All File Changes

v432_preview2 to v432_base (2022-05-31 to 2022-06-06) v432

• src/hg/hgc/rnaFoldClick.c
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    ab0b162f0b880aa7dce8cd25b840957b1bfa9656 Wed Jun 1 00:58:03 2022 -0700
    Fixing NOSQLINJv2, using safe functions for extraWhere for hExtendedChromQuery in hgc/rnaFoldClick.c. refs #29274
• src/hg/htdocs/FAQ/FAQformat.html
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    eb062a7423c03c0641a7877d99bad1e9e7f956a1 Thu Jun 2 06:31:01 2022 -0700
    added links to genes non-coding FAQ in bigGenePred and Gene Pred Formats refs #26086
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    a050a5d26e8cd5a70055da0e080980fa3bf45824 Thu Jun 2 07:31:09 2022 -0700
    Adding a link in the genePred FAQ to advertise bigGenePred and codon number/AA display in custom tracks refs #26086
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    bb41c497a130d9fa52390febf85927d58534517f Thu Jun 2 07:33:22 2022 -0700
    Reword codon number/AA display in custom tracks sentence refs #26086
• src/hg/htdocs/goldenPath/help/bigGenePred.html
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    eb062a7423c03c0641a7877d99bad1e9e7f956a1 Thu Jun 2 06:31:01 2022 -0700
    added links to genes non-coding FAQ in bigGenePred and Gene Pred Formats refs #26086
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
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    7038a4fdd383a996d3cd109bf46e1cb0274c58f5 Tue May 31 10:06:10 2022 -0700
    Adding a new Assembly Hub overview section to trackDbHub page and linked to existing docs to provide anchors for groups, twoBitPath, defaultPos #1629
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    b4aec3faf165901efc9fd333ba77f71c40da4e55 Fri Jun 3 06:45:47 2022 -0700
    adding useOneFile on doc to trackDbHub page #26512
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    3c8303fc9d59eccfe9386f64fe4b4ad21275df51 Sun Jun 5 09:06:58 2022 -0700
    added anchors for hub.txt settings in /hgTrackHubHelp.html #2651
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
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    5636e1c8e892ab640c371b5df317893ea86b6e45 Fri May 27 12:18:21 2022 -0700
    Code Review edit to logo Doc refs #29438
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    7038a4fdd383a996d3cd109bf46e1cb0274c58f5 Tue May 31 10:06:10 2022 -0700
    Adding a new Assembly Hub overview section to trackDbHub page and linked to existing docs to provide anchors for groups, twoBitPath, defaultPos #1629
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    b4aec3faf165901efc9fd333ba77f71c40da4e55 Fri Jun 3 06:45:47 2022 -0700
    adding useOneFile on doc to trackDbHub page #26512
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    5636e1c8e892ab640c371b5df317893ea86b6e45 Fri May 27 12:18:21 2022 -0700
    Code Review edit to logo Doc refs #29438
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    f03135c12fca462a41f39dc6604dd79406e57849 Wed Jun 1 04:19:10 2022 -0700
    fixing "urls" trackDb doc, refs #29309
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    b8eea06820c03eb32bf769e6a4152bcdc9dbfb1a Wed Jun 1 08:13:47 2022 -0700
    Adjusting some wording about the urls setting in trackDbLibrary refs #29309
• src/hg/htdocs/goldenPath/newsarch.html
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    8b4bbbbadbdc027c9fc2a8d8c583b1c28053d33a Fri Jun 3 17:07:27 2022 -0700
    Announcing GenCC refs #28166
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    b17dc39da7b8b002eabc409c792c022038e8e126 Mon Jun 6 10:36:33 2022 -0700
    Changes for code review, refs #29524
• src/hg/htdocs/indexNews.html
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    8b4bbbbadbdc027c9fc2a8d8c583b1c28053d33a Fri Jun 3 17:07:27 2022 -0700
    Announcing GenCC refs #28166
• src/hg/htdocs/util.html
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    47ec5874029cec229a412d95cf3d8c4e6ff1a05b Wed Jun 1 10:32:19 2022 -0700
    Adding G-OnRamp to list of outside group tools and closing ticket ref #24920
• src/hg/inc/versionInfo.h
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    04c4e71a347cfb4774bd1139996eebc48c936bdd Mon Jun 6 11:20:43 2022 -0700
    New version number v432
• src/hg/lib/bigBedFind.c
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    9aad0c71c8101b3566c50714139e3e6369ccc0a2 Fri Jun 3 11:57:47 2022 -0700
    fix a long-term problem in bigBed search. Why didn't we see this earlier?
• src/hg/lib/sqlSanity.c
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    b13a2a991ee5be9c88fe0f4baf7859900c7c8570 Tue May 31 23:29:23 2022 -0700
    correction for the SQL NOT operator in sqlSanity.c
• src/hg/lib/trackHub.c
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    057252c1e8078051276e327622b30cf49b68e637 Wed Jun 1 11:39:40 2022 -0700
    fix problem of duplicated results in #29447
• src/hg/makeDb/doc/asmHubs/master.run.list
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    d54e66241ccc3090b69255dcd3dedfed45146b71 Wed Jun 1 16:38:55 2022 -0700
    remember a forgotten build command for mRatBN7.2 no redmine
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
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    e31cf0a8c121c0d36707912926d4d6f6f80b3708 Fri Jun 3 12:05:39 2022 -0700
    now using chromAlias.bb, better mkSymlink progress, no more restriction on dynamicBlat server space and report total track count on verify
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
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    e31cf0a8c121c0d36707912926d4d6f6f80b3708 Fri Jun 3 12:05:39 2022 -0700
    now using chromAlias.bb, better mkSymlink progress, no more restriction on dynamicBlat server space and report total track count on verify
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
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    e31cf0a8c121c0d36707912926d4d6f6f80b3708 Fri Jun 3 12:05:39 2022 -0700
    now using chromAlias.bb, better mkSymlink progress, no more restriction on dynamicBlat server space and report total track count on verify
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
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    e31cf0a8c121c0d36707912926d4d6f6f80b3708 Fri Jun 3 12:05:39 2022 -0700
    now using chromAlias.bb, better mkSymlink progress, no more restriction on dynamicBlat server space and report total track count on verify
• src/hg/makeDb/doc/hg38/hg38.txt
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    80b6325af1a7076f71c1a9413d99a1784d2a7fbd Thu May 26 17:16:48 2022 -0700
    Uniq'd bed files refs #23591
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    1ba6b97d77a7cb3030eb2890342e82faec2b31ff Thu Jun 2 13:11:05 2022 -0700
    add C.inopinata per user request and a new version of D.sechellia no redmine
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    f1c530c0f196d3147de2448f0c32e2f76e3541fe Wed Jun 1 15:22:26 2022 -0700
    catching up some new assemblies no redmine
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    30227957f7eb315b291051a8b291e7a74f7764b2 Fri Jun 3 12:02:11 2022 -0700
    adding GCA_023515785.1_UTH_Rnor_SHR_Utx per user request no redmine
• src/hg/makeDb/trackDb/canFam4.gbdbList.txt
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    dbbc2b6aef27cb1c2cb421c7c7982f55ef8db41d Tue May 31 14:34:46 2022 -0700
    Removing crud, No RM
• src/hg/makeDb/trackDb/human/genCC.html
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    5f16f242b40b5bec9c193b2192c37b05d186526a Fri Jun 3 15:13:54 2022 -0700
    Pushing GenCC proofread and release date refs #2816^
• src/hg/makeDb/trackDb/human/genCC.ra
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    5f16f242b40b5bec9c193b2192c37b05d186526a Fri Jun 3 15:13:54 2022 -0700
    Pushing GenCC proofread and release date refs #2816^
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    1c687cc86e7b53520b80e1f84eebd87cd9f1f5d2 Fri Jun 3 17:08:51 2022 -0700
    Added space refs #28166
• src/hg/makeDb/trackDb/human/revel.html
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    17ade49f24bb4fb6398e1d5b508a35a770329a6c Tue May 31 12:58:25 2022 -0700
    Minor grammar edits to revel overlaps refs #29475
• src/hg/makeDb/trackDb/human/revel.ra
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    17ade49f24bb4fb6398e1d5b508a35a770329a6c Tue May 31 12:58:25 2022 -0700
    Minor grammar edits to revel overlaps refs #29475
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    682fc6600dffe2e0c2b4fb69b8da5318d34940f6 Tue May 31 13:39:16 2022 -0700
    Small changes refs #29475
• src/hg/utils/faToVcf/faToVcf.c
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    6212068bffa294be01c27e5e34f7b51def22f25a Tue Apr 12 17:58:51 2022 -0700
    Treat '-' bases as 'N' when counting differing bases between ref and input seq for -maxDiff.
• src/hg/utils/hubCheck/hubCheck.c
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    7a7dfcb3a90292be4ea9ac465e5649f128043f05 Thu Jun 2 14:29:21 2022 -0700
    Don't error out early when checking subtracks, instead show all possible warnings for bad subgroup memberships, refs #29525
• src/hg/utils/hubCheck/tests/expected/badSubGroups.output.txt
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    7a7dfcb3a90292be4ea9ac465e5649f128043f05 Thu Jun 2 14:29:21 2022 -0700
    Don't error out early when checking subtracks, instead show all possible warnings for bad subgroup memberships, refs #29525
• src/hg/utils/hubCheck/tests/expected/manyErrors.output.txt
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    7a7dfcb3a90292be4ea9ac465e5649f128043f05 Thu Jun 2 14:29:21 2022 -0700
    Don't error out early when checking subtracks, instead show all possible warnings for bad subgroup memberships, refs #29525
• src/hg/utils/hubCheck/tests/input/badSubGroups.txt
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    7a7dfcb3a90292be4ea9ac465e5649f128043f05 Thu Jun 2 14:29:21 2022 -0700
    Don't error out early when checking subtracks, instead show all possible warnings for bad subgroup memberships, refs #29525
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    4b526917c44114d3d9fa18e6dd31bee769b5a24f Mon Apr 4 09:44:28 2022 -0700
    Added proposed482. G210T in XS and proposed446 needs to be masked for pangolin. XD samples should have 29742; some do, some don't, so mask that in (HT Cornelius Roemer). Added miscRecombOrContam to prevent non-XM descendants of XM branch from being labeled XM (HT Cornelius Roemer).
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    046b5de9f797d101b1de3bf677fc7249672a9779 Thu Apr 14 09:48:12 2022 -0700
    Added BA.4, BA.5, BA.2.11, BA.2.12, BA.2.12.1, BA.2.3.2, BA.2.10.1, AY.112.3 (pango-designation v1.3). Added BA.2.9.1, BA.2.13, BA.1.20, BA.1.21, BA.1.21.1, BA.1.14.1, BA.1.14.2, BA.1.15.2, AY.122.6, AY.127.3 (pango-designation v1.4).
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    7d3899630ebc8e51b5ba9724645a7e2c5ec9cab5 Thu Apr 14 13:00:43 2022 -0700
    Renamed proposed478 to XT. Added new lineages BA.1.1.17, BA.1.16.2, BA.2.14, BA.2.15, BA.2.16, AY.4.2.5, AY.33.2, and AY.39.4 [which will be renamed to AY.134 in v1.6] (pango-designation v1.5).
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    0bdcc5b4d14cf7a66c4d1ce677de340a36a82949 Wed Apr 20 11:14:58 2022 -0700
    Mask some additional sites for proposed437 -- addition of a new sequence caused some shifting around. Rename miscRecombOrContam to miscBA1BA2Post17k and add more misc labels to cover not-quite-the-designated-recombinant branches.
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    c7b124d26dc2d6df9116b1ab73b871ea48b6e8ba Fri Apr 22 16:56:18 2022 -0700
    Renamed AY.39.4 to AY.134. Added new lineages BA.1.22, BA.1.1.18, BA.2.3.3, BA.2.3.4, BA.2.9.2, BA.2.17-34, BA.2.25.1, XU and AY.39.1.4 - pango-designation v1.7
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    9c35703727c4430d37385dfc2245224c34e4c8ec Fri Apr 22 20:00:52 2022 -0700
    Added new lineage BA.3.1 - pango-designation v1.8
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    0c307351d389eef43c1f8e6157319a64fc7dde6b Mon May 2 09:33:55 2022 -0700
    Don't require C2455T for B.1.640; new back-mutation-penalizing matOptimize puts it on the branches to B.1.640.1 and B.1.640.2.
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    7b5cc8d266fb8f0fe6bd3205aa9ecc0c5216b3ef Mon May 9 17:21:59 2022 -0700
    Changes since release 1.8: BA.2.3.3 withdrawn; BA.2.12.1 broadened; BA.2.13 tweaked for change in order of mutations; new lineages BA.2.23.1, BA.2.35-39. Also added markers for several proposed lineages.
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    8332e557ae10b5c28591af7a3f534ebfb237934b Tue May 10 11:20:38 2022 -0700
    Renamed proposed569 to BA.2.10.2 and proposed542 to BA.2.40.1, with its parent node as BA.2.40.
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    3a55344530eb4be149af6c7995fa0757c887afc7 Thu May 12 20:43:37 2022 -0700
    Renamed proposed463 to XV, proposed586 to BA.2.41 and proposed591 to XW. Added proposed606 and proposed607.
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    ba77c7da2bff16677e7d42484a74aac9c645e9f2 Fri May 13 14:21:05 2022 -0700
    Move definition of BA.2.41 to where I would expect to find it. We are now up to pango-designation v1.9.
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    491248ae0a0495930849ee36c56163cd07168eca Tue May 17 13:28:36 2022 -0700
    Tweak to B.1.637.1 for more back-mutation-averse matOptimize.
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    a67eeb144dcd0ff90df4de1ad726ea7b34b82a6c Fri May 27 09:39:44 2022 -0700
    Added new post-v1.9 lineages AY.98.1.1, BA.2.10.3, BA.2.42-45, BA.4.1; renamed proposed606 to XY. Added proposed636-7. Removed masked reversions from BA.2.13 since those have been cleaned up.
• src/inc/srcVersion.h
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    04c4e71a347cfb4774bd1139996eebc48c936bdd Mon Jun 6 11:20:43 2022 -0700
    New version number v432
• src/lib/linefile.c
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    48d497b991b74998ee79dfb1276235b0930863be Tue May 31 09:43:07 2022 -0700
    Increase hardcoded line size limit in linefile.c; the Newick-formatted SARS-CoV-2 tree with 10 million sequences breaks this limit. If/when we approach 20 million this may need to be redoubled.
• src/utils/qa/weeklybld/buildEnv.csh
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    56b8a20a8fabfefad74ccec3c6152857a4df8ae8 Mon Jun 6 11:18:23 2022 -0700
    v432 final build, refs #29479

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