Commits for hiram
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v470_preview to v470_preview2 (2024-08-12 to 2024-08-19) v470
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234509cf8d35819a18c9abdcd2f551d33e28fb8a Mon Aug 12 13:03:12 2024 -0700
- assembly has changed its name, temporarily out of action here, no redmine
- src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 1, context: html, text, full: html, text
2a3cf8e64ff3246c8f8b9d7171f13fb1d07cbdce Mon Aug 12 13:04:49 2024 -0700
- VGP update adding tailed frog haplotypes refs #29545
- src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text
cc23002f01956ee7defd57193092deb9223e7e52 Mon Aug 12 13:06:30 2024 -0700
- legacy genbank yeast assembly refs #29545
- src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text
a51acc6579a07f61464e35002581cb8860eb18d5 Mon Aug 12 13:09:36 2024 -0700
- legacy genbank yeast assembly refs #29545
- src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 1, context: html, text, full: html, text
5a99f2bfa1172d32fa041ee9dfb7e2c5ed28befe Mon Aug 12 13:47:33 2024 -0700
- correct position=lastDbPos on the assembly hubs no redmine
- src/hg/makeDb/trackDb/human/hs1/primates11way.html - lines changed 9, context: html, text, full: html, text
9231a1e85252bf75c90f5e545bed1aca9acdffa4 Mon Aug 12 13:48:03 2024 -0700
- correct position=lastDbPos on the assembly hubs no redmine
- src/hg/makeDb/trackDb/human/hg38/primates11way.html - lines changed 9, context: html, text, full: html, text
fc4f7ec33eee5a715faa117b1e2afb9fcb8a82c6 Mon Aug 12 16:44:38 2024 -0700
- update adds 3 assemblies refs #29545
- src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text
ca99ea9edfabe1feb9d487551a5c227f7dc1bca4 Mon Aug 12 16:47:32 2024 -0700
- obsolete assembly name GCA_018852615.2_ASM1885261v2 becomes GCA_018852615.2_Q100_hg002v1.0.1.mat refs #29545
- src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
5a00dc1ab5eaaaf1776558e2fedc99997471eb73 Tue Aug 13 14:38:20 2024 -0700
- ready to start cleaning up refs #32897
- src/hg/hubApi/findGenome.c - lines changed 156, context: html, text, full: html, text
f8c0ad0bbd396785452c18d9fc3473cfb75c73a5 Tue Aug 13 15:47:21 2024 -0700
- much cleaner at this time removed all the previous experiments refs #32897
- src/hg/hubApi/findGenome.c - lines changed 389, context: html, text, full: html, text
a52bdc2dcb5068501fbc48696d7ad85e8fb2608e Tue Aug 13 17:57:48 2024 -0700
- eliminate the DBG statements and get the query string construction into a dyPrintf refs #32897
- src/hg/hubApi/findGenome.c - lines changed 38, context: html, text, full: html, text
3e420ec829635a0f80f3790b312ab555d3ff2240 Tue Aug 13 18:03:07 2024 -0700
- helper function assemblyListTableName() refs #32897
- src/hg/inc/assemblyList.h - lines changed 12, context: html, text, full: html, text
- src/hg/lib/assemblyList.c - lines changed 16, context: html, text, full: html, text
1d9a7f5d0c88114f17c93574fb726a230a98e3f7 Tue Aug 13 18:07:40 2024 -0700
- adding assemblyList.o to the library refs #32897
a86dc83b44e3ef6ebbbe914cfba5ee145e52482e Tue Aug 13 18:17:14 2024 -0700
- correct set of arguments for findGenome refs #32897
afabfb46d123af83f0b66b48fb2d229c9fbc4df7 Wed Aug 14 16:32:27 2024 -0700
- efficient use of the SQL count function when statsOnly refs #32897
- src/hg/hubApi/findGenome.c - lines changed 23, context: html, text, full: html, text
ffe3440ffaebf92cdab371616731c5b0bae27c62 Thu Aug 15 12:04:39 2024 -0700
- the addAssemblyList needs to run each week even if the other business needs no update refs #32897
- src/hg/utils/otto/genArk/updateHgcentral.sh - lines changed 2, context: html, text, full: html, text
5d9ee32b367b0cce28e02c83b20101ecbd8e8c3d Fri Aug 16 00:09:46 2024 -0700
- now with the browserExists argument to eliminate the allowAll refs #32897
- src/hg/hubApi/findGenome.c - lines changed 53, context: html, text, full: html, text
0fdfd6d6edc06c6b9899fd1013e99fb1515babcb Fri Aug 16 00:10:32 2024 -0700
- now with the browserExists argument to eliminate the allowAll refs #32897
- src/hg/hubApi/dataApi.h - lines changed 2, context: html, text, full: html, text
395c03c87d8620ad52f4760aa39e2b0e6b1bda24 Fri Aug 16 13:13:24 2024 -0700
- adding GCA_000845665.1_ViralProj14458 Murine herpesvirus 68 (WUMS 2007) per user request refs #29545
- src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 1, context: html, text, full: html, text
04d9a71891504b2be49c6e72e9e2f80183a4b22b Fri Aug 16 14:44:31 2024 -0700
- eliminate allowAll argument, return used search string even when modified, return total assembly count available refs #32897
- src/hg/hubApi/dataApi.h - lines changed 1, context: html, text, full: html, text
- src/hg/hubApi/findGenome.c - lines changed 36, context: html, text, full: html, text
fe68c1b1ff0235428aefefd9e8f68679f73f3fd6 Sat Aug 17 07:16:35 2024 -0700
- initial prototype code for assemblySearch function refs #32596
- src/hg/htdocs/assemblySearch.html - lines changed 109, context: html, text, full: html, text
- src/hg/htdocs/style/assemblySearch.css - lines changed 165, context: html, text, full: html, text
- src/hg/js/assemblySearch.js - lines changed 153, context: html, text, full: html, text
0956e5536532f162f20c601bc3cfbf65705ef85e Sat Aug 17 08:15:54 2024 -0700
- fixup to work in this new location refs #32596
- src/hg/htdocs/assemblySearch.html - lines changed 7, context: html, text, full: html, text
- src/hg/js/assemblySearch.js - lines changed 1, context: html, text, full: html, text
659e1bb4271552d1d1056c529298fbccb039f95d Sat Aug 17 08:29:32 2024 -0700
- recording stats on results to stderr for apache error_log refs #32596
- src/hg/hubApi/findGenome.c - lines changed 12, context: html, text, full: html, text
ff24452dd4f8ae69c2f45c1fc481b71abbafb406 Sat Aug 17 23:52:49 2024 -0700
- refresh the header row so the sorttable will function properly refs #32596
- src/hg/js/assemblySearch.js - lines changed 15, context: html, text, full: html, text
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