All File Changes
v359_preview to v359_preview2 (2017-12-04 to 2017-12-11) v359
Show details
- src/hg/hgCollection/hgCollection.c
- lines changed 20, context: html, text, full: html, text
829a1a35cc3c5bbdfe2293c9152a57872b1b8b12 Fri Dec 8 14:22:03 2017 -0800
redesign of hgCollection UI
- src/hg/hgLiftOver/hgLiftOver.c
- lines changed 2, context: html, text, full: html, text
ba68274702714fed37a44f6e890f4f23c750bffc Thu Dec 7 12:07:09 2017 -0800
fix problem I introduced causing liftOver to only output ~50 regions
- src/hg/hgSession/hgSession.c
- lines changed 15, context: html, text, full: html, text
731eb75a1a1b0eeacfdaf5a1f48f74dbcee11302 Mon Dec 4 15:17:07 2017 -0800
fix #20575 and #20616
- src/hg/hgTables/filterFields.c
- lines changed 4, context: html, text, full: html, text
57ae0219750957cadcb4a639ad0d83bef11ec24b Mon Dec 11 11:24:20 2017 -0800
Yet another case of bigDataUrl-only track running into old hgTables assumption that everything is in mysql. refs #19638 note-136
- src/hg/hgTracks/longRangeTrack.c
- lines changed 17, context: html, text, full: html, text
406740c2dc67f2bb8e217627dcbbe00a204fd594 Mon Dec 4 15:37:32 2017 -0800
Add support for item color, using Ensembl extension (RGB instead of value). http://www.ensembl.org/info/website/upload/pairwise.html
- lines changed 37, context: html, text, full: html, text
3b51318fe05fce338719b56a70d44f1436ff5311 Tue Dec 5 12:37:26 2017 -0800
Fix problems with computing centers and position starts (esp. noticeable for SNPs). Also some cleanup. refs #17512
- src/hg/hgc/hgc.c
- lines changed 9, context: html, text, full: html, text
406740c2dc67f2bb8e217627dcbbe00a204fd594 Mon Dec 4 15:37:32 2017 -0800
Add support for item color, using Ensembl extension (RGB instead of value). http://www.ensembl.org/info/website/upload/pairwise.html
- lines changed 29, context: html, text, full: html, text
3b51318fe05fce338719b56a70d44f1436ff5311 Tue Dec 5 12:37:26 2017 -0800
Fix problems with computing centers and position starts (esp. noticeable for SNPs). Also some cleanup. refs #17512
- src/hg/htdocs/FAQ/FAQreleases.html
- lines changed 3, context: html, text, full: html, text
2c6b27e3942ffb969d013b93362ca3bebb384458 Wed Dec 6 10:16:51 2017 -0800
Staging xenTro9 announcement docs
- src/hg/htdocs/goldenPath/credits.html
- lines changed 3, context: html, text, full: html, text
2c6b27e3942ffb969d013b93362ca3bebb384458 Wed Dec 6 10:16:51 2017 -0800
Staging xenTro9 announcement docs
- src/hg/htdocs/goldenPath/help/bigNarrowPeak.html
- lines changed 17, context: html, text, full: html, text
7d93fee0b9c157497c623f994a254af194cf5e9f Thu Dec 7 11:03:24 2017 -0800
Small changes to bigNarrowPeak.html refs #20620
- lines changed 44, context: html, text, full: html, text
f549e45062e094ad9b74ff843fcc9f8a556e1392 Thu Dec 7 16:49:04 2017 -0800
Adding example 3 to bigNarrowPeak to share about the filters #20620
- lines changed 1, context: html, text, full: html, text
fb86e25fcaf79e6c686c7486e6fd4b513ada1409 Fri Dec 8 16:37:05 2017 -0800
Adding news update about new bigNarrowPeak format
- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
- lines changed 3, context: html, text, full: html, text
4e34a8a4d69769ac1375243eded4af5f5d9fed22 Thu Dec 7 11:28:01 2017 -0800
Small changes to bigNarrowPeak doc refs #20620
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
- lines changed 12, context: html, text, full: html, text
d22da71220424980df9eabb2736118c089bb4218 Thu Dec 7 12:32:02 2017 -0800
Adding name links in trackDbHub.v2.html so Table Of Contents will jump to spots and also typo fix in trackDbLibrary.shtml refs #20620
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 1, context: html, text, full: html, text
d22da71220424980df9eabb2736118c089bb4218 Thu Dec 7 12:32:02 2017 -0800
Adding name links in trackDbHub.v2.html so Table Of Contents will jump to spots and also typo fix in trackDbLibrary.shtml refs #20620
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 37, context: html, text, full: html, text
2c6b27e3942ffb969d013b93362ca3bebb384458 Wed Dec 6 10:16:51 2017 -0800
Staging xenTro9 announcement docs
- lines changed 2, context: html, text, full: html, text
b9d737ec7f2271dc168370e2a6649dca401bd309 Wed Dec 6 12:44:28 2017 -0800
Woops fixing date of announcement
- lines changed 1, context: html, text, full: html, text
95da6cac3830342add898a5a4b0c18b9c595106c Wed Dec 6 12:47:28 2017 -0800
Fixing link to xentro downloads section
- lines changed 11, context: html, text, full: html, text
ff744257b21ed616047826d28a9572b7b991fdb4 Fri Dec 8 11:45:17 2017 -0800
Adding a news note about ability to BLAT from search box refs #19784
- lines changed 5, context: html, text, full: html, text
67b0b7b6a776f12fe753d977cbd5cb0148a89916 Fri Dec 8 11:53:23 2017 -0800
Changing day to date at Ann's request and fixing some unclosed quotes on the newsarch.html page
- lines changed 20, context: html, text, full: html, text
fb86e25fcaf79e6c686c7486e6fd4b513ada1409 Fri Dec 8 16:37:05 2017 -0800
Adding news update about new bigNarrowPeak format
- lines changed 1, context: html, text, full: html, text
f4ee7d6b1487001629600cbdddbc120e70200c19 Mon Dec 11 08:28:01 2017 -0800
Small typo fix newsarch.html refs #20655
- lines changed 1, context: html, text, full: html, text
ab827038f3598347a13870e733e05c52e1db3a4b Mon Dec 11 08:59:29 2017 -0800
Small typo fix newsarch.html refs #20655
- src/hg/htdocs/inc/hgCollection.html
- lines changed 85, context: html, text, full: html, text
829a1a35cc3c5bbdfe2293c9152a57872b1b8b12 Fri Dec 8 14:22:03 2017 -0800
redesign of hgCollection UI
- src/hg/htdocs/indexNews.html
- lines changed 12, context: html, text, full: html, text
2c6b27e3942ffb969d013b93362ca3bebb384458 Wed Dec 6 10:16:51 2017 -0800
Staging xenTro9 announcement docs
- lines changed 11, context: html, text, full: html, text
ff744257b21ed616047826d28a9572b7b991fdb4 Fri Dec 8 11:45:17 2017 -0800
Adding a news note about ability to BLAT from search box refs #19784
- lines changed 12, context: html, text, full: html, text
fb86e25fcaf79e6c686c7486e6fd4b513ada1409 Fri Dec 8 16:37:05 2017 -0800
Adding news update about new bigNarrowPeak format
- lines changed 11, context: html, text, full: html, text
21053aa11c399bcdf2aa5de1f49be1a6bcbe0b0a Mon Dec 11 08:22:20 2017 -0800
Staging indexNews, putting NCBI RefSeq over BLAT search summary in announcing bigNarrowPeak refs #20655
- src/hg/htdocs/mirror.html
- lines changed 1, context: html, text, full: html, text
07ea0ffbb40787fc8bf1d4d203e7cd986c33d8e5 Mon Dec 4 13:03:26 2017 -0800
Fixing broken link to cshl website
- src/hg/htdocs/training/index.html
- lines changed 19, context: html, text, full: html, text
144f18da4b3a6221fab7a3d2edfd4e1cd55efbb9 Fri Dec 8 20:11:31 2017 -0800
dropping completed india workshop and cancelled NYC workshop
- src/hg/inc/cart.h
- lines changed 4, context: html, text, full: html, text
731eb75a1a1b0eeacfdaf5a1f48f74dbcee11302 Mon Dec 4 15:17:07 2017 -0800
fix #20575 and #20616
- src/hg/inc/longRange.h
- lines changed 3, context: html, text, full: html, text
406740c2dc67f2bb8e217627dcbbe00a204fd594 Mon Dec 4 15:37:32 2017 -0800
Add support for item color, using Ensembl extension (RGB instead of value). http://www.ensembl.org/info/website/upload/pairwise.html
- lines changed 18, context: html, text, full: html, text
3b51318fe05fce338719b56a70d44f1436ff5311 Tue Dec 5 12:37:26 2017 -0800
Fix problems with computing centers and position starts (esp. noticeable for SNPs). Also some cleanup. refs #17512
- src/hg/inc/variantProjector.h
- lines changed 1, context: html, text, full: html, text
e2abb3d38e8bf2296e4be847deff63409bc82d1c Thu Dec 7 12:55:15 2017 -0800
In vpPep, don't distinguish between spansUtrCds and cantPredict. (btw spansUtrCds was only used for 5' UTR/CDS boundary)
This should not affect output of anything because they were treated the same anyway.
- src/hg/js/hgCollection.js
- lines changed 220, context: html, text, full: html, text
829a1a35cc3c5bbdfe2293c9152a57872b1b8b12 Fri Dec 8 14:22:03 2017 -0800
redesign of hgCollection UI
- src/hg/lib/cart.c
- lines changed 27, context: html, text, full: html, text
731eb75a1a1b0eeacfdaf5a1f48f74dbcee11302 Mon Dec 4 15:17:07 2017 -0800
fix #20575 and #20616
- src/hg/lib/hgHgvs.c
- lines changed 1, context: html, text, full: html, text
e2abb3d38e8bf2296e4be847deff63409bc82d1c Thu Dec 7 12:55:15 2017 -0800
In vpPep, don't distinguish between spansUtrCds and cantPredict. (btw spansUtrCds was only used for 5' UTR/CDS boundary)
This should not affect output of anything because they were treated the same anyway.
- src/hg/lib/longRange.c
- lines changed 34, context: html, text, full: html, text
406740c2dc67f2bb8e217627dcbbe00a204fd594 Mon Dec 4 15:37:32 2017 -0800
Add support for item color, using Ensembl extension (RGB instead of value). http://www.ensembl.org/info/website/upload/pairwise.html
- lines changed 1, context: html, text, full: html, text
7f316821347265c823bf973b7466ad6236705cbe Tue Dec 5 11:40:11 2017 -0800
fix uninitialized variable no redmine
- src/hg/lib/variantProjector.c
- lines changed 7, context: html, text, full: html, text
e2abb3d38e8bf2296e4be847deff63409bc82d1c Thu Dec 7 12:55:15 2017 -0800
In vpPep, don't distinguish between spansUtrCds and cantPredict. (btw spansUtrCds was only used for 5' UTR/CDS boundary)
This should not affect output of anything because they were treated the same anyway.
- src/hg/makeDb/genbank/etc/hgwbeta.dbs
- lines changed 2, context: html, text, full: html, text
8e763c1082d981097d8f9349d300a48210145c5f Fri Dec 8 15:38:14 2017 -0800
Turning on Genbank updates for panPan2, refs #16036
- src/hg/makeDb/genbank/etc/rr.dbs
- lines changed 2, context: html, text, full: html, text
d62a8aae6ef50245fec31af203630354b76d8f83 Tue Dec 5 10:47:22 2017 -0800
turning on rr genbank updates for xenTro9
- src/hg/makeDb/trackDb/human/hg19/gtexEqtl.ra
- lines changed 368, context: html, text, full: html, text
aeb15fa79f6f6a1afc6b2845775994a84e55f5e7 Mon Dec 4 16:41:25 2017 -0800
Add search stanzas for GTEx eQTL tissue tables. refs #20409
- lines changed 13, context: html, text, full: html, text
12e1cd233b4b898510be8877d0708e7db8231ba5 Tue Dec 5 14:52:25 2017 -0800
Adding 'new' tags to GTEx eQTL tracks, refs #20270
- src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra
- lines changed 1, context: html, text, full: html, text
89cb63162cf4e08240c6077f5f03b973b754744f Mon Dec 4 13:45:17 2017 -0800
Reverting back to original phylogenic order as placed by Hiram, undo commit 840fc3b, refs #20216
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
- lines changed 16, context: html, text, full: html, text
c02766b801796158227dc2e7fb936b3b4c0bf519 Mon Dec 4 10:10:24 2017 -0800
Adding xenTro9 to mouse vertebrate composite
- lines changed 16, context: html, text, full: html, text
c1bf49eb13eb9908038e0e8b5b996aef07623c21 Mon Dec 4 10:22:31 2017 -0800
also adding xenLae2 into mm10 vertebrate compostite, this is basically just a placeholder to get the tracks visibile until the whole thing gets cleaned up
- src/hg/makeDb/trackDb/refGenePfam.html
- lines changed 1, context: html, text, full: html, text
a992543120295357363514b36b30285e7cad1706 Tue Dec 5 09:24:03 2017 -0800
Url edit on refGenePfam, RM #20636
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 1, context: html, text, full: html, text
77749ae782933230de73cb87041b024a9b4b3fd1 Fri Dec 8 11:47:02 2017 -0800
Adding the beta release tag to get the NCBI Functional Elements on hgwbeta, refs #19638
- lines changed 1, context: html, text, full: html, text
2af00290f855b4b9f38acaf89a74d0607c95216a Fri Dec 8 15:42:35 2017 -0800
Adding a 'New' icon on hgTracks for the NCBI RefSeq Functional Elements track, refs #19638
- src/hg/makeDb/trackDb/zebrafish/affyZebrafish.html
- lines changed 2, context: html, text, full: html, text
b3ea393fdb82688f1361de9d261635f001226b74 Mon Dec 4 13:35:54 2017 -0800
Fixing broken links for danRer3, no Redmine.
- src/hg/makeDb/trackDb/zebrafish/affyZonWildType.html
- lines changed 2, context: html, text, full: html, text
b3ea393fdb82688f1361de9d261635f001226b74 Mon Dec 4 13:35:54 2017 -0800
Fixing broken links for danRer3, no Redmine.
- src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndPairs.html
- lines changed 3, context: html, text, full: html, text
b3ea393fdb82688f1361de9d261635f001226b74 Mon Dec 4 13:35:54 2017 -0800
Fixing broken links for danRer3, no Redmine.
- src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndSingles.html
- lines changed 3, context: html, text, full: html, text
b3ea393fdb82688f1361de9d261635f001226b74 Mon Dec 4 13:35:54 2017 -0800
Fixing broken links for danRer3, no Redmine.
- src/hg/makeDb/trackDb/zebrafish/danRer3/ctgPos2.html
- lines changed 1, context: html, text, full: html, text
b3ea393fdb82688f1361de9d261635f001226b74 Mon Dec 4 13:35:54 2017 -0800
Fixing broken links for danRer3, no Redmine.
- src/hg/makeDb/trackDb/zebrafish/danRer3/gold.html
- lines changed 2, context: html, text, full: html, text
b3ea393fdb82688f1361de9d261635f001226b74 Mon Dec 4 13:35:54 2017 -0800
Fixing broken links for danRer3, no Redmine.
- src/hg/makeDb/trackDb/zebrafish/danRer3/multiz5way.html
- lines changed 3, context: html, text, full: html, text
b3ea393fdb82688f1361de9d261635f001226b74 Mon Dec 4 13:35:54 2017 -0800
Fixing broken links for danRer3, no Redmine.
- src/hg/makeDb/trackDb/zebrafish/danRer3/rhMap.html
- lines changed 4, context: html, text, full: html, text
b3ea393fdb82688f1361de9d261635f001226b74 Mon Dec 4 13:35:54 2017 -0800
Fixing broken links for danRer3, no Redmine.
- src/hg/utils/automation/HgAutomate.pm
- lines changed 32, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doAugustus.pl
- lines changed 2, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doBlastzChainNet.pl
- lines changed 20, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doCpgIslands.pl
- lines changed 4, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doCrispr.pl
- lines changed 25, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doDbSnpMaskSequence.pl
- lines changed 2, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doDbSnpOrthoAlleles.pl
- lines changed 4, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doGapOverlap.pl
- lines changed 4, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doGenscan.pl
- lines changed 8, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doIdKeys.pl
- lines changed 2, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doRepeatMasker.pl
- lines changed 10, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doSameSpeciesLiftOver.pl
- lines changed 8, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doSimpleRepeat.pl
- lines changed 8, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/doTandemDup.pl
- lines changed 5, context: html, text, full: html, text
b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800
removing strict UCSC dependencies refs #18874
- src/hg/utils/automation/openStack/README.txt
- lines changed 34, context: html, text, full: html, text
31af7965c5089fec986c85b9865604da7e6c728c Thu Dec 7 11:12:46 2017 -0800
initial notes for theory of operation refs #18874
- src/hg/utils/phyloTrees/218way.dissect.txt
- lines changed 3045, context: html, text, full: html, text
1c34cd950a1ab0e34fba3410f724b805c67704dc Mon Dec 4 11:29:39 2017 -0800
adding all the primates refs #20216
- src/hg/utils/phyloTrees/218wayChainNet.pl
- lines changed 220, context: html, text, full: html, text
1c34cd950a1ab0e34fba3410f724b805c67704dc Mon Dec 4 11:29:39 2017 -0800
adding all the primates refs #20216
- src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_patches.tab
- lines changed 18, context: html, text, full: html, text
98fefd88af86752bdad2f436c928cd7e02e59d19 Tue Dec 5 12:38:00 2017 -0800
Adding new vcfToHgvs test case for Personalis variants on patches/alt sequences that are only in hg38. Not adding it to top-level 'make test' because test.2bit is a link to hg19.2bit and reconstructing a 2bit from hg19.2bit and hg38.2bit would be costly in either git repo space or test time, and using hg38 instead of test means that as RefSeq versions increment, the expected result file will get out of date. Still important to capture the test case because it exposed a couple more bugs in github hgvslib example_test_set/hgvs_test_cases_reference.txt.
- src/hg/utils/vcfToHgvs/tests/input/PersonalisGroundTruth2017_patches.vcf
- lines changed 32, context: html, text, full: html, text
98fefd88af86752bdad2f436c928cd7e02e59d19 Tue Dec 5 12:38:00 2017 -0800
Adding new vcfToHgvs test case for Personalis variants on patches/alt sequences that are only in hg38. Not adding it to top-level 'make test' because test.2bit is a link to hg19.2bit and reconstructing a 2bit from hg19.2bit and hg38.2bit would be costly in either git repo space or test time, and using hg38 instead of test means that as RefSeq versions increment, the expected result file will get out of date. Still important to capture the test case because it exposed a couple more bugs in github hgvslib example_test_set/hgvs_test_cases_reference.txt.
- src/hg/utils/vcfToHgvs/tests/makefile
- lines changed 9, context: html, text, full: html, text
98fefd88af86752bdad2f436c928cd7e02e59d19 Tue Dec 5 12:38:00 2017 -0800
Adding new vcfToHgvs test case for Personalis variants on patches/alt sequences that are only in hg38. Not adding it to top-level 'make test' because test.2bit is a link to hg19.2bit and reconstructing a 2bit from hg19.2bit and hg38.2bit would be costly in either git repo space or test time, and using hg38 instead of test means that as RefSeq versions increment, the expected result file will get out of date. Still important to capture the test case because it exposed a couple more bugs in github hgvslib example_test_set/hgvs_test_cases_reference.txt.
- src/lib/longTabix.c
- lines changed 4, context: html, text, full: html, text
406740c2dc67f2bb8e217627dcbbe00a204fd594 Mon Dec 4 15:37:32 2017 -0800
Add support for item color, using Ensembl extension (RGB instead of value). http://www.ensembl.org/info/website/upload/pairwise.html
- src/makefile
- lines changed 1, context: html, text, full: html, text
36ce5c7b63d028001448c971e155cff04c6317f4 Tue Dec 5 11:49:28 2017 -0800
need parasol binaries in userApps refs #18874
- src/parasol/makefile
- lines changed 3, context: html, text, full: html, text
36ce5c7b63d028001448c971e155cff04c6317f4 Tue Dec 5 11:49:28 2017 -0800
need parasol binaries in userApps refs #18874
- src/utils/qa/updateTimesDb.sh
- lines changed 3, context: html, text, full: html, text
8283f85926f62192df95f95c17fe96e53dfe415f Tue Dec 5 08:33:20 2017 -0800
Fixing file globbing bug in updateTimesDb.sh
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
38dae373864fe1d6bfea3155422a5ee2abe0c3ab Mon Dec 11 13:06:26 2017 -0800
v359 preview2 refs #20654
- src/utils/userApps/mkREADME.sh
- lines changed 1, context: html, text, full: html, text
f7343a9a6a34ab63c3021c6d3353bba9b4554fdc Tue Dec 5 11:55:36 2017 -0800
broken redirect of stderr #18874
- lines changed: 4709
- files changed: 85