All File Changes

v445_preview2 to v445_base (2023-03-06 to 2023-03-13) v445

• confs/hgwdev.hg.conf
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    a4d2f9f977dfd295ff433715e79612357f1cedf1 Sun Mar 12 01:11:26 2023 -0800
    Installing updated hg.conf files from UCSC servers
• src/browserbox/root/updateBrowser.sh
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    10df7fe2b072b48d566689b7769bb94f272a9bab Thu Mar 9 11:21:35 2023 -0800
    restore the swapfile when upgrading gbibs from 14, refs #30708
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    7a7fb5b8ca16c8256b2886b784e55bdc69ac78d1 Thu Mar 9 15:13:32 2023 -0800
    Fix sql_mode setting on gbibs that self-upgrade, refs #24254
• src/hg/cgilib/cartTrackDb.c
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    cdb81647deb6096ff29d18a21b4f9e83f45b4ac9 Tue Mar 7 14:38:53 2023 -0800
    Fix bug where hubApi was allowing ranged requests for tracks with 'tableBrowser off' setting in trackDb. Fix cartTrackDbIsAccessDenied function to recognize correctly when 'tableBrowser off' setting is present on the same host as the CGI is running. Add tests to hubApi system to check more 'tableBrowser' settings and check getting data from more than one track at once
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    1222e084d7fcf20712ca66f438878eb71407d980 Wed Mar 8 10:12:17 2023 -0800
    Fix trackDb does not exist error in the Table Browser, refs #30805
• src/hg/hgGene/hgGeneData/links.ra
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    4745c92b18f0c01f24e255944c02140a8b231a22 Thu Mar 9 10:44:40 2023 -0800
    Commenting out CGAP lines since the database is defunct now, refs #30695
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 1, context: html, text, full: html, text
    4dc2ce3ec067b4ccb7987cbda16289d165954971 Thu Mar 9 20:04:39 2023 -0800
    Translate multiple changes to the same codon correctly, collecting all mutations on the path from root to node.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 2, context: html, text, full: html, text
    4dc2ce3ec067b4ccb7987cbda16289d165954971 Thu Mar 9 20:04:39 2023 -0800
    Translate multiple changes to the same codon correctly, collecting all mutations on the path from root to node.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 117, context: html, text, full: html, text
    4dc2ce3ec067b4ccb7987cbda16289d165954971 Thu Mar 9 20:04:39 2023 -0800
    Translate multiple changes to the same codon correctly, collecting all mutations on the path from root to node.
• src/hg/hgTables/schema.c
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    f3525939f7d36dac2de9cf4194f4f0695d1f6148 Thu Mar 9 09:23:05 2023 -0800
    Fix schema page when a non-assembly database table is selected out of a joiner related track, found by Jairo in #30730-note4
• src/hg/hgTracks/hgTracks.c
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    f1739937876c7272e5ceea0b6c8a421598e94e00 Mon Mar 13 06:42:49 2023 -0700
    bringing back the default tracks and default order buttons, refs #30809
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    8b39b9ebf1c40d89f951286b7ed20912254b44cc Mon Mar 13 06:48:36 2023 -0700
    adding keyboard shortcut to button mouse over text, refs #30809
• src/hg/hgTracks/pslTrack.c
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    40a345b04f483a7e67494e62afc8528675eb587e Mon Mar 6 12:06:43 2023 -0800
    make sure alignment blockse are single coverage over the query.
• src/hg/hgTracks/snake.c
  • lines changed 46, context: html, text, full: html, text
    40a345b04f483a7e67494e62afc8528675eb587e Mon Mar 6 12:06:43 2023 -0800
    make sure alignment blockse are single coverage over the query.
• src/hg/hgTracks/snake.h
  • lines changed 1, context: html, text, full: html, text
    40a345b04f483a7e67494e62afc8528675eb587e Mon Mar 6 12:06:43 2023 -0800
    make sure alignment blockse are single coverage over the query.
• src/hg/hgTracks/wigCommon.h
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    0a01f6a29963ba42555b02782532a5702b649f29 Fri Mar 10 10:18:36 2023 -0800
    first cut at drawing base probability logos in wiggle tracks calculated at run time using an associated MAF related
• src/hg/hgTracks/wigTrack.c
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    0a01f6a29963ba42555b02782532a5702b649f29 Fri Mar 10 10:18:36 2023 -0800
    first cut at drawing base probability logos in wiggle tracks calculated at run time using an associated MAF related
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    5cda54b32e44c89a0f49cf6e4e2d72f898d86ad9 Sat Mar 11 10:07:37 2023 -0800
    for multiWig defined logo wiggle, use the track colors instead of hardcoded values
• src/hg/hubApi/apiUtils.c
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    cdb81647deb6096ff29d18a21b4f9e83f45b4ac9 Tue Mar 7 14:38:53 2023 -0800
    Fix bug where hubApi was allowing ranged requests for tracks with 'tableBrowser off' setting in trackDb. Fix cartTrackDbIsAccessDenied function to recognize correctly when 'tableBrowser off' setting is present on the same host as the CGI is running. Add tests to hubApi system to check more 'tableBrowser' settings and check getting data from more than one track at once
• src/hg/hubApi/getData.c
  • lines changed 8, context: html, text, full: html, text
    cdb81647deb6096ff29d18a21b4f9e83f45b4ac9 Tue Mar 7 14:38:53 2023 -0800
    Fix bug where hubApi was allowing ranged requests for tracks with 'tableBrowser off' setting in trackDb. Fix cartTrackDbIsAccessDenied function to recognize correctly when 'tableBrowser off' setting is present on the same host as the CGI is running. Add tests to hubApi system to check more 'tableBrowser' settings and check getting data from more than one track at once
• src/hg/hubApi/tests/expected/err48.gz
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    cdb81647deb6096ff29d18a21b4f9e83f45b4ac9 Tue Mar 7 14:38:53 2023 -0800
    Fix bug where hubApi was allowing ranged requests for tracks with 'tableBrowser off' setting in trackDb. Fix cartTrackDbIsAccessDenied function to recognize correctly when 'tableBrowser off' setting is present on the same host as the CGI is running. Add tests to hubApi system to check more 'tableBrowser' settings and check getting data from more than one track at once
• src/hg/hubApi/tests/expected/err49.gz
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    cdb81647deb6096ff29d18a21b4f9e83f45b4ac9 Tue Mar 7 14:38:53 2023 -0800
    Fix bug where hubApi was allowing ranged requests for tracks with 'tableBrowser off' setting in trackDb. Fix cartTrackDbIsAccessDenied function to recognize correctly when 'tableBrowser off' setting is present on the same host as the CGI is running. Add tests to hubApi system to check more 'tableBrowser' settings and check getting data from more than one track at once
• src/hg/hubApi/tests/expected/multiTrack1.gz
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    cdb81647deb6096ff29d18a21b4f9e83f45b4ac9 Tue Mar 7 14:38:53 2023 -0800
    Fix bug where hubApi was allowing ranged requests for tracks with 'tableBrowser off' setting in trackDb. Fix cartTrackDbIsAccessDenied function to recognize correctly when 'tableBrowser off' setting is present on the same host as the CGI is running. Add tests to hubApi system to check more 'tableBrowser' settings and check getting data from more than one track at once
• src/hg/hubApi/tests/makefile
  • lines changed 22, context: html, text, full: html, text
    cdb81647deb6096ff29d18a21b4f9e83f45b4ac9 Tue Mar 7 14:38:53 2023 -0800
    Fix bug where hubApi was allowing ranged requests for tracks with 'tableBrowser off' setting in trackDb. Fix cartTrackDbIsAccessDenied function to recognize correctly when 'tableBrowser off' setting is present on the same host as the CGI is running. Add tests to hubApi system to check more 'tableBrowser' settings and check getting data from more than one track at once
• src/hg/inc/hgMaf.h
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    0a01f6a29963ba42555b02782532a5702b649f29 Fri Mar 10 10:18:36 2023 -0800
    first cut at drawing base probability logos in wiggle tracks calculated at run time using an associated MAF related
• src/hg/inc/versionInfo.h
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    ab909bd4cde74f88f5557180d33d9b2b6f508d86 Mon Mar 13 10:22:03 2023 -0700
    New version number v445
• src/hg/lib/bedDetail.c
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    dcb42ca54277d403ea36613201459567ddee8d88 Wed Mar 8 19:24:51 2023 -0800
    Fixing a couple of overzealous interpretations of bedParseRgb failing, refs #30569
• src/hg/lib/customFactory.c
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    dcb42ca54277d403ea36613201459567ddee8d88 Wed Mar 8 19:24:51 2023 -0800
    Fixing a couple of overzealous interpretations of bedParseRgb failing, refs #30569
• src/hg/lib/hgMaf.c
  • lines changed 2, context: html, text, full: html, text
    06571741ba5844ec3dfaba611d3ce29970fa6b0b Wed Mar 8 13:11:22 2023 -0800
    adding back a couple of lines that were inadvertantly deleted in da6e1451531ba0147ba54f531361515e55fde9af
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    0a01f6a29963ba42555b02782532a5702b649f29 Fri Mar 10 10:18:36 2023 -0800
    first cut at drawing base probability logos in wiggle tracks calculated at run time using an associated MAF related
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
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    394ef72060f80bfaa2ec5186aa2cb8672c5460fc Sat Mar 11 14:02:09 2023 -0800
    mm10 vs. GCA_001624675.1/GCA_001632575.1 lastz/chain/net runs for user, refs #30492
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    0b18750a9b3f3e0c461d980c4177bb67f7615a46 Sat Mar 11 14:19:30 2023 -0800
    hg19 vs. GCF_014441545.1 lastz/chain/net run for user, refs #30686
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    eb333e1e6a1c865f687c36213ffdb672986f7d49 Sat Mar 11 14:30:33 2023 -0800
    hg19 vs. GCF_017639785.1 lastz/chain/net run for user, refs #30696
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    535dddb318de27c64f5bb1d18a6e9db723606e6f Sat Mar 11 14:45:17 2023 -0800
    mm10 vs. GCF_017639785.1 lastz/chain/net run for user, refs #30696
• src/hg/makeDb/doc/asmHubs/master.run.list
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    6b9e9cccaa743133f2ab4c4cb33c91460888f094 Mon Mar 13 08:58:40 2023 -0700
    adding GCA_002270425.1_ASM227042v1 Starmerella bacillaris per user request refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
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    6b9e9cccaa743133f2ab4c4cb33c91460888f094 Mon Mar 13 08:58:40 2023 -0700
    adding GCA_002270425.1_ASM227042v1 Starmerella bacillaris per user request refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
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    e981dbff9d0656a9a01d582356d85bf14f6cb2aa Mon Mar 6 11:34:24 2023 -0800
    catching up RefSeq assemblies refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
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    954602fdbb9b230ed81e5e2d06ac0b64dc9aaf10 Mon Mar 6 13:14:54 2023 -0800
    updated RefSeq assemblies refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
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    b40982ea80ba60973910dc0c893d5af8da2cdfa0 Mon Mar 6 10:55:04 2023 -0800
    catching up RefSeq assemblies about 53 refs #29545
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    4c906212d302408f36c2125bebce52a92f350ff6 Mon Mar 6 15:34:32 2023 -0800
    remove duplicate assembly definitions refs #29545
• src/hg/makeDb/doc/hg38/problematic.txt
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    ef569dd16ce2136a61c5e0bb5eb450e496ea604e Wed Mar 8 07:20:22 2023 -0800
    adding problematic regions track for hg38, refs #30801
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
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    2f2d6d5555249fcbaf0ae7b53274f6d322a2c7e3 Mon Mar 6 14:57:38 2023 -0800
    RefSeq update moves some assemblies to legacy refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    1d56173dc8704419bb08be3c2c84bcfc26bc6d44 Mon Mar 6 13:55:56 2023 -0800
    catching up RefSeq assemblies refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
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    be45faeff1eb804c8290bf3a1afb25de900b51ef Mon Mar 6 14:35:14 2023 -0800
    catching up RefSeq assemblies refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    e31bab9ce9d88c6d651529dd55d7bab39a8aaac8 Mon Mar 6 16:40:51 2023 -0800
    Ugandan red Colobus v4 moved to legacy refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    f63fe3ded78e7532c09a857fc96e9d6d7e0ba245 Mon Mar 6 14:47:15 2023 -0800
    catching up RefSeq assemblies and fixup names refs #29545
• src/hg/makeDb/trackDb/evaSnp4.html
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    19248340c20f05707fb11f937edff1703c4ae98c Tue Mar 7 16:48:14 2023 -0800
    Adding the evaSnp4 description page, refs #30320
• src/hg/makeDb/trackDb/human/dgv.html
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    b82ec846ffc1bbe552cdc84cc439232f9cd6f04c Tue Mar 7 18:08:31 2023 -0800
    Adding Data Access section to description pages, refs #25566
• src/hg/makeDb/trackDb/human/dgvPlus.html
  • lines changed 19, context: html, text, full: html, text
    b82ec846ffc1bbe552cdc84cc439232f9cd6f04c Tue Mar 7 18:08:31 2023 -0800
    Adding Data Access section to description pages, refs #25566
• src/hg/makeDb/trackDb/human/hg19/dgvPlusGold.html
  • lines changed 20, context: html, text, full: html, text
    b82ec846ffc1bbe552cdc84cc439232f9cd6f04c Tue Mar 7 18:08:31 2023 -0800
    Adding Data Access section to description pages, refs #25566
• src/hg/makeDb/trackDb/human/hg19/problematic.ra
  • lines changed 2, context: html, text, full: html, text
    ef569dd16ce2136a61c5e0bb5eb450e496ea604e Wed Mar 8 07:20:22 2023 -0800
    adding problematic regions track for hg38, refs #30801
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 36, context: html, text, full: html, text
    ef569dd16ce2136a61c5e0bb5eb450e496ea604e Wed Mar 8 07:20:22 2023 -0800
    adding problematic regions track for hg38, refs #30801
• src/hg/makeDb/trackDb/human/hg38/problematic.html
  • lines changed 95, context: html, text, full: html, text
    ef569dd16ce2136a61c5e0bb5eb450e496ea604e Wed Mar 8 07:20:22 2023 -0800
    adding problematic regions track for hg38, refs #30801
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 35, context: html, text, full: html, text
    ef569dd16ce2136a61c5e0bb5eb450e496ea604e Wed Mar 8 07:20:22 2023 -0800
    adding problematic regions track for hg38, refs #30801
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    ef569dd16ce2136a61c5e0bb5eb450e496ea604e Wed Mar 8 07:20:22 2023 -0800
    adding problematic regions track for hg38, refs #30801
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
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    9f0511672e907484b4ef9cfbec085bb7651f0f18 Fri Mar 10 11:45:20 2023 -0800
    don't print out the "Variant Review Status" on the submission page
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    76abf9976eb5424081d97e0100e2f98548a4db25 Fri Mar 10 16:14:38 2023 -0800
    Adding maxWindowCoverage setting to a few tracks in RTS SNVs which take too long to load in big windows, refs #30815
• src/hg/makeDb/trackDb/human/trackDb.ra
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    76abf9976eb5424081d97e0100e2f98548a4db25 Fri Mar 10 16:14:38 2023 -0800
    Adding maxWindowCoverage setting to a few tracks in RTS SNVs which take too long to load in big windows, refs #30815
• src/hg/makeDb/trackDb/mouse/mm10/liftOverMm39.html
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    ff02c6f3e8bcc0a791b5f4ec2ed5100e0b137fbd Mon Mar 6 16:43:20 2023 -0800
    adding liftOver mm10 mm39 tracks refs #30736
• src/hg/makeDb/trackDb/mouse/mm10/liftOverMm39.ra
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    ff02c6f3e8bcc0a791b5f4ec2ed5100e0b137fbd Mon Mar 6 16:43:20 2023 -0800
    adding liftOver mm10 mm39 tracks refs #30736
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    401fac4f62d7d4d2b88647e65144629c7927f3b3 Mon Mar 6 16:48:56 2023 -0800
    adding lift over tracks for mm10 to mm39 and mm39 to mm10 refs #30736
• src/hg/makeDb/trackDb/mouse/mm39/liftOverMm10.html
  • lines changed 43, context: html, text, full: html, text
    ff02c6f3e8bcc0a791b5f4ec2ed5100e0b137fbd Mon Mar 6 16:43:20 2023 -0800
    adding liftOver mm10 mm39 tracks refs #30736
• src/hg/makeDb/trackDb/mouse/mm39/liftOverMm10.ra
  • lines changed 12, context: html, text, full: html, text
    ff02c6f3e8bcc0a791b5f4ec2ed5100e0b137fbd Mon Mar 6 16:43:20 2023 -0800
    adding liftOver mm10 mm39 tracks refs #30736
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    401fac4f62d7d4d2b88647e65144629c7927f3b3 Mon Mar 6 16:48:56 2023 -0800
    adding lift over tracks for mm10 to mm39 and mm39 to mm10 refs #30736
• src/hg/makeDb/trackDb/relatedTracks.ra
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    514fe8fab2dc0ad37220e33bf7cbb786ee3b4b02 Wed Mar 8 15:55:29 2023 -0800
    tweaks to problematic regions track on hg38, refs #30801
• src/hg/makeDb/trackDb/tagTypes.tab
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    9f0511672e907484b4ef9cfbec085bb7651f0f18 Fri Mar 10 11:45:20 2023 -0800
    don't print out the "Variant Review Status" on the submission page
• src/hg/makeDb/trackDb/trackDb.ra
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    fba0bd9bb1eb54ead37e38b5d6ac9cc040c77ffd Tue Mar 7 16:51:30 2023 -0800
    Adding pennantIcon for new track, refs #30320
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    76abf9976eb5424081d97e0100e2f98548a4db25 Fri Mar 10 16:14:38 2023 -0800
    Adding maxWindowCoverage setting to a few tracks in RTS SNVs which take too long to load in big windows, refs #30815
• src/hg/makeDb/trackDb/uniprot.html
  • lines changed 54, context: html, text, full: html, text
    d23e93330f5b7acd3403ea3ea68731820d234a2b Fri Mar 10 02:44:26 2023 -0800
    trying to improve docs page for uniprot, email with markd and jonathan, no redmine
• src/hg/utils/otto/clinGen/clinGenWrapper.sh
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/dbVar/dbVarWrapper.sh
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/decipher/checkDecipher.sh
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    d93d32ad4b79aff0c9ac7d10f62609183287cd66 Wed Mar 8 17:01:16 2023 -0800
    Removing a heartbeat message. It has been running this way on hive for a while and it all seems well. No RM.
• src/hg/utils/otto/decipher/decipherWrapper.sh
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
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    1cb645d2d695768372404159511419112e4000f6 Wed Mar 8 17:11:32 2023 -0800
    Disabling heartbeat messages to reduce spam. These have been running this way for a while with no noticible issues. Refs #28331
• src/hg/utils/otto/genArk/updateHgcentral.sh
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/geneReviews/geneReviewsWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/grcIncident/grcUpdate.sh
  • lines changed 1, context: html, text, full: html, text
    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/grcIncident/runUpdate.sh
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    4fe29cc807f90b379abec789ccd1f2512ac2dbdb Mon Mar 6 21:53:10 2023 -0800
    adding GRCm39 to the update list refs #30735
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/gwas/gwasWrapper.sh
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/isca/iscaWrapper.sh
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/lrg/lrgWrapper.sh
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/mastermind/hg19/chromAlias.tab
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    ac7f504f80766b1d4c5734136d5fcd7e8dd3bc44 Thu Mar 9 03:02:34 2023 -0800
    removing unnecessary files from git repo, email from lou, no redmine
• src/hg/utils/otto/mastermind/hg38/chromAlias.tab
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    ac7f504f80766b1d4c5734136d5fcd7e8dd3bc44 Thu Mar 9 03:02:34 2023 -0800
    removing unnecessary files from git repo, email from lou, no redmine
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    821e5e9d2150d9423bc2710fc79bfaa41576f788 Fri Mar 10 15:15:51 2023 -0800
    Committing change that Max made some time ago adding additional alt/fix chroms to mastermind otto, no RM.
• src/hg/utils/otto/ncbiRefSeq/runUcscDb.sh
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/omim/checkOmimUpload.sh
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    1cb645d2d695768372404159511419112e4000f6 Wed Mar 8 17:11:32 2023 -0800
    Disabling heartbeat messages to reduce spam. These have been running this way for a while with no noticible issues. Refs #28331
• src/hg/utils/otto/omim/omimUploadWrapper.sh
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/omim/omimWrapper.sh
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/orphanet/orphanetWrapper.sh
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
• src/hg/utils/otto/orphanet/parseOrphadata.py
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    4476efe0390552715279bd7c24063248f46c60ba Thu Mar 9 03:03:50 2023 -0800
    fixing error in orphanet otto build, orphanet never replied, but this field seems to be gone, no redmine, email with Lou
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    c02df7dc1559b72b91e2592dbadd63ca34d3d2fb Fri Mar 10 15:09:46 2023 -0800
    Adding a change to the orphanet otto that make made a while ago but wasn't committed. Removes a field that isn't in the file any longer. No RM.
• src/hg/utils/otto/otto.crontab
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    f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800
    Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
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    29c64e32c9e82878484db141eec2365526b32d8a Fri Mar 10 15:36:22 2023 -0800
    Adding the md5sum checker script to otto user and crontab, no RM.
• src/hg/utils/otto/ottoCompareGitVsHiveFiles.py
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    13943290b9a9a2d653074a5a59d5b3cde2bc4ecf Fri Mar 10 15:32:46 2023 -0800
    Adding a script I've had running for a while officially to the tree and under otto. This script checks the md5sums of the files in the otto git tree to the actual scripts being run on hive. Often engineers will tinker with the script directly and forget to commit their changes, because a trial period of the changes is typical. No RM.
• src/hg/utils/otto/panelApp/genes.py
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    dbd5ff960fd0321d74d1c995752cbe919eb14f72 Fri Mar 10 15:07:34 2023 -0800
    Committing a change that Max made some time ago to have the otto job be more resillient when panelApp is being weird. No RM.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    d936f6666770ec1a86f10344a828dceb213ee6f8 Wed Mar 8 10:41:48 2023 -0800
    Add public tree download limited to 6M sequences for ShUShER so it doesn't run out of browser mem.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    a9106d91accc695dc149bca8976342aa84e82179 Wed Mar 8 10:42:20 2023 -0800
    A few new lineages.
• src/inc/common.h
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    4dc2ce3ec067b4ccb7987cbda16289d165954971 Thu Mar 9 20:04:39 2023 -0800
    Translate multiple changes to the same codon correctly, collecting all mutations on the path from root to node.
• src/inc/srcVersion.h
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    ab909bd4cde74f88f5557180d33d9b2b6f508d86 Mon Mar 13 10:22:03 2023 -0700
    New version number v445
• src/lib/common.c
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    4dc2ce3ec067b4ccb7987cbda16289d165954971 Thu Mar 9 20:04:39 2023 -0800
    Translate multiple changes to the same codon correctly, collecting all mutations on the path from root to node.
• src/utils/qa/weeklybld/buildEnv.csh
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    a4b6fb893ced5b995515d37e5d7d49ff533c5371 Mon Mar 13 10:20:23 2023 -0700
    v445 final build, refs #30708

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