All File Changes
v445_base to v446_preview (2023-03-13 to 2023-03-20) v446
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- README
- lines changed 80, context: html, text, full: html, text
8f4dade376c8abc619b98cae61b054414ab4326f Thu Mar 16 04:02:41 2023 -0700
cleaning up the main README file a little, pointing to all the new docs we have and adding links to kent-core
- build/kent-core/README.md
- lines changed 11, context: html, text, full: html, text
1b30f5184294b113da69c347441a238e7cc61cd4 Thu Mar 16 03:41:22 2023 -0700
updating kent-core README
- build/kent-core/makeKentCore
- lines changed 1, context: html, text, full: html, text
86d972102a4fe9b77b62cf5efe1003864c25df9e Thu Mar 16 02:50:52 2023 -0700
clean kent first, no redmine, github #75
- lines changed 13, context: html, text, full: html, text
06ee0f8f3e1a1a1c1ce07e5a408629389ea6e795 Thu Mar 16 03:31:52 2023 -0700
updating makeKentCore and added to build wiki page CGI_Build_Process
- build/kent-core/makeKentCore.rules
- lines changed 4, context: html, text, full: html, text
06ee0f8f3e1a1a1c1ce07e5a408629389ea6e795 Thu Mar 16 03:31:52 2023 -0700
updating makeKentCore and added to build wiki page CGI_Build_Process
- src/hg/gar/mkAlias.pl
- lines changed 205, context: html, text, full: html, text
da5c2bf40e5fa78b2e072c52069d6bbf71a6f469 Thu Mar 16 14:32:36 2023 -0700
script to make the alias table tsv after the assemblyRequest page has been made refs #30474
- src/hg/hgGene/hgGeneData/C_elegans/links.ra
- lines changed 2, context: html, text, full: html, text
e0b3a8e4497a0953cf6689431d1b287f6d4456a7 Thu Mar 16 10:04:43 2023 -0700
Getting rid of the rest of the CGAP hgGene entries, refs #30695
- src/hg/hgGene/hgGeneData/D_melanogaster/dm1/links.ra
- lines changed 2, context: html, text, full: html, text
e0b3a8e4497a0953cf6689431d1b287f6d4456a7 Thu Mar 16 10:04:43 2023 -0700
Getting rid of the rest of the CGAP hgGene entries, refs #30695
- src/hg/hgGene/hgGeneData/D_melanogaster/dm2/links.ra
- lines changed 2, context: html, text, full: html, text
e0b3a8e4497a0953cf6689431d1b287f6d4456a7 Thu Mar 16 10:04:43 2023 -0700
Getting rid of the rest of the CGAP hgGene entries, refs #30695
- src/hg/hgGene/hgGeneData/D_melanogaster/dm3/links.ra
- lines changed 2, context: html, text, full: html, text
e0b3a8e4497a0953cf6689431d1b287f6d4456a7 Thu Mar 16 10:04:43 2023 -0700
Getting rid of the rest of the CGAP hgGene entries, refs #30695
- src/hg/hgGene/hgGeneData/Mouse/links.ra
- lines changed 2, context: html, text, full: html, text
e0b3a8e4497a0953cf6689431d1b287f6d4456a7 Thu Mar 16 10:04:43 2023 -0700
Getting rid of the rest of the CGAP hgGene entries, refs #30695
- src/hg/hgGene/hgGeneData/Rat/links.ra
- lines changed 2, context: html, text, full: html, text
e0b3a8e4497a0953cf6689431d1b287f6d4456a7 Thu Mar 16 10:04:43 2023 -0700
Getting rid of the rest of the CGAP hgGene entries, refs #30695
- src/hg/hgGene/hgGeneData/S_cerevisiae/links.ra
- lines changed 2, context: html, text, full: html, text
e0b3a8e4497a0953cf6689431d1b287f6d4456a7 Thu Mar 16 10:04:43 2023 -0700
Getting rid of the rest of the CGAP hgGene entries, refs #30695
- src/hg/hgGene/hgGeneData/Zebrafish/links.ra
- lines changed 2, context: html, text, full: html, text
e0b3a8e4497a0953cf6689431d1b287f6d4456a7 Thu Mar 16 10:04:43 2023 -0700
Getting rid of the rest of the CGAP hgGene entries, refs #30695
- src/hg/hgTracks/hgTracks.c
- lines changed 12, context: html, text, full: html, text
904babadd41551f2b2be6e44159fd53665e3e0c9 Wed Mar 15 13:38:50 2023 -0700
Fixing issues with highlights in image/PDF, particularly with multi-region. refs #30833
- lines changed 10, context: html, text, full: html, text
f5bc011a1d5dd3daa3211c93eead19e8c7f50ce3 Thu Mar 16 16:53:32 2023 -0700
polishing up squishyPack for release
- lines changed 5, context: html, text, full: html, text
108ec2796d49d37c04454bcf3c89c353c44e9cdf Fri Mar 17 01:44:27 2023 -0700
removing buttons again, I misunderstood QA, refs #30827
- src/hg/hgTracks/hgTracks.h
- lines changed 1, context: html, text, full: html, text
f5bc011a1d5dd3daa3211c93eead19e8c7f50ce3 Thu Mar 16 16:53:32 2023 -0700
polishing up squishyPack for release
- src/hg/hgTracks/longRangeTrack.c
- lines changed 6, context: html, text, full: html, text
c47b72480a741cb22f2d0b0d9f0bff9b3dd8809a Fri Mar 17 09:51:58 2023 -0700
Updating a couple of other minor locations to better reflect transparency code, refs #30569
- src/hg/hgTracks/simpleTracks.c
- lines changed 10, context: html, text, full: html, text
f5bc011a1d5dd3daa3211c93eead19e8c7f50ce3 Thu Mar 16 16:53:32 2023 -0700
polishing up squishyPack for release
- src/hg/hubApi/tests/expected/err48.gz
- lines changed 0, context: html, text, full: html, text
cd9835e35a7381da350289f1eb287005bfac1826 Fri Mar 17 13:22:45 2023 -0700
fixup makefile to show server and allow other targets for convenient server setting refs #30457
- src/hg/hubApi/tests/expected/err49.gz
- lines changed 0, context: html, text, full: html, text
cd9835e35a7381da350289f1eb287005bfac1826 Fri Mar 17 13:22:45 2023 -0700
fixup makefile to show server and allow other targets for convenient server setting refs #30457
- src/hg/hubApi/tests/makefile
- lines changed 168, context: html, text, full: html, text
cd9835e35a7381da350289f1eb287005bfac1826 Fri Mar 17 13:22:45 2023 -0700
fixup makefile to show server and allow other targets for convenient server setting refs #30457
- lines changed 25, context: html, text, full: html, text
4c458a517cc3ea3cfa4f26a2c136d3641647edd2 Fri Mar 17 15:03:41 2023 -0700
adding a search test refs #24113
- src/hg/js/hgTracks.js
- lines changed 1, context: html, text, full: html, text
2ebbf76a87337459b3137c01283a4fa706538f14 Sat Mar 18 14:57:23 2023 -0700
turn on phylo logo on dev. Turn off track download for squish
auxilliary tracks
- src/hg/js/jquery.imgareaselect.js
- lines changed 8, context: html, text, full: html, text
86d972102a4fe9b77b62cf5efe1003864c25df9e Thu Mar 16 02:50:52 2023 -0700
clean kent first, no redmine, github #75
- src/hg/lib/hubConnect.c
- lines changed 1, context: html, text, full: html, text
18d9591883af29405f3870fc649acbae9a798cd6 Wed Mar 15 17:03:51 2023 -0700
check asmAlias BEFORE looking for curated hubs
- src/hg/makeDb/doc/asmHubs/commonHtml.pm
- lines changed 12, context: html, text, full: html, text
790b166f17ba0ef2f8cfe220dbc6c2a67035ede9 Wed Mar 15 21:16:40 2023 -0700
adding HPRC links to the index pages refs #30508
- src/hg/makeDb/doc/asmHubs/hubIndex.pl
- lines changed 14, context: html, text, full: html, text
c44435c2093a2967aa189ef7394595edcc7cbf3d Wed Mar 15 21:25:07 2023 -0700
adding viral and bacteria index pointers no redmine
- lines changed 13, context: html, text, full: html, text
653a69b696a8534261a8ff0dcbf1ef3af7d7c816 Wed Mar 15 21:45:32 2023 -0700
adding link to HPRC collection no redmine
- lines changed 1, context: html, text, full: html, text
620c0f6f7951ebe04d3599ed66ac6a46e36edbaf Wed Mar 15 21:48:36 2023 -0700
extra table header can center its text no redmine
- lines changed 2, context: html, text, full: html, text
bc7b8c2d05214b6e6ebe5d7b99d8361394d3c3d5 Wed Mar 15 21:50:12 2023 -0700
do not want sortable table since it now has an extra header in the middle no redmine
- src/hg/makeDb/doc/asmHubs/master.run.list
- lines changed 1, context: html, text, full: html, text
540d6e9c29612d2a2a932e04bc917ab73a442401 Mon Mar 13 11:00:47 2023 -0700
adding GCF_027579735.1_aBomBom1.pri fire-bellied toad (aBomBom1 primary hap 2023) per user for RefSeq update refs #29545
- lines changed 2, context: html, text, full: html, text
37421ec79ef8877da0fd40cb21335fa61e36475a Mon Mar 13 11:33:59 2023 -0700
starting two example HPRC assemblies refs #30508
- lines changed 1, context: html, text, full: html, text
6d95fbd4185c76a8bedb7e5115bd0b5bd34ac0e0 Mon Mar 13 13:43:28 2023 -0700
adding GCA_904849725.1_MorexV3_pseudomolecules_assembly domesticated barley (H.vulgare 2021 genbank) per user request refs #29545
- lines changed 6, context: html, text, full: html, text
2e5bad70bb2d00c524f3b3ee630b67c1b67b7d89 Mon Mar 13 15:22:27 2023 -0700
adding 4 more for RefSeq update refs #29545
- lines changed 5, context: html, text, full: html, text
7fb4fbe8a776a07fd04922670e4ffac45e7dae60 Wed Mar 15 14:28:41 2023 -0700
adding 5 more HPRC builds ref #29545
- lines changed 14, context: html, text, full: html, text
d2d394ba518c610ec0a1a23a114b2f7bb518828c Thu Mar 16 11:15:19 2023 -0700
catching up the 20 HPRC assemblies refs #30508
- lines changed 4, context: html, text, full: html, text
90006ce50a15349235c0defdc272526fe1b48aa1 Sat Mar 18 09:13:46 2023 -0700
adding three per user request refs #29545
- src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
- lines changed 23, context: html, text, full: html, text
790b166f17ba0ef2f8cfe220dbc6c2a67035ede9 Wed Mar 15 21:16:40 2023 -0700
adding HPRC links to the index pages refs #30508
- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
- lines changed 23, context: html, text, full: html, text
790b166f17ba0ef2f8cfe220dbc6c2a67035ede9 Wed Mar 15 21:16:40 2023 -0700
adding HPRC links to the index pages refs #30508
- lines changed 18, context: html, text, full: html, text
3227ff50033faf22cb1199ad40610f9042c7fd10 Fri Mar 17 16:19:21 2023 -0700
add special section for the VGP index page to point to the special listings of files no redmine
- src/hg/makeDb/doc/asmHubs/trackData.pl
- lines changed 23, context: html, text, full: html, text
790b166f17ba0ef2f8cfe220dbc6c2a67035ede9 Wed Mar 15 21:16:40 2023 -0700
adding HPRC links to the index pages refs #30508
- src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
- lines changed 3, context: html, text, full: html, text
4516d025b57857bdddbf393f5d82c6c2b91e22c3 Sat Mar 18 09:26:01 2023 -0700
adding three per user request refs #29545
- src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
- lines changed 2, context: html, text, full: html, text
923105258f47bd9b394d707c53e8626856403bfb Mon Mar 13 16:39:26 2023 -0700
adding four to catch up RefSeq assemblies refs #29545
- src/hg/makeDb/doc/hprcAsmHub/HPRC_PanGenome_Logo.png
- lines changed 0, context: html, text, full: html, text
ff3005ab6eb18c0111dc8a08c5a5ff057c79a1d5 Wed Mar 15 20:44:33 2023 -0700
HPRC logo from https://humanpangenome.org/img/Logo-3.png refs #30508
- src/hg/makeDb/doc/hprcAsmHub/hprc.orderList.tsv
- lines changed 9, context: html, text, full: html, text
23afc99533e828beee0252880a28eee1bd885870 Wed Mar 15 20:31:40 2023 -0700
starting HPRC with 9 genomes refs #30508
- src/hg/makeDb/doc/hprcAsmHub/hub.txt
- lines changed 6, context: html, text, full: html, text
23afc99533e828beee0252880a28eee1bd885870 Wed Mar 15 20:31:40 2023 -0700
starting HPRC with 9 genomes refs #30508
- src/hg/makeDb/doc/hprcAsmHub/makefile
- lines changed 23, context: html, text, full: html, text
23afc99533e828beee0252880a28eee1bd885870 Wed Mar 15 20:31:40 2023 -0700
starting HPRC with 9 genomes refs #30508
- src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
- lines changed 11, context: html, text, full: html, text
674e99d2258f5a334cb0badb20a1e437debe7ca1 Mon Mar 13 13:45:05 2023 -0700
adding GCA_904849725.1_MorexV3_pseudomolecules_assembly domesticated barley (H.vulgare 2021 genbank) per user request refs #29545
- src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
- lines changed 1, context: html, text, full: html, text
6d95fbd4185c76a8bedb7e5115bd0b5bd34ac0e0 Mon Mar 13 13:43:28 2023 -0700
adding GCA_904849725.1_MorexV3_pseudomolecules_assembly domesticated barley (H.vulgare 2021 genbank) per user request refs #29545
- src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
- lines changed 1, context: html, text, full: html, text
923105258f47bd9b394d707c53e8626856403bfb Mon Mar 13 16:39:26 2023 -0700
adding four to catch up RefSeq assemblies refs #29545
- src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
- lines changed 1, context: html, text, full: html, text
6d95fbd4185c76a8bedb7e5115bd0b5bd34ac0e0 Mon Mar 13 13:43:28 2023 -0700
adding GCA_904849725.1_MorexV3_pseudomolecules_assembly domesticated barley (H.vulgare 2021 genbank) per user request refs #29545
- lines changed 2, context: html, text, full: html, text
923105258f47bd9b394d707c53e8626856403bfb Mon Mar 13 16:39:26 2023 -0700
adding four to catch up RefSeq assemblies refs #29545
- src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
- lines changed 4, context: html, text, full: html, text
37421ec79ef8877da0fd40cb21335fa61e36475a Mon Mar 13 11:33:59 2023 -0700
starting two example HPRC assemblies refs #30508
- lines changed 5, context: html, text, full: html, text
8d8aeeae86fd9c8d88d199fb03b4fe8c2e381c1d Wed Mar 15 14:45:34 2023 -0700
adding 5 more HPRC builds ref #29545
- lines changed 14, context: html, text, full: html, text
f436af2460ce80a02f8e6c12dc9482c1a0957172 Thu Mar 16 12:01:34 2023 -0700
catching up 20 HPRC genomes refs #30508
- src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
- lines changed 1, context: html, text, full: html, text
540d6e9c29612d2a2a932e04bc917ab73a442401 Mon Mar 13 11:00:47 2023 -0700
adding GCF_027579735.1_aBomBom1.pri fire-bellied toad (aBomBom1 primary hap 2023) per user for RefSeq update refs #29545
- src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
- lines changed 56, context: html, text, full: html, text
f5bc011a1d5dd3daa3211c93eead19e8c7f50ce3 Thu Mar 16 16:53:32 2023 -0700
polishing up squishyPack for release
- src/hg/makeDb/trackDb/human/hg38/trackDb.100way.alpha.ra
- lines changed 114, context: html, text, full: html, text
2ebbf76a87337459b3137c01283a4fa706538f14 Sat Mar 18 14:57:23 2023 -0700
turn on phylo logo on dev. Turn off track download for squish
auxilliary tracks
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 2, context: html, text, full: html, text
f5bc011a1d5dd3daa3211c93eead19e8c7f50ce3 Thu Mar 16 16:53:32 2023 -0700
polishing up squishyPack for release
- lines changed 2, context: html, text, full: html, text
2ebbf76a87337459b3137c01283a4fa706538f14 Sat Mar 18 14:57:23 2023 -0700
turn on phylo logo on dev. Turn off track download for squish
auxilliary tracks
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 2, context: html, text, full: html, text
f5bc011a1d5dd3daa3211c93eead19e8c7f50ce3 Thu Mar 16 16:53:32 2023 -0700
polishing up squishyPack for release
- lines changed 1, context: html, text, full: html, text
2ebbf76a87337459b3137c01283a4fa706538f14 Sat Mar 18 14:57:23 2023 -0700
turn on phylo logo on dev. Turn off track download for squish
auxilliary tracks
- src/hg/utils/bedMergeOverlappingBlocks/bedMergeOverlappingBlocks.c
- lines changed 1, context: html, text, full: html, text
c47b72480a741cb22f2d0b0d9f0bff9b3dd8809a Fri Mar 17 09:51:58 2023 -0700
Updating a couple of other minor locations to better reflect transparency code, refs #30569
- src/hg/utils/rts/dumpSessions
- lines changed 11, context: html, text, full: html, text
767e3f123a734a5c0623b2e635c7cdc59e9fb61f Mon Mar 13 10:48:38 2023 -0700
starting on work to purge recommend track sets of all that is not
relevant to the rts
- lines changed 1, context: html, text, full: html, text
d81de2e463562bf4591506561b16594173fb76b9 Tue Mar 14 14:18:57 2023 -0700
remove duplicates in RTS sessions
- src/hg/utils/rts/getTracks
- lines changed 14, context: html, text, full: html, text
767e3f123a734a5c0623b2e635c7cdc59e9fb61f Mon Mar 13 10:48:38 2023 -0700
starting on work to purge recommend track sets of all that is not
relevant to the rts
- src/hg/utils/rts/hg19/CNVs%20Clinical
- lines changed 689, context: html, text, full: html, text
767e3f123a734a5c0623b2e635c7cdc59e9fb61f Mon Mar 13 10:48:38 2023 -0700
starting on work to purge recommend track sets of all that is not
relevant to the rts
- lines changed 324, context: html, text, full: html, text
d81de2e463562bf4591506561b16594173fb76b9 Tue Mar 14 14:18:57 2023 -0700
remove duplicates in RTS sessions
- src/hg/utils/rts/hg19/Non%20coding%20SNVs
- lines changed 619, context: html, text, full: html, text
767e3f123a734a5c0623b2e635c7cdc59e9fb61f Mon Mar 13 10:48:38 2023 -0700
starting on work to purge recommend track sets of all that is not
relevant to the rts
- src/hg/utils/rts/hg19/Problematic%20Regions
- lines changed 247, context: html, text, full: html, text
767e3f123a734a5c0623b2e635c7cdc59e9fb61f Mon Mar 13 10:48:38 2023 -0700
starting on work to purge recommend track sets of all that is not
relevant to the rts
- lines changed 2, context: html, text, full: html, text
d81de2e463562bf4591506561b16594173fb76b9 Tue Mar 14 14:18:57 2023 -0700
remove duplicates in RTS sessions
- src/hg/utils/rts/hg19/SNVs%20Clinical
- lines changed 739, context: html, text, full: html, text
767e3f123a734a5c0623b2e635c7cdc59e9fb61f Mon Mar 13 10:48:38 2023 -0700
starting on work to purge recommend track sets of all that is not
relevant to the rts
- lines changed 303, context: html, text, full: html, text
d81de2e463562bf4591506561b16594173fb76b9 Tue Mar 14 14:18:57 2023 -0700
remove duplicates in RTS sessions
- src/hg/utils/rts/hg38/Clinical_CNVs_hg38
- lines changed 297, context: html, text, full: html, text
767e3f123a734a5c0623b2e635c7cdc59e9fb61f Mon Mar 13 10:48:38 2023 -0700
starting on work to purge recommend track sets of all that is not
relevant to the rts
- lines changed 1, context: html, text, full: html, text
d81de2e463562bf4591506561b16594173fb76b9 Tue Mar 14 14:18:57 2023 -0700
remove duplicates in RTS sessions
- src/hg/utils/rts/hg38/Clinical_SNVs_hg38
- lines changed 292, context: html, text, full: html, text
767e3f123a734a5c0623b2e635c7cdc59e9fb61f Mon Mar 13 10:48:38 2023 -0700
starting on work to purge recommend track sets of all that is not
relevant to the rts
- lines changed 2, context: html, text, full: html, text
d81de2e463562bf4591506561b16594173fb76b9 Tue Mar 14 14:18:57 2023 -0700
remove duplicates in RTS sessions
- src/hg/utils/rts/hg38/Non_Coding_SNVs_hg38
- lines changed 353, context: html, text, full: html, text
767e3f123a734a5c0623b2e635c7cdc59e9fb61f Mon Mar 13 10:48:38 2023 -0700
starting on work to purge recommend track sets of all that is not
relevant to the rts
- lines changed 2, context: html, text, full: html, text
d81de2e463562bf4591506561b16594173fb76b9 Tue Mar 14 14:18:57 2023 -0700
remove duplicates in RTS sessions
- src/hg/utils/rts/hg38/Problematic_Regions_hg38
- lines changed 318, context: html, text, full: html, text
767e3f123a734a5c0623b2e635c7cdc59e9fb61f Mon Mar 13 10:48:38 2023 -0700
starting on work to purge recommend track sets of all that is not
relevant to the rts
- lines changed 2, context: html, text, full: html, text
d81de2e463562bf4591506561b16594173fb76b9 Tue Mar 14 14:18:57 2023 -0700
remove duplicates in RTS sessions
- src/inc/common.mk
- lines changed 3, context: html, text, full: html, text
46d1b1ddb8160c5203eca5ae39302374eea74c64 Wed Mar 15 10:43:28 2023 -0700
enforce using HAL *only* on hgwdev, no other machine, breaks userApps build on hgcompute-01 no redmine
- src/lib/basicBed.c
- lines changed 2, context: html, text, full: html, text
2118fb80386b56219609bb0e50a2565092a72dae Fri Mar 17 09:53:14 2023 -0700
bedParseRgb doesn't need to add alpha for 3-value color - that's added later when colors
are translated to the graphics level. So we'll accept 255,255,255 as a color again. refs #30569
- src/utils/hubPublicMail
- lines changed 2, context: html, text, full: html, text
882695ead3a63c68053ad2bad8b6be4b2da68cf0 Thu Mar 16 16:45:10 2023 -0700
Changing a verbose print to debug only to reduce the amount of emails sent from this script. Will still email when sending out to a hub provider. No RM.
- src/utils/qa/checkGbdbDiffs.csh
- lines changed 2, context: html, text, full: html, text
6d65d261218d44d751559cc954b8c9df83c1558a Thu Mar 16 16:46:49 2023 -0700
Commenting out a verbose line so this cron is silent unless it finds a difference in gbdb. No RM.
- src/utils/qa/hubSearchUpdate
- lines changed 1, context: html, text, full: html, text
3729c3c6b2ac6dab93c80c3dcccc9151f66da151 Thu Mar 16 16:46:04 2023 -0700
Appending the date to the log file so the email is clear adnt he cron only messages when there is an error, no RM.
- lines changed: 5226
- files changed: 88