All File Changes
v449_preview to v449_preview2 (2023-05-22 to 2023-05-30) v449
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- confs/hgwdev.hg.conf
- lines changed 1, context: html, text, full: html, text
4ea50430ea105dbe8cb3f8461a814fe6ccd90d49 Sun May 28 01:11:19 2023 -0700
Installing updated hg.conf files from UCSC servers
- src/hg/hgTables/mainPage.c
- lines changed 1, context: html, text, full: html, text
5c2aaf5c9e5cce3360e476917f7b8e09dc510b39 Fri May 26 10:51:05 2023 -0700
skip hub prefix on link to hgdownload for GTF files
- src/hg/hgTracks/hgTracks.c
- lines changed 2, context: html, text, full: html, text
413714d95b7ac57dbd5d08f9ecc1c4cf01345317 Mon May 29 06:46:57 2023 -0700
disable squishyPack mode when in multi-exon mode
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 1, context: html, text, full: html, text
3b3ce5f1e11f04b4a4919f8aa05bac11c8310067 Tue May 16 16:36:12 2023 -0700
Fixing grammar errors for the DGV Gold Standard track announcement found by b0b, refs #30908
- src/hg/makeDb/doc/asmHubs/master.run.list
- lines changed 88, context: html, text, full: html, text
50f711447b7b3c2dfa65a490bd018e7b62e08b83 Fri May 26 13:47:26 2023 -0700
a number of new RefSeq assemblies in invertebrates refs #29545
- src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
- lines changed 2, context: html, text, full: html, text
3d33d00c61f8aa1e2dde2400388d78ebffaced0f Fri May 26 15:50:15 2023 -0700
RefSeq catch up refs #29545
- src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
- lines changed 2, context: html, text, full: html, text
3d33d00c61f8aa1e2dde2400388d78ebffaced0f Fri May 26 15:50:15 2023 -0700
RefSeq catch up refs #29545
- src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
- lines changed 116, context: html, text, full: html, text
50f711447b7b3c2dfa65a490bd018e7b62e08b83 Fri May 26 13:47:26 2023 -0700
a number of new RefSeq assemblies in invertebrates refs #29545
- src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
- lines changed 20, context: html, text, full: html, text
d3f09e41b76b680a22b29d6a1d5b6c8547695096 Fri May 26 15:15:05 2023 -0700
some invertebrates became obsolete refs #29545
- src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
- lines changed 12, context: html, text, full: html, text
d3f09e41b76b680a22b29d6a1d5b6c8547695096 Fri May 26 15:15:05 2023 -0700
some invertebrates became obsolete refs #29545
- lines changed 3, context: html, text, full: html, text
3d33d00c61f8aa1e2dde2400388d78ebffaced0f Fri May 26 15:50:15 2023 -0700
RefSeq catch up refs #29545
- src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
- lines changed 1, context: html, text, full: html, text
3d33d00c61f8aa1e2dde2400388d78ebffaced0f Fri May 26 15:50:15 2023 -0700
RefSeq catch up refs #29545
- src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
- lines changed 1, context: html, text, full: html, text
3d33d00c61f8aa1e2dde2400388d78ebffaced0f Fri May 26 15:50:15 2023 -0700
RefSeq catch up refs #29545
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 2, context: html, text, full: html, text
dccfa46e499c59cc36ba8591dd4f44e3927d966a Wed May 24 16:30:59 2023 -0700
Re-adding evaSnp3, no RM
- src/hg/mouseStuff/axtChain/axtChain.c
- lines changed 30, context: html, text, full: html, text
7106942562801f0a7a7c9dc4c101c9f7e8afc1a8 Fri May 26 15:55:20 2023 -0700
User reported in MLQ #31322 that axtChain gave fewer results for fasta inputs than for 2bit inputs.
It turned out to be an almost 20-year-old bug that we never noticed because we always use 2bit:
loadFaSeq mimiced the strand-change detection logic in loadIfNewSeq but ignored the fact that
loadIfNewSeq gets a fresh new sequence on the + strand every time the name changes, and only compares
to the previous value of strand when the sequence name has not changed. Instead of unsuccessfully
mimicing that code, just let the caller reverse-complement the sequence when strand is - and then
restore it to + strand after use.
- src/hg/utils/automation/asmHubChromAlias.pl
- lines changed 21, context: html, text, full: html, text
57a2bac4726971e593dc92902803e55667782882 Mon May 22 13:34:49 2023 -0700
adding Ensembl relations in chromAlias and new extended ensGene track to host Rapid Release ensGene refs #31332
- src/hg/utils/automation/asmHubTrackDb.sh
- lines changed 43, context: html, text, full: html, text
57a2bac4726971e593dc92902803e55667782882 Mon May 22 13:34:49 2023 -0700
adding Ensembl relations in chromAlias and new extended ensGene track to host Rapid Release ensGene refs #31332
- src/hg/utils/automation/doNcbiRefSeq.pl
- lines changed 2, context: html, text, full: html, text
5e98a4b579ae9b7efbcc20c0314b7b51e88b7caf Mon May 29 12:13:19 2023 -0700
do not look for a database when it is an assembly hub (hs1) refs #31342
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
- lines changed 1, context: html, text, full: html, text
52cebd83cd791590bbd74bbae30df228dc4b8244 Wed May 24 10:58:24 2023 -0700
Different representative for XBB - nodes have been shuffled around a bit.
- src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
- lines changed 19, context: html, text, full: html, text
4d771afe20833a75ac19216081a730846bb4bb5f Wed May 24 10:59:03 2023 -0700
Run more things in parallel where possible.
- src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
- lines changed 2, context: html, text, full: html, text
693b252e4597e0d97badea0f19b9836ded21ddae Wed May 24 11:02:16 2023 -0700
Added 23A, 23B.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
- lines changed 145, context: html, text, full: html, text
99936258b0be1c69c8017993091ee6c6cb219119 Tue May 9 10:31:45 2023 -0700
Another hundred-odd new lineages and a couple minor corrections.
- lines changed 8, context: html, text, full: html, text
01ad4bc701089c54f7a738b808eab4f422740b60 Wed May 24 10:52:15 2023 -0700
Added XBB.2.9 -- pango-designation v1.20.
Add BA.4_dropout, BA.5_dropout, XBB_dropout to catch more of those in pangolin.
Corrected paths to Q.4, BA.5.2.62, XC.
Add more Ns to B.1.1.529_dropout since a lot of intermediate nodes went away with cleanup.
- lines changed 9, context: html, text, full: html, text
3e8756ab36ff31538dfc529aca39f9c8ef720e31 Wed May 24 11:00:45 2023 -0700
More new lineages.
- src/utils/hubPublicMail
- lines changed 3, context: html, text, full: html, text
d078d44eb66ddc5ec304b69ec9d66a67a1f5d4eb Wed May 24 12:27:22 2023 -0700
Updating the cron to also point to hgcentral, no RM
- lines changed 258, context: html, text, full: html, text
18969d7b729d4b72ea555cbb7d29a74960d91cfe Wed May 24 14:43:45 2023 -0700
Removing the script which now lives under utis/qa, Gera made the addition and I deleted. No RM.
- src/utils/makefile
- lines changed 1, context: html, text, full: html, text
18969d7b729d4b72ea555cbb7d29a74960d91cfe Wed May 24 14:43:45 2023 -0700
Removing the script which now lives under utis/qa, Gera made the addition and I deleted. No RM.
- src/utils/qa/hubPublicMail
- lines changed 258, context: html, text, full: html, text
562f32705c036a421f44da1865add2ef2c2cd803 Wed May 24 14:44:10 2023 -0700
moving script to qa directory, No RM
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
551582f58256a4829f72f8ababc034e83c36b8fc Tue May 30 10:10:39 2023 -0700
v449 preview2, refs #31355
- lines changed: 1054
- files changed: 29