All File Changes

v394_preview2 to v394_base (2020-02-10 to 2020-02-17) v394

• src/hg/cirm/cdw/cdwRenameDataset/cdwRenameDataset.c
  • lines changed 14, context: html, text, full: html, text
    ecebacc98890dd849cd57dca6cf136c0b4352c7c Wed Feb 12 22:51:58 2020 -0800
    fixing some metadata that we overlooked in cdwRenameDataset. fixed typo in help for cdwUnlockSubmittedFiles.
• src/hg/cirm/cdw/cdwUnlockSubmittedFiles/cdwUnlockSubmittedFiles.c
  • lines changed 2, context: html, text, full: html, text
    ecebacc98890dd849cd57dca6cf136c0b4352c7c Wed Feb 12 22:51:58 2020 -0800
    fixing some metadata that we overlooked in cdwRenameDataset. fixed typo in help for cdwUnlockSubmittedFiles.
• src/hg/cirm/cdw/lib/cdwPageFooter.h
  • lines changed 1, context: html, text, full: html, text
    20a1b1aeaa8ccde3b9136c58a19a0b89a92c8c13 Thu Feb 13 14:43:59 2020 -0800
    CIRM changing default html page from index.html to cirmIndex.html so that it does not collide with htdocs from genome browser and both software projects can have htdocs made without colliding. This also requires an apache config change which has already taken place and is backwards-compatible.
• src/hg/cirm/cdw/lib/cdwPageHeader.h
  • lines changed 2, context: html, text, full: html, text
    20a1b1aeaa8ccde3b9136c58a19a0b89a92c8c13 Thu Feb 13 14:43:59 2020 -0800
    CIRM changing default html page from index.html to cirmIndex.html so that it does not collide with htdocs from genome browser and both software projects can have htdocs made without colliding. This also requires an apache config change which has already taken place and is backwards-compatible.
• src/hg/cirm/gateway/htdocs/README
  • lines changed 3, context: html, text, full: html, text
    50d467281f8b23157c18f32327de0dc3703338a1 Thu Feb 13 15:31:03 2020 -0800
    The rest of the changes for cirm from index.html to cirmIndex.html
• src/hg/cirm/gateway/htdocs/cescg/cescgPeople.html
  • lines changed 54, context: html, text, full: html, text
    a42a17f6842e06fcf8dea3254e0485d5f53327be Sun Feb 16 20:02:40 2020 -0800
    Add credit images and update publications
• src/hg/cirm/gateway/htdocs/cescg/cescgPubs.html
  • lines changed 268, context: html, text, full: html, text
    a42a17f6842e06fcf8dea3254e0485d5f53327be Sun Feb 16 20:02:40 2020 -0800
    Add credit images and update publications
• src/hg/cirm/gateway/htdocs/cirmIndex.html
  • lines changed 189, context: html, text, full: html, text
    20a1b1aeaa8ccde3b9136c58a19a0b89a92c8c13 Thu Feb 13 14:43:59 2020 -0800
    CIRM changing default html page from index.html to cirmIndex.html so that it does not collide with htdocs from genome browser and both software projects can have htdocs made without colliding. This also requires an apache config change which has already taken place and is backwards-compatible.
• src/hg/cirm/gateway/htdocs/inc/footer.html
  • lines changed 1, context: html, text, full: html, text
    50d467281f8b23157c18f32327de0dc3703338a1 Thu Feb 13 15:31:03 2020 -0800
    The rest of the changes for cirm from index.html to cirmIndex.html
• src/hg/cirm/gateway/htdocs/inc/header.html
  • lines changed 2, context: html, text, full: html, text
    50d467281f8b23157c18f32327de0dc3703338a1 Thu Feb 13 15:31:03 2020 -0800
    The rest of the changes for cirm from index.html to cirmIndex.html
• src/hg/cirm/gateway/htdocs/index.html
  • lines changed 5, context: html, text, full: html, text
    4541a837f817dcd09a71a03b728e34dea744796a Thu Feb 13 11:49:58 2020 -0800
    fixing little typos
  • lines changed 189, context: html, text, full: html, text
    20a1b1aeaa8ccde3b9136c58a19a0b89a92c8c13 Thu Feb 13 14:43:59 2020 -0800
    CIRM changing default html page from index.html to cirmIndex.html so that it does not collide with htdocs from genome browser and both software projects can have htdocs made without colliding. This also requires an apache config change which has already taken place and is backwards-compatible.
  • lines changed 2, context: html, text, full: html, text
    a42a17f6842e06fcf8dea3254e0485d5f53327be Sun Feb 16 20:02:40 2020 -0800
    Add credit images and update publications
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 151, context: html, text, full: html, text
    749bdccc1d80e53df351a2eefe81783ab942adf7 Wed Feb 12 09:57:01 2020 -0800
    Edited icons and links on project.html
  • lines changed 1, context: html, text, full: html, text
    8735d9b69ce55206a574df348e1eb85b5c8951cb Wed Feb 12 10:47:08 2020 -0800
    Add link to quake Tumor Profiling
  • lines changed 1, context: html, text, full: html, text
    ce4fa8a874a207e3363debe9004c4d17aec2f755 Wed Feb 12 11:04:47 2020 -0800
    Fixed link to quakeAdultAgingPancreas
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 20, context: html, text, full: html, text
    a42a17f6842e06fcf8dea3254e0485d5f53327be Sun Feb 16 20:02:40 2020 -0800
    Add credit images and update publications
• src/hg/geneBounds/clusterGenes/clusterGenes.c
  • lines changed 57, context: html, text, full: html, text
    7687cf920f88accdb12ab70c718f3add9bf88131 Wed Feb 12 09:16:51 2020 -0800
    added -minOverlappingBases option to set a threshold for merging transcripts into a gene cluster
• src/hg/geneBounds/clusterGenes/tests/expected/minOverlappingBasesTest.gl
  • lines changed 3, context: html, text, full: html, text
    7687cf920f88accdb12ab70c718f3add9bf88131 Wed Feb 12 09:16:51 2020 -0800
    added -minOverlappingBases option to set a threshold for merging transcripts into a gene cluster
• src/hg/geneBounds/clusterGenes/tests/input/smallOverlap.gp
  • lines changed 2, context: html, text, full: html, text
    7687cf920f88accdb12ab70c718f3add9bf88131 Wed Feb 12 09:16:51 2020 -0800
    added -minOverlappingBases option to set a threshold for merging transcripts into a gene cluster
• src/hg/geneBounds/clusterGenes/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    7687cf920f88accdb12ab70c718f3add9bf88131 Wed Feb 12 09:16:51 2020 -0800
    added -minOverlappingBases option to set a threshold for merging transcripts into a gene cluster
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    393c8a7bb0e4dc56856fcbe514a4aa65914f096b Wed Feb 12 11:25:50 2020 -0800
    Fixing linkout to GTF files on download server refs #24810
• src/hg/hgTracks/chainTrack.c
  • lines changed 2, context: html, text, full: html, text
    53cf1948cc8b9ea8a06f0285e2824e2a2b62353f Mon Feb 10 15:09:37 2020 -0800
    hgTracks: chain trackDb scoreFilter setting was ignored. refs #24695
• src/hg/htdocs/goldenPath/help/bam.html
  • lines changed 1, context: html, text, full: html, text
    c6294826e3c81aee41b14394ca5109be755bc32c Wed Feb 12 11:32:23 2020 -0800
    adding mention of doWiggle option to turn on density graph in track header line
  • lines changed 1, context: html, text, full: html, text
    73e5ffe87841338f4519f9a88558d9d7e7aa6bc8 Wed Feb 12 12:33:24 2020 -0800
    expanded descripiton of doWiggle a little
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 17, context: html, text, full: html, text
    2c8afb0254c9e2781bd844f87569fd165ae6bfc6 Fri Feb 14 01:56:37 2020 -0800
    removing webspace provider note in track hub hosting help, no redmine, but Brian Lee email
  • lines changed 9, context: html, text, full: html, text
    66cfea495661d45e1b078536d0ad4b54ccbf9390 Fri Feb 14 01:59:59 2020 -0800
    small change to hosting FAQ
  • lines changed 11, context: html, text, full: html, text
    41fe77fcd45f63a661782177344c2518dc345c76 Fri Feb 14 11:42:19 2020 -0800
    Small changes to Max's edits to the #hosting section on the Track Hub help page
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    21b89caeeff57687cedae973fb44d388555adad8 Thu Feb 13 15:31:47 2020 -0800
    Removed double word from CR refs #24940
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 36, context: html, text, full: html, text
    809d9dc5361c47b83d020b88ffef60704aef097d Tue Feb 11 13:13:46 2020 -0800
    News release for updated GENCODE for mouse and human refs #24948 #24948 #24501
  • lines changed 2, context: html, text, full: html, text
    9e6cf3574a98eb42d0d402834b8a5484f5765c36 Tue Feb 11 13:50:19 2020 -0800
    Announcing ncbi refSeq update refs #24604
  • lines changed 38, context: html, text, full: html, text
    0f899681f739d9ea4d7b4b7a5d7730a92e3c8c7b Tue Feb 11 13:54:08 2020 -0800
    Announcing ncbi refSeq update, fixing merge refs #24604
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    809d9dc5361c47b83d020b88ffef60704aef097d Tue Feb 11 13:13:46 2020 -0800
    News release for updated GENCODE for mouse and human refs #24948 #24948 #24501
  • lines changed 3, context: html, text, full: html, text
    9e6cf3574a98eb42d0d402834b8a5484f5765c36 Tue Feb 11 13:50:19 2020 -0800
    Announcing ncbi refSeq update refs #24604
  • lines changed 15, context: html, text, full: html, text
    0f899681f739d9ea4d7b4b7a5d7730a92e3c8c7b Tue Feb 11 13:54:08 2020 -0800
    Announcing ncbi refSeq update, fixing merge refs #24604
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    2e0a3ac9ce2ed0281b2e17d71fd35fb2f9875b37 Thu Feb 13 07:02:45 2020 -0800
    making configure word on composite dialog look like a link, refs #24372
• src/hg/htdocs/training/index.html
  • lines changed 28, context: html, text, full: html, text
    70cbab41f5d66337a973322afc75633b7cb425e6 Thu Feb 13 15:14:25 2020 -0800
    dropping completed uscf workshop. moving pidtc asilomar into next-four list. fixing date on acmg. fixing spelling of iasi romania. adding link to veptc barcelona
• src/hg/htdocs/util.html
  • lines changed 3, context: html, text, full: html, text
    bd581d82ac22f11cbe6d2db5aa4507b8897cb0ba Wed Feb 12 09:32:36 2020 -0800
    Code Review changes for util.html refs #24941
  • lines changed 10, context: html, text, full: html, text
    077edaf4f72269a2517551cf8ed559183fe180bf Wed Feb 12 09:35:20 2020 -0800
    Adding periods to end of util.html descriptions to match style on the top of the page refs #24941
  • lines changed 10, context: html, text, full: html, text
    e7d8f628f59803799145e7d5088cc651af47e40d Wed Feb 12 09:38:39 2020 -0800
    On second thought, instead of adding sentence fragments doing a Revert "Adding periods to end of util.html descriptions to match style on the top of the page refs #24941" This reverts commit 077edaf4f72269a2517551cf8ed559183fe180bf.
  • lines changed 1, context: html, text, full: html, text
    630f0009d94838a356f89e46e37871598e5149b4 Wed Feb 12 09:39:59 2020 -0800
    Removing stray period in util.html
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    e5e8c31dd056d42cee8356af6228db4da7f28e3d Mon Feb 17 10:10:08 2020 -0800
    New version number v394
• src/hg/lib/hubConnect.c
  • lines changed 3, context: html, text, full: html, text
    ca932f3523dd1d830482cffebb2036a94163e790 Fri Feb 14 15:47:25 2020 -0800
    when checking cache, don't assume trackDb file exists
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    db5a31cf51189eb8703ccbaef599eae2c3985730 Thu Feb 13 06:18:24 2020 -0800
    adding the word "configure" after the wrench icon, refs #24372
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 22, context: html, text, full: html, text
    3a103914b717293d5a2723c2306db20a889a31c7 Fri Feb 14 14:47:59 2020 -0800
    now with new path names for download access refs #23891
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 23, context: html, text, full: html, text
    3a103914b717293d5a2723c2306db20a889a31c7 Fri Feb 14 14:47:59 2020 -0800
    now with new path names for download access refs #23891
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 18, context: html, text, full: html, text
    3a103914b717293d5a2723c2306db20a889a31c7 Fri Feb 14 14:47:59 2020 -0800
    now with new path names for download access refs #23891
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 18, context: html, text, full: html, text
    3a103914b717293d5a2723c2306db20a889a31c7 Fri Feb 14 14:47:59 2020 -0800
    now with new path names for download access refs #23891
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 36, context: html, text, full: html, text
    3a103914b717293d5a2723c2306db20a889a31c7 Fri Feb 14 14:47:59 2020 -0800
    now with new path names for download access refs #23891
• src/hg/makeDb/doc/hg19.txt
  • lines changed 39, context: html, text, full: html, text
    c11dda620b2fd111b46877fa8b05e7250a61b9f8 Tue Feb 11 12:50:33 2020 -0800
    Instructions for loading up NCBI's ReMap alignments as a chain track. refs #24449
  • lines changed 2, context: html, text, full: html, text
    94d6890bdac9d6c53a6070eef9bcb82611c7d25f Fri Feb 14 11:32:08 2020 -0800
    Adding mouseOver to missense constraint track and finishing up track description, refs #20394
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 208, context: html, text, full: html, text
    c1c71601b337d480f3e17ad3a1c72aac2b255352 Tue Feb 11 10:12:37 2020 -0800
    Rebuilt hg38 chainSelf: dropSelf with pslDropOverlap, fixed undetected errors that caused loss of chains, added -minScore=10000 filtering. refs #24695
  • lines changed 11, context: html, text, full: html, text
    8c68b963e315759727569797b7b32f2bc009a619 Tue Feb 11 11:25:10 2020 -0800
    oops, forgot download files for rebuilt hg38 Self Chain. refs #24695
  • lines changed 44, context: html, text, full: html, text
    c11dda620b2fd111b46877fa8b05e7250a61b9f8 Tue Feb 11 12:50:33 2020 -0800
    Instructions for loading up NCBI's ReMap alignments as a chain track. refs #24449
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 1680, context: html, text, full: html, text
    71c598c89ce19f939c11c661699e9f0f2a6e4465 Thu Feb 13 14:00:15 2020 -0800
    Ensembl v99 release refs #24963
• src/hg/makeDb/gnomad/aaToGenomic.py
  • lines changed 2, context: html, text, full: html, text
    94d6890bdac9d6c53a6070eef9bcb82611c7d25f Fri Feb 14 11:32:08 2020 -0800
    Adding mouseOver to missense constraint track and finishing up track description, refs #20394
• src/hg/makeDb/trackDb/chicken/snp147.shared.html
  • lines changed 1, context: html, text, full: html, text
    b53ca06391134031e25470547b8a2cbfe34c6f85 Tue Feb 11 09:54:55 2020 -0800
    Updating redirected links found for galGal5, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/gnomadPLI.html
  • lines changed 37, context: html, text, full: html, text
    3454b18249705d49114125631b628ccd8e498fe3 Thu Feb 13 18:26:43 2020 -0800
    Fixing up the pLI description page after feedback from Lou and Ana, still need to add a small part about the track methods used to generate teh missense constraint track, refs #20394
  • lines changed 8, context: html, text, full: html, text
    94d6890bdac9d6c53a6070eef9bcb82611c7d25f Fri Feb 14 11:32:08 2020 -0800
    Adding mouseOver to missense constraint track and finishing up track description, refs #20394
• src/hg/makeDb/trackDb/human/hg19/hic.ra
  • lines changed 1, context: html, text, full: html, text
    35aa24c64658013d08a2eb506728fc253d6b00af Mon Feb 10 16:31:51 2020 -0800
    Squashing stale pennantIcons no RM
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    eef8d460ec846cfae2b95b4ac80936916c3a540b Mon Feb 10 14:17:49 2020 -0800
    Adding pennantIcons for recent releases and fixing GENCODE visibilities refs #24156 #24501 #24785 #24502
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    94d6890bdac9d6c53a6070eef9bcb82611c7d25f Fri Feb 14 11:32:08 2020 -0800
    Adding mouseOver to missense constraint track and finishing up track description, refs #20394
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    35aa24c64658013d08a2eb506728fc253d6b00af Mon Feb 10 16:31:51 2020 -0800
    Squashing stale pennantIcons no RM
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 2, context: html, text, full: html, text
    a6eb1d8d1b9253035fc7585111b83b2309d9ff19 Wed Feb 12 10:31:51 2020 -0800
    Fixing some broken GENCODE linkouts, no RM
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.ra
  • lines changed 1, context: html, text, full: html, text
    eef8d460ec846cfae2b95b4ac80936916c3a540b Mon Feb 10 14:17:49 2020 -0800
    Adding pennantIcons for recent releases and fixing GENCODE visibilities refs #24156 #24501 #24785 #24502
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV33lift37.ra
  • lines changed 1, context: html, text, full: html, text
    eef8d460ec846cfae2b95b4ac80936916c3a540b Mon Feb 10 14:17:49 2020 -0800
    Adding pennantIcons for recent releases and fixing GENCODE visibilities refs #24156 #24501 #24785 #24502
• src/hg/makeDb/trackDb/human/hg38/hic.ra
  • lines changed 1, context: html, text, full: html, text
    35aa24c64658013d08a2eb506728fc253d6b00af Mon Feb 10 16:31:51 2020 -0800
    Squashing stale pennantIcons no RM
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    eef8d460ec846cfae2b95b4ac80936916c3a540b Mon Feb 10 14:17:49 2020 -0800
    Adding pennantIcons for recent releases and fixing GENCODE visibilities refs #24156 #24501 #24785 #24502
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    35aa24c64658013d08a2eb506728fc253d6b00af Mon Feb 10 16:31:51 2020 -0800
    Squashing stale pennantIcons no RM
  • lines changed 1, context: html, text, full: html, text
    25d0ad24bdfdecb23813ac4ac751e8d7c8503ba7 Tue Feb 11 09:52:46 2020 -0800
    Add scoreFilter 20000 to hg38 chainSelf per Jim. refs #24695
  • lines changed 20, context: html, text, full: html, text
    8d89592cc2ddc307ab8d75f68cdc4caa1411792c Wed Feb 12 16:24:21 2020 -0800
    Adding filters to dgv tracks on hg38, refs #24749
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 2, context: html, text, full: html, text
    a6eb1d8d1b9253035fc7585111b83b2309d9ff19 Wed Feb 12 10:31:51 2020 -0800
    Fixing some broken GENCODE linkouts, no RM
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV31.ra
  • lines changed 1, context: html, text, full: html, text
    eef8d460ec846cfae2b95b4ac80936916c3a540b Mon Feb 10 14:17:49 2020 -0800
    Adding pennantIcons for recent releases and fixing GENCODE visibilities refs #24156 #24501 #24785 #24502
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV33.ra
  • lines changed 1, context: html, text, full: html, text
    eef8d460ec846cfae2b95b4ac80936916c3a540b Mon Feb 10 14:17:49 2020 -0800
    Adding pennantIcons for recent releases and fixing GENCODE visibilities refs #24156 #24501 #24785 #24502
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    eef8d460ec846cfae2b95b4ac80936916c3a540b Mon Feb 10 14:17:49 2020 -0800
    Adding pennantIcons for recent releases and fixing GENCODE visibilities refs #24156 #24501 #24785 #24502
  • lines changed 1, context: html, text, full: html, text
    35aa24c64658013d08a2eb506728fc253d6b00af Mon Feb 10 16:31:51 2020 -0800
    Squashing stale pennantIcons no RM
• src/hg/makeDb/trackDb/mouse/igtc.html
  • lines changed 1, context: html, text, full: html, text
    0b7445617861c8c1e9c73be88c6a450fd72e4e49 Thu Feb 13 11:46:18 2020 -0800
    Updating http to https for redirected links on mm9, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    eef8d460ec846cfae2b95b4ac80936916c3a540b Mon Feb 10 14:17:49 2020 -0800
    Adding pennantIcons for recent releases and fixing GENCODE visibilities refs #24156 #24501 #24785 #24502
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
  • lines changed 2, context: html, text, full: html, text
    a6eb1d8d1b9253035fc7585111b83b2309d9ff19 Wed Feb 12 10:31:51 2020 -0800
    Fixing some broken GENCODE linkouts, no RM
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM22.ra
  • lines changed 1, context: html, text, full: html, text
    eef8d460ec846cfae2b95b4ac80936916c3a540b Mon Feb 10 14:17:49 2020 -0800
    Adding pennantIcons for recent releases and fixing GENCODE visibilities refs #24156 #24501 #24785 #24502
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM24.ra
  • lines changed 1, context: html, text, full: html, text
    eef8d460ec846cfae2b95b4ac80936916c3a540b Mon Feb 10 14:17:49 2020 -0800
    Adding pennantIcons for recent releases and fixing GENCODE visibilities refs #24156 #24501 #24785 #24502
• src/hg/makeDb/trackDb/mouse/mm9/laminB1Mm9.html
  • lines changed 1, context: html, text, full: html, text
    0b7445617861c8c1e9c73be88c6a450fd72e4e49 Thu Feb 13 11:46:18 2020 -0800
    Updating http to https for redirected links on mm9, uiLinks cronjob.
• src/hg/mouseStuff/chainBridge/chainBridge.c
  • lines changed 140, context: html, text, full: html, text
    0e15377650ad1a2f32303ac3323b6a998b9ff937 Mon Feb 3 14:14:20 2020 -0800
    chainBridge: add -diffTolerance option; run bandExt in both directions in case best alignment is at end not start. refs #21650 When using chainBridge to extend through "gaps" in AGP correspondences, use large -diffTolerance, no need to require that t & q have similar sizes.
• src/hg/mouseStuff/chainBridge/tests/expected/someChange.bridged.chain
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    0e15377650ad1a2f32303ac3323b6a998b9ff937 Mon Feb 3 14:14:20 2020 -0800
    chainBridge: add -diffTolerance option; run bandExt in both directions in case best alignment is at end not start. refs #21650 When using chainBridge to extend through "gaps" in AGP correspondences, use large -diffTolerance, no need to require that t & q have similar sizes.
• src/hg/utils/archiveTracks.sh
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    be6bc76d6d45a41a4bf9c7ca96b404ea38ab306c Mon Feb 10 15:45:43 2020 -0800
    Fixing a bunch of archiveTracks.sh typos pointed out by code review, refs #24936
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    336ccdf9413a7b2e54a99e9384ce1b2d73431b41 Tue Feb 11 08:02:40 2020 -0800
    Noting that archiveTracks works on a list of databases too, refs #24936
• src/hg/utils/automation/EnsGeneAutomate.pm
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    8edeca715fd909f21ec673b9e879788da8f44d6c Thu Feb 13 12:49:57 2020 -0800
    beginning to add version 99 definitions and allow the process to skip download step already done refs #24963
• src/hg/utils/automation/asmHubGatewayPage.pl
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    4257b7f552eb7d6bf044fc2edf27b462dd890c79 Fri Feb 14 14:47:29 2020 -0800
    now with new path names for download access refs #23891
• src/hg/utils/automation/blastz-run-ucsc
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    a76cda6a69557a8c71016489147e4afd31266295 Mon Feb 3 15:19:13 2020 -0800
    blastz-run-ucsc: catch pipe errors; use pslDropOverlap for -dropSelf, for both lav and axt output. refs #24694, #24695 In MLQ #24587 a user reported some trivial self-alignments that should have been filtered - but when lastz produced axt output (for 2bit without suffix), we were not doing anything to filter those out. Now we use pslDropOverlap there. Worse, lavToAxt was failing when lastz output included double-sided gaps, and the failure was not propagated through the piped system() command, so undetected errors caused lots of alignments to be lost. So instead of using lavToAxt because of its -dropSelf option, use lavToPsl | pslDropOverlap.
• src/hg/utils/automation/doEnsGeneUpdate.pl
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    8edeca715fd909f21ec673b9e879788da8f44d6c Thu Feb 13 12:49:57 2020 -0800
    beginning to add version 99 definitions and allow the process to skip download step already done refs #24963
• src/hg/utils/otto/clinvar/clinVarToBed
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    cbbdd7331c4477e84f01020a41e44d8ccec900a0 Thu Feb 13 12:56:22 2020 -0800
    Fixing bad decoding problem in clinvar build script
• src/hg/utils/otto/lovd/checkAndLoad.sh
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    4351a6f72e80bce13726edf01d8a404557c8ae63 Thu Feb 13 10:57:09 2020 -0800
    Make lovd otto build script more descriptive when it fails
• src/inc/srcVersion.h
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    e5e8c31dd056d42cee8356af6228db4da7f28e3d Mon Feb 17 10:10:08 2020 -0800
    New version number v394
• src/lib/gapCalc.c
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    5834a31cf2b9000f0e268647d47f03f6944f9e9d Fri Feb 7 13:44:20 2020 -0800
    Watch out for integer overflow for large gap penalties in gapCalcCost. refs #21650
• src/product/ex.hg.conf
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    7fde049250a05b2804e5674676d84d0bcbbbf7b9 Thu Feb 13 16:31:55 2020 -0800
    added documentation on cart.* variables
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    8b6b553fc9340254d55f57661df382706bcdc10d Thu Feb 13 16:33:20 2020 -0800
    added some new (old) config variables
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    4c58030b95ea4e15ed5361b6f54f7304bf2c4a3b Thu Feb 13 17:23:42 2020 -0800
    add some more undocumented hg.conf variables
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    2cbb554c410d05d093ed0ded0b50ebb66c96091e Fri Feb 14 03:26:03 2020 -0800
    documenting rare hg.conf options, email from braney
• src/utils/qa/weeklybld/buildEnv.csh
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    0940985d85d8810989a8247ab808539cb9acc863 Mon Feb 17 10:08:27 2020 -0800
    v394 final build, refs #24908

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• files changed: 99