All File Changes
v466_preview to v466_preview2 (2024-05-20 to 2024-05-27) v466
Show details
- confs/hgwdev.hg.conf
- lines changed 2, context: html, text, full: html, text
35de98e7042d6dcf9372b62be5d23a4494ef7516 Sun May 26 01:11:17 2024 -0700
Installing updated hg.conf files from UCSC servers
- src/hg/hgPhyloPlace/hgPhyloPlace.c
- lines changed 2, context: html, text, full: html, text
1d72deb939d79331f80c9fffc1bef03d3c284186 Tue May 21 13:08:04 2024 -0700
Updating a couple instances of db-->org that I missed previously.
- src/hg/hgPhyloPlace/phyloPlace.c
- lines changed 127, context: html, text, full: html, text
0b186effb2d2b536d2c280ec31bec6e153e6bd7e Tue May 21 13:26:39 2024 -0700
Add support for uploaded names/IDs for the multi-ref/tree organism.ra case. Add new config option anchorSamples, pass to usher-sampled/matUtils/server if present.
anchorSamples is a file with names of sequences that should always be included in the subtree to provide some larger-scale context, e.g. well-known vaccine or reference material strains. Influenza user request.
- src/hg/hgPhyloPlace/phyloPlace.h
- lines changed 3, context: html, text, full: html, text
0b186effb2d2b536d2c280ec31bec6e153e6bd7e Tue May 21 13:26:39 2024 -0700
Add support for uploaded names/IDs for the multi-ref/tree organism.ra case. Add new config option anchorSamples, pass to usher-sampled/matUtils/server if present.
anchorSamples is a file with names of sequences that should always be included in the subtree to provide some larger-scale context, e.g. well-known vaccine or reference material strains. Influenza user request.
- src/hg/hgPhyloPlace/runUsher.c
- lines changed 32, context: html, text, full: html, text
0b186effb2d2b536d2c280ec31bec6e153e6bd7e Tue May 21 13:26:39 2024 -0700
Add support for uploaded names/IDs for the multi-ref/tree organism.ra case. Add new config option anchorSamples, pass to usher-sampled/matUtils/server if present.
anchorSamples is a file with names of sequences that should always be included in the subtree to provide some larger-scale context, e.g. well-known vaccine or reference material strains. Influenza user request.
- src/hg/hgTracks/baseTrack.c
- lines changed 142, context: html, text, full: html, text
866749c9bbb85a5f82999f298af6a68ef01e4151 Wed May 22 10:11:13 2024 -0700
new track type to draw coordinates in track
- lines changed 18, context: html, text, full: html, text
df6cf391270cbbfe12f9ec3869948c2813002a87 Thu May 23 13:47:45 2024 -0700
add support for baseView track type
- src/hg/hgTracks/bedTrack.c
- lines changed 1, context: html, text, full: html, text
283f449c6c5370757305f0904971f6a792ea3524 Wed May 22 10:10:04 2024 -0700
increase the size of a buffer
- src/hg/hgTracks/hgTracks.c
- lines changed 1, context: html, text, full: html, text
2154c402b569cb4a7acbd4c36710219e8a5b20dd Thu May 23 00:34:27 2024 -0700
fix typo in error message
- lines changed 16, context: html, text, full: html, text
6f3056fb1c519aeb262d6c1cc9f352652e3086ae Mon May 27 07:49:54 2024 -0700
not setting pix if run from command line, email from Lou that qa scripts are not running anymore
- src/hg/hgTracks/hgTracks.h
- lines changed 4, context: html, text, full: html, text
df6cf391270cbbfe12f9ec3869948c2813002a87 Thu May 23 13:47:45 2024 -0700
add support for baseView track type
- src/hg/hgTracks/makefile
- lines changed 1, context: html, text, full: html, text
df6cf391270cbbfe12f9ec3869948c2813002a87 Thu May 23 13:47:45 2024 -0700
add support for baseView track type
- src/hg/hgTracks/simpleTracks.c
- lines changed 5, context: html, text, full: html, text
df6cf391270cbbfe12f9ec3869948c2813002a87 Thu May 23 13:47:45 2024 -0700
add support for baseView track type
- lines changed 1, context: html, text, full: html, text
f441916bec96b3640c4a9c4af81202fc8e64599b Fri May 24 17:19:40 2024 -0700
remove weird infinite loop when maxItems differs between composite
parent and child and composite parent has bigBed for a type
- src/hg/hgc/hgc.c
- lines changed 1, context: html, text, full: html, text
e55d5d49dfead30ba3c279307ed460f25d729d0a Fri May 24 14:48:39 2024 -0700
Fixing broken links, No redmine
- src/hg/htdocs/FAQ/FAQformat.html
- lines changed 2, context: html, text, full: html, text
9a0dafc324c11ebf400522f85c74355718d50687 Fri May 24 14:54:03 2024 -0700
Adding Decorator format to the FAQ: Data File Formats page, refs #32818
- src/hg/htdocs/conditions.html
- lines changed 7, context: html, text, full: html, text
0d60bff4ed1adb5ca5cbb7a9545ec8592e2cae81 Wed May 22 09:27:06 2024 -0700
Adding a general clinical disclaimer in our conditions page, refs #26059
- src/hg/htdocs/goldenPath/help/customTrackText.html
- lines changed 17, context: html, text, full: html, text
7f4c9f08fb12830d1c0b16ef96a21b38ae680cd7 Mon May 20 17:20:18 2024 -0700
Making changes from Lou's code review, refs #33716
- lines changed 1, context: html, text, full: html, text
061a6e85c0092b5aedc7174c577293fb0668502a Thu May 23 17:56:10 2024 -0700
Fixing a typo of an extra <br> tag, refs #33759
- lines changed 3, context: html, text, full: html, text
daff241ad7cf5bbb51cd54e07d84b3863bda4fa4 Fri May 24 10:35:57 2024 -0700
Adding the word NOTE: and making the sentence bold to match the other notes in the section.
- src/hg/htdocs/goldenPath/help/trackDb/changes.html
- lines changed 6, context: html, text, full: html, text
25e992ce826a1546ec0bf93626286f289d5f4157 Wed May 22 06:55:43 2024 -0700
adding decorators to changelog, no redmine
- lines changed 6, context: html, text, full: html, text
981c352ff2365c4d725eefa6a9053a4da5ad6ca9 Thu May 23 00:50:13 2024 -0700
documenting mouseover for the other track types
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 2, context: html, text, full: html, text
981c352ff2365c4d725eefa6a9053a4da5ad6ca9 Thu May 23 00:50:13 2024 -0700
documenting mouseover for the other track types
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 50, context: html, text, full: html, text
f75be6cdc179d7ce11539664b23406306976052d Tue May 21 12:27:38 2024 -0700
Staging and releasing the new GENCODE Known Gene tracks V46 and VM35, refs #33080 #33083
- lines changed 4, context: html, text, full: html, text
b39ad84412ed9a69cfcd7ae9ca05384cb17e40e9 Sat May 25 08:03:25 2024 -0700
Removing repetition of text, refs #33080 #33083
- src/hg/htdocs/indexNews.html
- lines changed 12, context: html, text, full: html, text
f75be6cdc179d7ce11539664b23406306976052d Tue May 21 12:27:38 2024 -0700
Staging and releasing the new GENCODE Known Gene tracks V46 and VM35, refs #33080 #33083
- src/hg/js/hgTracks.js
- lines changed 8, context: html, text, full: html, text
c1824ffc854245b1ab7f72a8e8afedf2d37f8edb Wed May 22 10:43:01 2024 -0700
Revert "Better fix for broken drag select. The map click code that now tries to open up hgc needs to first check whether we are currently allowed to click to begin with. Then we can try to open up the details pages. If we aren't doing a details page, then we need to submit the form like we would do before I added hgc pop ups, refs #33584"
This reverts commit 12acb7943615ead2b77b0eebaedf70b8ca1d7a96.
- lines changed 8, context: html, text, full: html, text
9b6103be7485ef3fd43b3f2ce8d67a86e73e409d Wed May 22 10:46:04 2024 -0700
Revert "Revert "Better fix for broken drag select. The map click code that now tries to open up hgc needs to first check whether we are currently allowed to click to begin with. Then we can try to open up the details pages. If we aren't doing a details page, then we need to submit the form like we would do before I added hgc pop ups, refs #33584""
This reverts commit c1824ffc854245b1ab7f72a8e8afedf2d37f8edb.
- lines changed 2, context: html, text, full: html, text
e016f7eae81edd3cfac1f65219dc6c18e91c7e22 Wed May 22 10:47:12 2024 -0700
Unify the different color pickers (drag select highlights, track item highlights and track item colors) into hui.js. Ensure the text box and palette selector work, refs #24507
- src/hg/js/hui.js
- lines changed 23, context: html, text, full: html, text
e016f7eae81edd3cfac1f65219dc6c18e91c7e22 Wed May 22 10:47:12 2024 -0700
Unify the different color pickers (drag select highlights, track item highlights and track item colors) into hui.js. Ensure the text box and palette selector work, refs #24507
- lines changed 2, context: html, text, full: html, text
002a32a1207879eb9f001d444be05ce8eab33314 Wed May 22 12:47:47 2024 -0700
Fix track drag re-order not working after including hui.js in hgTracks javascript includes, refs #33775
- src/hg/js/utils.js
- lines changed 26, context: html, text, full: html, text
e016f7eae81edd3cfac1f65219dc6c18e91c7e22 Wed May 22 10:47:12 2024 -0700
Unify the different color pickers (drag select highlights, track item highlights and track item colors) into hui.js. Ensure the text box and palette selector work, refs #24507
- src/hg/lib/hubConnect.c
- lines changed 8, context: html, text, full: html, text
036b5fab2f643a3db6064a44eeb9580b00eae0cd Sun May 26 10:59:30 2024 -0700
get hgc and hgTrackUi to use trackDb cache
- src/hg/lib/hui.c
- lines changed 13, context: html, text, full: html, text
e016f7eae81edd3cfac1f65219dc6c18e91c7e22 Wed May 22 10:47:12 2024 -0700
Unify the different color pickers (drag select highlights, track item highlights and track item colors) into hui.js. Ensure the text box and palette selector work, refs #24507
- src/hg/lib/quickLift.c
- lines changed 12, context: html, text, full: html, text
70e4f023e0cd98a096dfe959142bbada59c4e7a9 Mon May 20 17:28:31 2024 -0700
ongoing work on pair browser
- src/hg/lib/trackHub.c
- lines changed 1, context: html, text, full: html, text
df6cf391270cbbfe12f9ec3869948c2813002a87 Thu May 23 13:47:45 2024 -0700
add support for baseView track type
- src/hg/logCrawl/dbTrackAndSearchUsage/generateUsageStats.py
- lines changed 1, context: html, text, full: html, text
5e1a5bda35707ab546e0a70c6b8b38f91d1b4160 Wed May 22 14:33:13 2024 -0700
Adding a new variable needed to run hgTracks on the command line due to a change Max made. Refs #32237
- src/hg/makeDb/doc/asmHubs/asmHubs.mk
- lines changed 2, context: html, text, full: html, text
8fd2016b6c0e6a6c0bccbf47f2133124c5e6657e Mon May 20 12:48:30 2024 -0700
this will make symLinks happen twice but it is needed and now making a chain net listing while running refs #29545
- lines changed 11, context: html, text, full: html, text
13488a498e6b5238accdbf32c140ed30e30d173c Mon May 20 14:48:43 2024 -0700
correctly get mkSymLinks to run before mkGenomes refs #29545
- src/hg/makeDb/doc/asmHubs/commonNames.pl
- lines changed 5, context: html, text, full: html, text
f81d9d27f273824d88236ee48736f674fe441092 Mon May 27 08:52:41 2024 -0700
sciName for mosquitoes, bees, moths and sponges no redmine
- src/hg/makeDb/doc/asmHubs/master.run.list
- lines changed 18, context: html, text, full: html, text
6b4b6d8db2ca21b06d57b1507c0e67f01338bf33 Mon May 20 12:39:06 2024 -0700
update underway this the first 18 done refs #29545
- lines changed 1, context: html, text, full: html, text
48f681077c8d2fbfdc37cd446a96f6c55e20551c Mon May 20 17:00:51 2024 -0700
adding GCA_902167015.1_Zm-Oh43-REFERENCE-NAM-1.0 Zea_mays per user request, refs #29545
- lines changed 1, context: html, text, full: html, text
f22a96abc0a0fe44ef9a12d57571609f13473435 Fri May 24 15:54:27 2024 -0700
adding assembly GCA_002743455.1_CAU_duck1.0 common mallard (Pekin duck 2017) per user request refs #29545
- lines changed 3, context: html, text, full: html, text
13d6c761cb546b415419da0671931101f5f9a5be Sun May 26 16:57:57 2024 -0700
RefSeq update finished primates refs #29545
- lines changed 8, context: html, text, full: html, text
a1e069cada2a0a440988bc879b09a8c146e284a2 Mon May 27 09:32:24 2024 -0700
catch up run.list with tsv entries no redmine
- src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
- lines changed 1, context: html, text, full: html, text
f22a96abc0a0fe44ef9a12d57571609f13473435 Fri May 24 15:54:27 2024 -0700
adding assembly GCA_002743455.1_CAU_duck1.0 common mallard (Pekin duck 2017) per user request refs #29545
- src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
- lines changed 21, context: html, text, full: html, text
5a43b9ffe0eae7367e4b59e9ae9422d7718621bd Mon May 27 09:33:30 2024 -0700
refseq update adding 8 refs #29545
- src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
- lines changed 1, context: html, text, full: html, text
4f8c175be20be4b98420acdce67d003cc89d8f88 Mon May 20 17:09:40 2024 -0700
adding GCA_902167015.1_Zm-Oh43-REFERENCE-NAM-1.0 Zea_mays maize (OH43 2020) per user request, refs #29545
- src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
- lines changed 8, context: html, text, full: html, text
1e8c52aca6900f6f3ce8b31e79cd6b625715ca39 Mon May 20 13:11:37 2024 -0700
four updates genbank to refseq refs #29545
- lines changed 6, context: html, text, full: html, text
13d6c761cb546b415419da0671931101f5f9a5be Sun May 26 16:57:57 2024 -0700
RefSeq update finished primates refs #29545
- src/hg/makeDb/trackDb/drosophila/dm6/reMap.ra
- lines changed 1, context: html, text, full: html, text
90f2d18f85f8fe8749293cfd6b01ff843be2ffab Fri May 24 15:54:42 2024 -0700
commenting out the maxItems line as it is causing issues for the ReMap track, refs #33791
- src/hg/makeDb/trackDb/human/hg18/omimAvSnp.html
- lines changed 1, context: html, text, full: html, text
e55d5d49dfead30ba3c279307ed460f25d729d0a Fri May 24 14:48:39 2024 -0700
Fixing broken links, No redmine
- src/hg/makeDb/trackDb/human/hg19/reMap.ra
- lines changed 1, context: html, text, full: html, text
90f2d18f85f8fe8749293cfd6b01ff843be2ffab Fri May 24 15:54:42 2024 -0700
commenting out the maxItems line as it is causing issues for the ReMap track, refs #33791
- src/hg/makeDb/trackDb/human/hg38/knownGene.ra
- lines changed 7, context: html, text, full: html, text
f75be6cdc179d7ce11539664b23406306976052d Tue May 21 12:27:38 2024 -0700
Staging and releasing the new GENCODE Known Gene tracks V46 and VM35, refs #33080 #33083
- src/hg/makeDb/trackDb/human/hg38/knownGeneV46.html
- lines changed 1, context: html, text, full: html, text
25e4ae4de9f1d1fd1e59be96621e5bdb0cd97703 Wed May 22 11:23:46 2024 -0700
Updating the month in the html for the latest hg38 and mm39 knownGene tracks, refs #33080 #33083
- src/hg/makeDb/trackDb/human/hg38/mane.ra
- lines changed 2, context: html, text, full: html, text
0ece0de4cc06223e83cba70f32f6a48beb62b253 Wed May 22 09:40:07 2024 -0700
Adding mane higher in search priority as requested by SAB, refs #33477
- src/hg/makeDb/trackDb/human/hg38/reMap.ra
- lines changed 1, context: html, text, full: html, text
90f2d18f85f8fe8749293cfd6b01ff843be2ffab Fri May 24 15:54:42 2024 -0700
commenting out the maxItems line as it is causing issues for the ReMap track, refs #33791
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 2, context: html, text, full: html, text
f75be6cdc179d7ce11539664b23406306976052d Tue May 21 12:27:38 2024 -0700
Staging and releasing the new GENCODE Known Gene tracks V46 and VM35, refs #33080 #33083
- src/hg/makeDb/trackDb/human/omimAvSnp.html
- lines changed 2, context: html, text, full: html, text
e55d5d49dfead30ba3c279307ed460f25d729d0a Fri May 24 14:48:39 2024 -0700
Fixing broken links, No redmine
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 1, context: html, text, full: html, text
2a3426a3f255a5cbc66c2665c7592ac1c8e2732a Wed May 22 09:42:10 2024 -0700
Adding hgnc higher in search priority, refs #33477
- src/hg/makeDb/trackDb/mouse/mm10/reMap.ra
- lines changed 1, context: html, text, full: html, text
90f2d18f85f8fe8749293cfd6b01ff843be2ffab Fri May 24 15:54:42 2024 -0700
commenting out the maxItems line as it is causing issues for the ReMap track, refs #33791
- src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
- lines changed 7, context: html, text, full: html, text
f75be6cdc179d7ce11539664b23406306976052d Tue May 21 12:27:38 2024 -0700
Staging and releasing the new GENCODE Known Gene tracks V46 and VM35, refs #33080 #33083
- src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM35.html
- lines changed 1, context: html, text, full: html, text
25e4ae4de9f1d1fd1e59be96621e5bdb0cd97703 Wed May 22 11:23:46 2024 -0700
Updating the month in the html for the latest hg38 and mm39 knownGene tracks, refs #33080 #33083
- src/hg/makeDb/trackDb/mouse/mm39/reMap.ra
- lines changed 1, context: html, text, full: html, text
90f2d18f85f8fe8749293cfd6b01ff843be2ffab Fri May 24 15:54:42 2024 -0700
commenting out the maxItems line as it is causing issues for the ReMap track, refs #33791
- src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
- lines changed 2, context: html, text, full: html, text
f75be6cdc179d7ce11539664b23406306976052d Tue May 21 12:27:38 2024 -0700
Staging and releasing the new GENCODE Known Gene tracks V46 and VM35, refs #33080 #33083
- src/hg/utils/automation/asmHubChainNetTrackDb.pl
- lines changed 26, context: html, text, full: html, text
ed7414028de9887b9fe8d562758a0af09dedcd8f Thu May 23 18:31:52 2024 -0700
better default visibilities no redmine
- src/hg/utils/automation/asmHubHtml.pl
- lines changed 1, context: html, text, full: html, text
27a61987f2692b2fad37a9faada47b927f568e1e Fri May 24 10:11:44 2024 -0700
correct ftp to https for references to ftp.ncbi.nih.gov no redmine
- src/hg/utils/automation/asmHubNcbiGene.pl
- lines changed 2, context: html, text, full: html, text
27a61987f2692b2fad37a9faada47b927f568e1e Fri May 24 10:11:44 2024 -0700
correct ftp to https for references to ftp.ncbi.nih.gov no redmine
- src/hg/utils/automation/asmHubNcbiRefSeq.pl
- lines changed 16, context: html, text, full: html, text
9374faeb653ab0653e07e6ba890d6531395ae476 Fri May 24 09:59:56 2024 -0700
correctly identify the source for the genes when coming from GCF onto GCA no redmine
- lines changed 3, context: html, text, full: html, text
e76c704d9c5c6dfa06f7d7e15387fd14f651d9bf Fri May 24 10:09:39 2024 -0700
correct FTP path no redmine
- src/hg/utils/automation/asmHubWindowMasker.pl
- lines changed 1, context: html, text, full: html, text
27a61987f2692b2fad37a9faada47b927f568e1e Fri May 24 10:11:44 2024 -0700
correct ftp to https for references to ftp.ncbi.nih.gov no redmine
- src/hg/utils/automation/doNcbiRefSeq.pl
- lines changed 18, context: html, text, full: html, text
1391f50a576e35bd691d3e3898475b5637b88976 Thu May 23 18:32:31 2024 -0700
correct naming of files when porting GCF refSeq to equivalent GCA assembly no redmine
- src/hg/utils/automation/refSeqOnGenBank.py
- lines changed 194, context: html, text, full: html, text
08300d3c6b6f4211a16bf497c40ae6722242d4d4 Fri May 24 14:05:36 2024 -0700
script to add RefSeq genes to a GenBank assembly no redmine
- lines changed 13, context: html, text, full: html, text
d258476e0cc734212538e8ab0a7509acb8b24aaa Fri May 24 14:10:17 2024 -0700
remove cruft no redmine
- lines changed 13, context: html, text, full: html, text
8c99a44e8855b4d78a741f91c02abc603c7ca7ca Fri May 24 14:29:24 2024 -0700
the version check stuff does not actually work
- src/hg/utils/buildPairAssembly/buildPairAssembly.c
- lines changed 5, context: html, text, full: html, text
70e4f023e0cd98a096dfe959142bbada59c4e7a9 Mon May 20 17:28:31 2024 -0700
ongoing work on pair browser
- lines changed 33, context: html, text, full: html, text
df6cf391270cbbfe12f9ec3869948c2813002a87 Thu May 23 13:47:45 2024 -0700
add support for baseView track type
- src/hg/utils/buildPairAssembly/makePair
- lines changed 67, context: html, text, full: html, text
70e4f023e0cd98a096dfe959142bbada59c4e7a9 Mon May 20 17:28:31 2024 -0700
ongoing work on pair browser
- lines changed 15, context: html, text, full: html, text
df6cf391270cbbfe12f9ec3869948c2813002a87 Thu May 23 13:47:45 2024 -0700
add support for baseView track type
- src/hg/utils/otto/genCC/doGenCC.py
- lines changed 3, context: html, text, full: html, text
409b76b74d5e20204f44a74ef250aca5b7ca61db Wed May 22 04:24:46 2024 -0700
Commenting out the part of genCC otto that prints out bad format lines, it causes a lot of spam and is not accionable unless the number of entries suddenly explodes. No RM.
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
- lines changed 9, context: html, text, full: html, text
99b4f6868e8f0fad4985f6e94e46908eeb744ffe Tue May 21 13:28:45 2024 -0700
Adding a few more requested sites.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
- lines changed 21, context: html, text, full: html, text
ac192b6e6f18b63359e0aa30bf096e6883b85588 Thu May 23 13:51:34 2024 -0700
More new lineages; JN.1.33 redesignated to JN.1.39.3; correction to XDV path.
- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
- lines changed 17, context: html, text, full: html, text
19b943548e4c4987365430f090582cc0061156b9 Tue May 21 13:31:43 2024 -0700
Generate memory-mapped hash tables for metadata and name lookup.
- src/inc/cheapcgi.h
- lines changed 3, context: html, text, full: html, text
6f3056fb1c519aeb262d6c1cc9f352652e3086ae Mon May 27 07:49:54 2024 -0700
not setting pix if run from command line, email from Lou that qa scripts are not running anymore
- src/lib/cheapcgi.c
- lines changed 16, context: html, text, full: html, text
6f3056fb1c519aeb262d6c1cc9f352652e3086ae Mon May 27 07:49:54 2024 -0700
not setting pix if run from command line, email from Lou that qa scripts are not running anymore
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
1ef1eefc2445b35d905f227ac3fbea2b8b547941 Mon May 27 10:57:49 2024 -0700
v466 preview2, refs #33762
- lines changed: 1165
- files changed: 86