All File Changes

v413_preview2 to v413_base (2021-04-05 to 2021-04-12) v413

• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    4c3fbb7999fe549d13dd854c451ee72699fc0978 Sun Apr 11 01:11:41 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/gfClient/gfClient.c
  • lines changed 32, context: html, text, full: html, text
    4e762a020077ea49d08f2c60b4d56a0d59e1bd29 Mon Apr 5 14:37:55 2021 -0700
    better error message in gfClient when dynamic blat server failure refs #26658
• src/hg/hgBlat/hgBlat.c
  • lines changed 19, context: html, text, full: html, text
    24662cf7d67a02bc0a1dab62b3be93cdc97eb800 Mon Apr 5 12:42:49 2021 -0700
    improving errro messages in case of dynamic server overload refs #26658
  • lines changed 2, context: html, text, full: html, text
    4e762a020077ea49d08f2c60b4d56a0d59e1bd29 Mon Apr 5 14:37:55 2021 -0700
    better error message in gfClient when dynamic blat server failure refs #26658
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 46, context: html, text, full: html, text
    8b379e58f89d4a779e768f8c41b042bda714d101 Thu Apr 8 15:26:18 2021 -0700
    Print out nearest neighbor & lineage for each sample in ascii tree (requested by Joe deRisi).
• src/hg/hgTracks/config.c
  • lines changed 3, context: html, text, full: html, text
    e68383a591384d56176313e147d126961d6b13c1 Tue Apr 6 14:45:25 2021 -0700
    turn freeType fonts on by default. Look for them in ../htdocs/urw-fonts by default
• src/hg/hgc/hgc.c
  • lines changed 12, context: html, text, full: html, text
    f42aedac7eaf850e2df8200dfbded43936b9dc76 Thu Apr 8 14:34:25 2021 -0700
    fix chain click-throughs from assembly hubs to native assemblies and vice-versa
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 1, context: html, text, full: html, text
    f53a35ac112b3b7c1410c626c974476ea9cd0541 Thu Apr 8 10:42:38 2021 -0700
    Removing a dupicated word from Code Reveiw, refs #27325
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 1, context: html, text, full: html, text
    64ecc1f91c3af45e46b802450fcd14bd8ab26133 Fri Apr 9 11:41:38 2021 -0700
    Updating old info No RM
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    aef58922506b3be2ea46e1a8d58338a69a0f6423 Mon Apr 5 13:14:08 2021 -0700
    Adding mm39 to the list, refs #27333
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 11, context: html, text, full: html, text
    7df84a167388930011a25e442c4bc7483f4b9745 Thu Apr 8 09:26:30 2021 -0700
    Removing second interact_example in library added by acf6e4da causing error Non unique ID found in library: interact_example in trackDbHub doc refs #27339
  • lines changed 2, context: html, text, full: html, text
    f67e79c7d280aa19d6425ccaefe26404486524f5 Thu Apr 8 09:30:35 2021 -0700
    Adding a note that allButtonPair on setting will prevent matrix from displaying discovered in MLQ refs #27339
• src/hg/htdocs/images/singleCell/muscle-fig1a.png
  • lines changed 0, context: html, text, full: html, text
    026f444a44a6ef1d3f38ee5a178aef70c7e62934 Wed Apr 7 10:45:01 2021 -0700
    Adding images for figures 1a and 1e from paper for muscleDeMicheli track. refs #26968
• src/hg/htdocs/images/singleCell/muscle-fig1e.png
  • lines changed 0, context: html, text, full: html, text
    026f444a44a6ef1d3f38ee5a178aef70c7e62934 Wed Apr 7 10:45:01 2021 -0700
    Adding images for figures 1a and 1e from paper for muscleDeMicheli track. refs #26968
• src/hg/hubApi/tests/expected/schema10.gz
  • lines changed 0, context: html, text, full: html, text
    0cf6d0bf916e95eede2ab70d04efc35de51573a2 Mon Apr 5 11:41:57 2021 -0700
    track has removed its priority line no redmine;
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    f42aedac7eaf850e2df8200dfbded43936b9dc76 Thu Apr 8 14:34:25 2021 -0700
    fix chain click-throughs from assembly hubs to native assemblies and vice-versa
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    02f273a3899445ed872fd366177ae693faec2c7d Mon Apr 12 10:05:05 2021 -0700
    New version number v413
• src/hg/lib/chainNetDbLoad.c
  • lines changed 3, context: html, text, full: html, text
    f42aedac7eaf850e2df8200dfbded43936b9dc76 Thu Apr 8 14:34:25 2021 -0700
    fix chain click-throughs from assembly hubs to native assemblies and vice-versa
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    07d10481f82757c5b853be2c3800959852481918 Thu Apr 8 05:16:10 2021 -0700
    adding tracking code for gbdb redirects to GBIB/GBIC, refs #27121
• src/hg/lib/hui.c
  • lines changed 10, context: html, text, full: html, text
    bd4567974fda4dceb15dba92e45f6512554e50db Tue Apr 6 17:05:32 2021 -0700
    hopefully fixes #27254... though it probably breaks something else.
• src/hg/lib/trackHub.c
  • lines changed 21, context: html, text, full: html, text
    f42aedac7eaf850e2df8200dfbded43936b9dc76 Thu Apr 8 14:34:25 2021 -0700
    fix chain click-throughs from assembly hubs to native assemblies and vice-versa
• src/hg/lib/trackLayout.c
  • lines changed 1, context: html, text, full: html, text
    e68383a591384d56176313e147d126961d6b13c1 Tue Apr 6 14:45:25 2021 -0700
    turn freeType fonts on by default. Look for them in ../htdocs/urw-fonts by default
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 5, context: html, text, full: html, text
    105dbccea1c736dbd8393e3e3d55d85a2f8f922d Tue Apr 6 13:52:53 2021 -0700
    now with host argument on verify to verify with different servers refs #26658
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 3, context: html, text, full: html, text
    31cfa0823734a570e9aabdbfd730dbd01f0b0a85 Tue Apr 6 13:51:13 2021 -0700
    eliminate the trailing ^M on the taxId and testing blat-backup refs #26658
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 15, context: html, text, full: html, text
    105dbccea1c736dbd8393e3e3d55d85a2f8f922d Tue Apr 6 13:52:53 2021 -0700
    now with host argument on verify to verify with different servers refs #26658
• src/hg/makeDb/doc/grcM38P6.txt
  • lines changed 4, context: html, text, full: html, text
    ec42546aa8efd2a5801969e60dd52bb7d9d5948d Sat Apr 10 01:33:17 2021 -0700
    fixing small error
• src/hg/makeDb/doc/hg19.patchUpdate.13.txt
  • lines changed 12, context: html, text, full: html, text
    6bb4a70d43ca7391a27cebc24726be25d639d500 Sat Apr 10 15:23:18 2021 -0700
    hg19 gc5Base makedoc tweak for consistency.
  • lines changed 12, context: html, text, full: html, text
    ea88d6b1ce6aaff5f1e3574f9607de1276b929c9 Sun Apr 11 11:15:22 2021 -0700
    Revert "hg19 gc5Base makedoc tweak for consistency." This reverts commit 6bb4a70d43ca7391a27cebc24726be25d639d500.
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 32, context: html, text, full: html, text
    44e8a323a9251919f1dada93f0d389a555fda1a2 Tue Apr 6 23:14:27 2021 -0700
    Import gencode V38 pre-release
• src/hg/makeDb/doc/hg38/grcH38P13.txt
  • lines changed 383, context: html, text, full: html, text
    44fc09ac64d99b7426d53102d4aa972509f50644 Wed Apr 7 19:47:33 2021 -0700
    Oops, overdue adding this work done over a year ago to git.
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 103, context: html, text, full: html, text
    d5849c76b7b13e3189e1ce67035ba9695a821122 Wed Apr 7 16:02:04 2021 -0700
    lastz chainNet to assembly hub GCF_002742125.1 refs #27321
• src/hg/makeDb/doc/hg38/patchUpdate.11.txt
  • lines changed 16, context: html, text, full: html, text
    76aada406b7f8e257b9c6e975138735c3328eff3 Sat Apr 10 01:52:47 2021 -0700
    improving hg38 bigZips downloads for gc5Base
• src/hg/makeDb/doc/hg38/patchUpdate.13.txt
  • lines changed 771, context: html, text, full: html, text
    4f93d78f61f85b8b7553e1ea8afb033b8db78d03 Thu Apr 8 15:23:24 2021 -0700
    Adding steps for updating hg13 files & tracks to GRCh38.p13 -- some steps done, most not yet.
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 37, context: html, text, full: html, text
    f74b788fef738178f0e2f85588f196c26d8f60e2 Wed Apr 7 10:58:29 2021 -0700
    import of gencode VM27 pre-release
• src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM26.sh
  • lines changed 739, context: html, text, full: html, text
    386557411c4eaea7faa46ebfdc279e660a06eb58 Mon Apr 5 17:34:17 2021 -0700
    starting on knownGene VM26 for mm39
• src/hg/makeDb/doc/wuhCor1/vaccines.txt
  • lines changed 204, context: html, text, full: html, text
    c8d4a396979b1bcf0ec166d9ce5ce9e707f68d8d Fri Apr 9 11:06:24 2021 -0700
    procedure for vaccine track refs #27312
  • lines changed 2, context: html, text, full: html, text
    fee59e80dfd2be9c42c19eaba8a5e84f98f82151 Fri Apr 9 15:45:04 2021 -0700
    add CDS to vaccines track
• src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema
  • lines changed 2, context: html, text, full: html, text
    44e8a323a9251919f1dada93f0d389a555fda1a2 Tue Apr 6 23:14:27 2021 -0700
    Import gencode V38 pre-release
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 5, context: html, text, full: html, text
    44e8a323a9251919f1dada93f0d389a555fda1a2 Tue Apr 6 23:14:27 2021 -0700
    Import gencode V38 pre-release
  • lines changed 4, context: html, text, full: html, text
    f74b788fef738178f0e2f85588f196c26d8f60e2 Wed Apr 7 10:58:29 2021 -0700
    import of gencode VM27 pre-release
• src/hg/makeDb/schema/all.joiner
  • lines changed 95, context: html, text, full: html, text
    44e8a323a9251919f1dada93f0d389a555fda1a2 Tue Apr 6 23:14:27 2021 -0700
    Import gencode V38 pre-release
  • lines changed 95, context: html, text, full: html, text
    f74b788fef738178f0e2f85588f196c26d8f60e2 Wed Apr 7 10:58:29 2021 -0700
    import of gencode VM27 pre-release
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 50, context: html, text, full: html, text
    68d6d9b391f13a9f09724ee7943e60ebf1df108b Wed Apr 7 10:07:26 2021 -0700
    add definitions for sheep/GCF_002742125.1 rn7 and xenTro10 refs #27321
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 19, context: html, text, full: html, text
    68d6d9b391f13a9f09724ee7943e60ebf1df108b Wed Apr 7 10:07:26 2021 -0700
    add definitions for sheep/GCF_002742125.1 rn7 and xenTro10 refs #27321
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    f74b788fef738178f0e2f85588f196c26d8f60e2 Wed Apr 7 10:58:29 2021 -0700
    import of gencode VM27 pre-release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV38.html
  • lines changed 47, context: html, text, full: html, text
    44e8a323a9251919f1dada93f0d389a555fda1a2 Tue Apr 6 23:14:27 2021 -0700
    Import gencode V38 pre-release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV38.ra
  • lines changed 286, context: html, text, full: html, text
    44e8a323a9251919f1dada93f0d389a555fda1a2 Tue Apr 6 23:14:27 2021 -0700
    Import gencode V38 pre-release
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
  • lines changed 51, context: html, text, full: html, text
    386557411c4eaea7faa46ebfdc279e660a06eb58 Mon Apr 5 17:34:17 2021 -0700
    starting on knownGene VM26 for mm39
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    f74b788fef738178f0e2f85588f196c26d8f60e2 Wed Apr 7 10:58:29 2021 -0700
    import of gencode VM27 pre-release
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    386557411c4eaea7faa46ebfdc279e660a06eb58 Mon Apr 5 17:34:17 2021 -0700
    starting on knownGene VM26 for mm39
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM27.html
  • lines changed 30, context: html, text, full: html, text
    f74b788fef738178f0e2f85588f196c26d8f60e2 Wed Apr 7 10:58:29 2021 -0700
    import of gencode VM27 pre-release
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM27.ra
  • lines changed 286, context: html, text, full: html, text
    f74b788fef738178f0e2f85588f196c26d8f60e2 Wed Apr 7 10:58:29 2021 -0700
    import of gencode VM27 pre-release
• src/hg/makeDb/trackDb/rat/rn7/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    d6d80a608dbaff14ea7d9703b1adbae70c6eaa27 Wed Apr 7 09:11:08 2021 -0700
    Changing tracks priority and changing shortLabel name to display mm10
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 66, context: html, text, full: html, text
    d17d8aa5904721432031873676eb9fdef45a1c25 Wed Apr 7 09:44:38 2021 -0700
    adding sheep vs. hg38 refs #27231
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    697433c3bb2bfd1ea3a61f9715ed2bff32210071 Thu Apr 8 10:00:06 2021 -0700
    adding vaccine track refs #27312
• src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html
  • lines changed 78, context: html, text, full: html, text
    9e8bdeb3e12205577bff31b067a4b54aec7059f5 Thu Apr 8 12:27:18 2021 -0700
    initial discussion refs #27312
  • lines changed 34, context: html, text, full: html, text
    b18ba7e510b3924376e1119d8bec7f308fbaf680 Thu Apr 8 15:05:05 2021 -0700
    filling in the description page refs #27312
  • lines changed 1, context: html, text, full: html, text
    c99c3332ebb86e79017f2a9687a637b6c6f9da68 Thu Apr 8 15:06:54 2021 -0700
    filling in the description page refs #27312
  • lines changed 40, context: html, text, full: html, text
    8802f297ea83400417f0554c50c41cf922ba14df Fri Apr 9 10:42:03 2021 -0700
    completed track description page refs #27312
  • lines changed 7, context: html, text, full: html, text
    4588a5528433ea59ad7a9a5c53df3db57dc9426d Fri Apr 9 12:23:35 2021 -0700
    adding references refs #27312
  • lines changed 3, context: html, text, full: html, text
    fee59e80dfd2be9c42c19eaba8a5e84f98f82151 Fri Apr 9 15:45:04 2021 -0700
    add CDS to vaccines track
  • lines changed 13, context: html, text, full: html, text
    964019044e25ffa2e215e658f470d647a487bfa6 Fri Apr 9 16:46:39 2021 -0700
    correct discussion of the two AA differences refs #27312
  • lines changed 1, context: html, text, full: html, text
    c975a54c98d0d9df901018c20622bbf14cc4e029 Fri Apr 9 16:51:24 2021 -0700
    color the PP AAs in the sequence refs #27312
  • lines changed 1, context: html, text, full: html, text
    a9bb1f10c8525ec26075305820047acba867d8fb Fri Apr 9 17:03:26 2021 -0700
    correct variation notation refs #27312
  • lines changed 1, context: html, text, full: html, text
    680a791e910f94be537ad381e06bbb68afd9f4ca Fri Apr 9 20:14:52 2021 -0700
    bold text on the PP AAs refs #27312
• src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.ra
  • lines changed 18, context: html, text, full: html, text
    697433c3bb2bfd1ea3a61f9715ed2bff32210071 Thu Apr 8 10:00:06 2021 -0700
    adding vaccine track refs #27312
  • lines changed 2, context: html, text, full: html, text
    8802f297ea83400417f0554c50c41cf922ba14df Fri Apr 9 10:42:03 2021 -0700
    completed track description page refs #27312
  • lines changed 1, context: html, text, full: html, text
    4b34f0f7f41bc83f4944cd82416656354cb8438a Fri Apr 9 10:53:30 2021 -0700
    correct track name refs #27312
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    61caa523f9d5b4fa0a65f08ef60dcb4d4a9d2e3d Fri Apr 9 10:55:11 2021 -0700
    correct track group refs #27312
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 23, context: html, text, full: html, text
    8b9550f224b17e9118820b82f88655a589d9e383 Tue Apr 6 13:55:04 2021 -0700
    eliminate single gapOverlap track and getting ready for lastz chainNet tracks refs #26658
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 1, context: html, text, full: html, text
    bef062c8d38d8813621688d6cb115d9f9f9e0b3d Tue Apr 6 13:58:19 2021 -0700
    correctly send gtf file to bigZips/genes refs #26428
• src/hg/utils/otto/uniprot/bed12UniProtAnnot.as
  • lines changed 4, context: html, text, full: html, text
    7adb1d36b6e6f5ce11d882f348af4b1194ad17b6 Wed Apr 7 01:05:10 2021 -0700
    comitting a few changes to the uniprot pipeline to make it more stable for ottomatization, but also to get the filters to work correctly, refs #27069
• src/hg/utils/otto/uniprot/bed12UniProtAnnotBgp.as
  • lines changed 33, context: html, text, full: html, text
    7adb1d36b6e6f5ce11d882f348af4b1194ad17b6 Wed Apr 7 01:05:10 2021 -0700
    comitting a few changes to the uniprot pipeline to make it more stable for ottomatization, but also to get the filters to work correctly, refs #27069
• src/hg/utils/otto/uniprot/bed12UniProtFullSeqBgp.as
  • lines changed 48, context: html, text, full: html, text
    7adb1d36b6e6f5ce11d882f348af4b1194ad17b6 Wed Apr 7 01:05:10 2021 -0700
    comitting a few changes to the uniprot pipeline to make it more stable for ottomatization, but also to get the filters to work correctly, refs #27069
• src/hg/utils/otto/uniprot/bed12UniProtMut.as
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    7adb1d36b6e6f5ce11d882f348af4b1194ad17b6 Wed Apr 7 01:05:10 2021 -0700
    comitting a few changes to the uniprot pipeline to make it more stable for ottomatization, but also to get the filters to work correctly, refs #27069
• src/hg/utils/otto/uniprot/bigPslUniprot.as
  • lines changed 57, context: html, text, full: html, text
    7adb1d36b6e6f5ce11d882f348af4b1194ad17b6 Wed Apr 7 01:05:10 2021 -0700
    comitting a few changes to the uniprot pipeline to make it more stable for ottomatization, but also to get the filters to work correctly, refs #27069
• src/hg/utils/otto/uniprot/doUpdate.sh
  • lines changed 11, context: html, text, full: html, text
    7adb1d36b6e6f5ce11d882f348af4b1194ad17b6 Wed Apr 7 01:05:10 2021 -0700
    comitting a few changes to the uniprot pipeline to make it more stable for ottomatization, but also to get the filters to work correctly, refs #27069
• src/hg/utils/otto/uniprot/makefile
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    7adb1d36b6e6f5ce11d882f348af4b1194ad17b6 Wed Apr 7 01:05:10 2021 -0700
    comitting a few changes to the uniprot pipeline to make it more stable for ottomatization, but also to get the filters to work correctly, refs #27069
• src/hg/utils/vcfRenameAndPrune/vcfRenameAndPrune.c
  • lines changed 7, context: html, text, full: html, text
    21e42695bd70f58fcd48b6080764a5c2ddad907a Wed Apr 7 19:50:25 2021 -0700
    When a row has a million columns, throwing words[] on the stack just won't do. Alloc the array once and use for all rows.
• src/inc/errCatch.h
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    4e762a020077ea49d08f2c60b4d56a0d59e1bd29 Mon Apr 5 14:37:55 2021 -0700
    better error message in gfClient when dynamic blat server failure refs #26658
• src/inc/srcVersion.h
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    02f273a3899445ed872fd366177ae693faec2c7d Mon Apr 12 10:05:05 2021 -0700
    New version number v413
• src/utils/qa/weeklybld/buildEnv.csh
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    b04a77c94519a1917f2261352ee715cf95badcad Mon Apr 12 10:04:07 2021 -0700
    v413 final build, refs #27311
• src/utils/vcfFilter/vcfFilter.c
  • lines changed 9, context: html, text, full: html, text
    21e42695bd70f58fcd48b6080764a5c2ddad907a Wed Apr 7 19:50:25 2021 -0700
    When a row has a million columns, throwing words[] on the stack just won't do. Alloc the array once and use for all rows.

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• files changed: 83