cc188859e75622549292ff3a5c7ff2bd Tue Nov 1 16:51:40 2016 -0700
updated GENCODE credits section
- lines changed 5, context: html, text, full: html, text
60a8742482f1c4cb169a020d4ff6980936e87e2c Wed Nov 2 08:34:54 2016 -0700
Fixing broken td tag, removing extra comma, making APPRIS link open in new tab, and making APPRIS lines fit within our less 100 char limits, refs #18295
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
- lines changed 122, context: html, text, full: html, text
7ba9ed84cc188859e75622549292ff3a5c7ff2bd Tue Nov 1 16:51:40 2016 -0700
updated GENCODE credits section
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM11.html
- lines changed 319, context: html, text, full: html, text
7ba9ed84cc188859e75622549292ff3a5c7ff2bd Tue Nov 1 16:51:40 2016 -0700
updated GENCODE credits section
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM11.ra
- lines changed 1, context: html, text, full: html, text
f7d15a2fd90040351e6b92c4e1dac320ac68e63b Tue Nov 1 15:29:40 2016 -0700
updated hgFindSpec to match naming convention change on GENCODE 2-way pseudogene track
- src/hg/pslCheck/pslCheck.c
- lines changed 26, context: html, text, full: html, text
f1ed9037745e40b85f0e3908f6e8f1aa497cf753 Sun Nov 6 16:09:27 2016 -0800
added option to pslCheck to string qName uniqueness modifiers
- src/hg/utils/automation/extractSource.pl
- lines changed 44, context: html, text, full: html, text
bed79fc1964b5e7f176df34bbdf5d6675bc9a28b Tue Nov 1 10:49:34 2016 -0700
to fixup extraction of source identity from Ensembl gtf file refs #18240
- src/inc/bamFile.h
- lines changed 4, context: html, text, full: html, text
6d90b13178a35682a27514cf704f7b05794e7192 Wed Nov 2 14:18:48 2016 -0700
Refactoring code to convert bam to a psl from hgTracks/bamTrack.c refs #13673
- src/lib/bamFile.c
- lines changed 78, context: html, text, full: html, text
07f0e0134a6eee29337add57582421937c617e9a Wed Nov 2 14:17:47 2016 -0700
Refactoring code to convert bam to a psl from hgTracks/bamTrack.c refs #13673
- lines changed 5, context: html, text, full: html, text
196d206a199ee47dc303b5ddf54170f89e4daa75 Thu Nov 3 17:13:25 2016 -0700
correctly counting matches and mis matches refs #13673
- src/lib/htmlPage.c
- lines changed 16, context: html, text, full: html, text
596fceb9da320bd456bbd4cda8571d4a62cc329f Mon Oct 31 12:03:18 2016 -0700
Relaxing some validations to accommodate newer web pages.
- lines changed 3, context: html, text, full: html, text
9562808bb257905689c06d196305e0b8234bf05b Mon Oct 31 12:14:08 2016 -0700
Improving behavior when missing technically optional head section.
- lines changed 2, context: html, text, full: html, text
41f2f92517eff6f5b8477bdd90bfe33799eeedd0 Mon Oct 31 12:28:42 2016 -0700
Adding DIV SCRIPT and SVG to tags checked for nesting.
- src/tagStorm/tagStormQuery/tagStormQuery.c
- lines changed 1, context: html, text, full: html, text
12c561f936552b6604e16e209cbff155516966ca Wed Nov 2 15:16:44 2016 -0700
Fixed year old typo!
- src/utils/bamToFastq/bamToFastq.c
- lines changed 6, context: html, text, full: html, text
a14d8dea71b926b326385cdd03a50b5db372240c Wed Nov 2 14:22:24 2016 -0700
Updating to use htslib.
- src/utils/bamToFastq/makefile
- lines changed 3, context: html, text, full: html, text
a14d8dea71b926b326385cdd03a50b5db372240c Wed Nov 2 14:22:24 2016 -0700
Updating to use htslib.
- src/utils/bamToPsl/bamToPsl.c
- lines changed 80, context: html, text, full: html, text
3ad4f4c509134534060643ed1152f4629aab172e Wed Nov 2 14:15:58 2016 -0700
First cut of a bamToPsl utility.
- lines changed 90, context: html, text, full: html, text
2bd5caf8ce518d13cefc69de0d084228cf7712fe Fri Nov 4 13:36:48 2016 -0700
adding useful options refs #13673
- src/utils/bamToPsl/makefile
- lines changed 4, context: html, text, full: html, text
3ad4f4c509134534060643ed1152f4629aab172e Wed Nov 2 14:15:58 2016 -0700
First cut of a bamToPsl utility.
- src/utils/doLocusName
- lines changed 1, context: html, text, full: html, text
a823a26a0ed014c44482f50eb1c4072b3860f9de Mon Oct 31 14:27:59 2016 -0700
small fix to doLocusName to handle genes with with spaces in names
- src/utils/htmlCheck/htmlCheck.c
- lines changed 9, context: html, text, full: html, text
4d0515666d53ed314b503f52a80cfb5a3744af28 Mon Oct 31 12:54:32 2016 -0700
Fixing so that you can run htmlCheck on local files rather than just URLS.
- src/utils/makefile
- lines changed 1, context: html, text, full: html, text
93115ea6e9d63814f717023f1e798d1025ad494c Fri Nov 4 13:37:30 2016 -0700
adding bamToPsl to utils refs #13673
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 3, context: html, text, full: html, text
8b5a8239d2432475ec19002c09963f7d3956de03 Mon Nov 7 10:05:28 2016 -0800
v341 final build refs #18302
- lines changed: 3317
- files changed: 68