All File Changes

v362_base to v363_preview (2018-03-05 to 2018-03-12) v363

• src/hg/genePredToFakePsl/genePredToFakePsl.c
  • lines changed 67, context: html, text, full: html, text
    bc3bbb2794e3067f0ff35ac2003fd69362e2ed58 Thu Mar 8 11:34:17 2018 -0800
    Libified genePredToFakePsl's code for extracting PSL and CDS from genePred so I can use it to infer PSL+CDS from genePred tracks like Gencode for HGVS. refs #21076
• src/hg/hgCollection/hgCollection.c
  • lines changed 61, context: html, text, full: html, text
    eb78be0ea632442a7ff6c55321f5bb6cafb2c7d2 Tue Mar 6 09:36:21 2018 -0800
    add tool tips and the ability to put multiwigs into collections from hgTracks
  • lines changed 3, context: html, text, full: html, text
    749553d06451930286cb888d66e8b665c33dcaf5 Wed Mar 7 12:42:26 2018 -0800
    fix a couple problems with not cleaning up trackDb entries
  • lines changed 21, context: html, text, full: html, text
    d0e307bce55e3d3a02252ad9fdac0375e1e0893b Wed Mar 7 22:26:14 2018 -0800
    escape single quotes in strings in the JSON that contains the trackDb contents
  • lines changed 6, context: html, text, full: html, text
    ed8dbd64ca36974846ce471161da56c58a8d224a Thu Mar 8 08:54:54 2018 -0800
    don't use Javascript sets because IE doesn't completely support them.
  • lines changed 4, context: html, text, full: html, text
    c839a278e4118d72f938b7b65253ec3fdea04f50 Thu Mar 8 13:44:55 2018 -0800
    fix problem with hubs that don't specify the group of subtracks
  • lines changed 5, context: html, text, full: html, text
    5b52f94be8580d3538787e63d0828de8376b181e Thu Mar 8 17:11:45 2018 -0800
    add a specific warning for collections that disappear telling users to save them in a session
  • lines changed 4, context: html, text, full: html, text
    44e3dc026187c8f73c1f93316dd9ee5cbd829c8c Fri Mar 9 13:48:01 2018 -0800
    add times to collection names to make them more unique
  • lines changed 48, context: html, text, full: html, text
    0bd11409624970f87f46089c184f38bc9360f136 Sat Mar 10 11:18:22 2018 -0800
    make sure auto-generated short labels are unique within the collection
• src/hg/hgTracks/hgTracks.c
  • lines changed 26, context: html, text, full: html, text
    a6177bc07e5dbb520e06cd0b341036efc2ecd3b3 Tue Mar 6 14:23:29 2018 -0800
    In hgFind, when adding a highlight via URL that the user clicks on, use a new cart variable addHighlight instead of appending to the current highlight string because that can get too long for a URL. refs #21056
  • lines changed 1, context: html, text, full: html, text
    ef39e447f159ff068789ce02e4a658b7bad9caec Wed Mar 7 16:15:27 2018 -0800
    checkAddHighlight also needs to be run after tracksDisplay because it may call findGenomePos which may set addHighlight again. refs #21056
• src/hg/hgTracks/interactTrack.c
  • lines changed 11, context: html, text, full: html, text
    c2c780666cf30f764fe4eb81b7fad350b0a7391a Thu Mar 8 15:56:39 2018 -0800
    Add trackDb setting to indicate if there is a direction to the interaction (interactDirectional). refs #17512
  • lines changed 5, context: html, text, full: html, text
    d6350cf4a7f0802301568b4aba4b3ee5adccb5fa Fri Mar 9 10:34:18 2018 -0800
    Improve dense mode. It now shows end points full height (like long range track). refs #17512
  • lines changed 4, context: html, text, full: html, text
    e5244b1de921b0252f9e62b383b06be78ec140a6 Fri Mar 9 10:53:48 2018 -0800
    Additional detail on dense mode: highlight cross-chrom items by coloring magenta. refs #17512
  • lines changed 5, context: html, text, full: html, text
    6035ae51559998e5f45beeb52d371498622d639d Fri Mar 9 10:58:57 2018 -0800
    Additional detail on dense mode: highlight cross-chrom items by coloring magenta. refs #17512
  • lines changed 17, context: html, text, full: html, text
    4915a88e2c772b27f402db699413ef28a5d4e08d Fri Mar 9 11:36:51 2018 -0800
    Add some info to mouseovers of unnamed interactions. refs #17512
• src/hg/hgc/gencodeClick.c
  • lines changed 26, context: html, text, full: html, text
    5899cbd4120fc82ba0939dce519582841db961f7 Thu Mar 8 11:38:07 2018 -0800
    Add support for GENCODE protein id to wgEncodeGencodeAttrs* table. For backwards compatibility with existing tables, this was added as the last column of the table and the code checks for it's presences. RM 21077
• src/hg/hgc/interactClick.c
  • lines changed 47, context: html, text, full: html, text
    c2c780666cf30f764fe4eb81b7fad350b0a7391a Thu Mar 8 15:56:39 2018 -0800
    Add trackDb setting to indicate if there is a direction to the interaction (interactDirectional). refs #17512
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 5, context: html, text, full: html, text
    4409b6329b5bb716ef0acf83f03e4f85bd65c462 Tue Mar 6 15:31:19 2018 -0800
    Adding a note about -type=bedN+P in searchIndex note in trackDb Library refs #20773
• src/hg/htdocs/images/hgCollectionRtClickAddFromBrowser.jpg
  • lines changed 0, context: html, text, full: html, text
    ac3fa5dd1a1fa400401808e605b184e9cc6a5dec Fri Mar 9 11:09:39 2018 -0800
    Adding hgCollection help doc image for rt-click from browser, refs #11630
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 2, context: html, text, full: html, text
    305b36225604001d547208ec39658fa414c5bfb9 Thu Mar 8 18:11:40 2018 -0800
    add a <tr> around a <td> to make htmlCheck happy
• src/hg/htdocs/inc/hgCollectionHelpInclude.html
  • lines changed 8, context: html, text, full: html, text
    8ead0a9b94ea9f1e8f62f3fde6e85e305fcc22e0 Wed Mar 7 13:48:49 2018 -0800
    Minor fixes to hgCollection help, refs #11630
  • lines changed 97, context: html, text, full: html, text
    a27b22e72c78a2fde4488889705ef5be776cb710 Fri Mar 9 15:41:05 2018 -0800
    hgCollection help doc revisions for code review, video is placeholder for now, refs #21064
• src/hg/htdocs/training/index.html
  • lines changed 25, context: html, text, full: html, text
    e411d3e46e96bd6cd14cbee29338476f7c286621 Fri Mar 9 02:19:43 2018 -0800
    dropping completed Florida State and Texas Med workshops
• src/hg/inc/encode/wgEncodeGencodeAttrs.h
  • lines changed 9, context: html, text, full: html, text
    5899cbd4120fc82ba0939dce519582841db961f7 Thu Mar 8 11:38:07 2018 -0800
    Add support for GENCODE protein id to wgEncodeGencodeAttrs* table. For backwards compatibility with existing tables, this was added as the last column of the table and the code checks for it's presences. RM 21077
• src/hg/inc/genePred.h
  • lines changed 9, context: html, text, full: html, text
    bc3bbb2794e3067f0ff35ac2003fd69362e2ed58 Thu Mar 8 11:34:17 2018 -0800
    Libified genePredToFakePsl's code for extracting PSL and CDS from genePred so I can use it to infer PSL+CDS from genePred tracks like Gencode for HGVS. refs #21076
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    5f9ba1691bd3051146f2f9464c9d1375e42f6ff4 Thu Mar 8 11:36:57 2018 -0800
    Added support for ENS*T* transcript IDs in HGVS position search, using the latest Gencode. Added support for parsing ENS*P* protein IDs, but can't yet map those to the genome because our Gencode tables don't yet include a mapping between transcript and protein IDs. refs #21076
• src/hg/inc/interact.h
  • lines changed 10, context: html, text, full: html, text
    c2c780666cf30f764fe4eb81b7fad350b0a7391a Thu Mar 8 15:56:39 2018 -0800
    Add trackDb setting to indicate if there is a direction to the interaction (interactDirectional). refs #17512
• src/hg/inc/interactUi.h
  • lines changed 6, context: html, text, full: html, text
    c2c780666cf30f764fe4eb81b7fad350b0a7391a Thu Mar 8 15:56:39 2018 -0800
    Add trackDb setting to indicate if there is a direction to the interaction (interactDirectional). refs #17512
• src/hg/js/hgCollection.js
  • lines changed 3, context: html, text, full: html, text
    eb78be0ea632442a7ff6c55321f5bb6cafb2c7d2 Tue Mar 6 09:36:21 2018 -0800
    add tool tips and the ability to put multiwigs into collections from hgTracks
  • lines changed 4, context: html, text, full: html, text
    ed8dbd64ca36974846ce471161da56c58a8d224a Thu Mar 8 08:54:54 2018 -0800
    don't use Javascript sets because IE doesn't completely support them.
  • lines changed 4, context: html, text, full: html, text
    44e3dc026187c8f73c1f93316dd9ee5cbd829c8c Fri Mar 9 13:48:01 2018 -0800
    add times to collection names to make them more unique
  • lines changed 23, context: html, text, full: html, text
    0bd11409624970f87f46089c184f38bc9360f136 Sat Mar 10 11:18:22 2018 -0800
    make sure auto-generated short labels are unique within the collection
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    eb78be0ea632442a7ff6c55321f5bb6cafb2c7d2 Tue Mar 6 09:36:21 2018 -0800
    add tool tips and the ability to put multiwigs into collections from hgTracks
  • lines changed 1, context: html, text, full: html, text
    d382c74441f7982f225a1fc6052aa7ff69e2834b Wed Mar 7 13:34:27 2018 -0800
    only show sorting options for custom collections when they're not being merged
• src/hg/lib/customFactory.c
  • lines changed 5, context: html, text, full: html, text
    c2c780666cf30f764fe4eb81b7fad350b0a7391a Thu Mar 8 15:56:39 2018 -0800
    Add trackDb setting to indicate if there is a direction to the interaction (interactDirectional). refs #17512
• src/hg/lib/encode/wgEncodeGencodeAttrs.as
  • lines changed 1, context: html, text, full: html, text
    5899cbd4120fc82ba0939dce519582841db961f7 Thu Mar 8 11:38:07 2018 -0800
    Add support for GENCODE protein id to wgEncodeGencodeAttrs* table. For backwards compatibility with existing tables, this was added as the last column of the table and the code checks for it's presences. RM 21077
• src/hg/lib/encode/wgEncodeGencodeAttrs.c
  • lines changed 22, context: html, text, full: html, text
    5899cbd4120fc82ba0939dce519582841db961f7 Thu Mar 8 11:38:07 2018 -0800
    Add support for GENCODE protein id to wgEncodeGencodeAttrs* table. For backwards compatibility with existing tables, this was added as the last column of the table and the code checks for it's presences. RM 21077
• src/hg/lib/encode/wgEncodeGencodeAttrs.sql
  • lines changed 1, context: html, text, full: html, text
    5899cbd4120fc82ba0939dce519582841db961f7 Thu Mar 8 11:38:07 2018 -0800
    Add support for GENCODE protein id to wgEncodeGencodeAttrs* table. For backwards compatibility with existing tables, this was added as the last column of the table and the code checks for it's presences. RM 21077
  • lines changed 2, context: html, text, full: html, text
    2b39fab6c6a54dde12024faaef0f32c8af0f7f16 Thu Mar 8 12:18:30 2018 -0800
    added index to wgEncodeGencodeAttrs proteinId column
• src/hg/lib/genePred.c
  • lines changed 74, context: html, text, full: html, text
    bc3bbb2794e3067f0ff35ac2003fd69362e2ed58 Thu Mar 8 11:34:17 2018 -0800
    Libified genePredToFakePsl's code for extracting PSL and CDS from genePred so I can use it to infer PSL+CDS from genePred tracks like Gencode for HGVS. refs #21076
• src/hg/lib/hdb.c
  • lines changed 50, context: html, text, full: html, text
    5f9ba1691bd3051146f2f9464c9d1375e42f6ff4 Thu Mar 8 11:36:57 2018 -0800
    Added support for ENS*T* transcript IDs in HGVS position search, using the latest Gencode. Added support for parsing ENS*P* protein IDs, but can't yet map those to the genome because our Gencode tables don't yet include a mapping between transcript and protein IDs. refs #21076
• src/hg/lib/hgFind.c
  • lines changed 20, context: html, text, full: html, text
    a6177bc07e5dbb520e06cd0b341036efc2ecd3b3 Tue Mar 6 14:23:29 2018 -0800
    In hgFind, when adding a highlight via URL that the user clicks on, use a new cart variable addHighlight instead of appending to the current highlight string because that can get too long for a URL. refs #21056
  • lines changed 13, context: html, text, full: html, text
    5f9ba1691bd3051146f2f9464c9d1375e42f6ff4 Thu Mar 8 11:36:57 2018 -0800
    Added support for ENS*T* transcript IDs in HGVS position search, using the latest Gencode. Added support for parsing ENS*P* protein IDs, but can't yet map those to the genome because our Gencode tables don't yet include a mapping between transcript and protein IDs. refs #21076
• src/hg/lib/hgHgvs.c
  • lines changed 339, context: html, text, full: html, text
    5f9ba1691bd3051146f2f9464c9d1375e42f6ff4 Thu Mar 8 11:36:57 2018 -0800
    Added support for ENS*T* transcript IDs in HGVS position search, using the latest Gencode. Added support for parsing ENS*P* protein IDs, but can't yet map those to the genome because our Gencode tables don't yet include a mapping between transcript and protein IDs. refs #21076
  • lines changed 108, context: html, text, full: html, text
    31744b6e479fbe5e49b3188e651a328cf3374ed0 Thu Mar 8 13:40:51 2018 -0800
    Added support for ENS*P* accessions in HGVS position search. Thanks Mark for the new Attrs proteinId column! refs #21076
• src/hg/lib/hubConnect.c
  • lines changed 13, context: html, text, full: html, text
    5b52f94be8580d3538787e63d0828de8376b181e Thu Mar 8 17:11:45 2018 -0800
    add a specific warning for collections that disappear telling users to save them in a session
• src/hg/lib/interact.as
  • lines changed 9, context: html, text, full: html, text
    c2c780666cf30f764fe4eb81b7fad350b0a7391a Thu Mar 8 15:56:39 2018 -0800
    Add trackDb setting to indicate if there is a direction to the interaction (interactDirectional). refs #17512
• src/hg/lib/interactUi.c
  • lines changed 16, context: html, text, full: html, text
    c2c780666cf30f764fe4eb81b7fad350b0a7391a Thu Mar 8 15:56:39 2018 -0800
    Add trackDb setting to indicate if there is a direction to the interaction (interactDirectional). refs #17512
• src/hg/lib/mathWig.c
  • lines changed 1, context: html, text, full: html, text
    30e53467883676e7fb5c8aad1a4f303c40ffaf73 Tue Mar 6 14:37:57 2018 -0800
    do GBiB gbdb replacement magic on mathWig bigWigs.
• src/hg/lib/trackHub.c
  • lines changed 4, context: html, text, full: html, text
    c2c780666cf30f764fe4eb81b7fad350b0a7391a Thu Mar 8 15:56:39 2018 -0800
    Add trackDb setting to indicate if there is a direction to the interaction (interactDirectional). refs #17512
• src/hg/makeDb/doc/hg19.txt
  • lines changed 36, context: html, text, full: html, text
    e09f1a98e3dca1819c5fd9c834d2c85469c3df2d Fri Mar 9 10:05:25 2018 -0800
    added proteinId to attributes for GENCODE V19, VM16, and V27 for use by VAI
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 14, context: html, text, full: html, text
    e09f1a98e3dca1819c5fd9c834d2c85469c3df2d Fri Mar 9 10:05:25 2018 -0800
    added proteinId to attributes for GENCODE V19, VM16, and V27 for use by VAI
• src/hg/makeDb/doc/mm10.txt
  • lines changed 17, context: html, text, full: html, text
    e09f1a98e3dca1819c5fd9c834d2c85469c3df2d Fri Mar 9 10:05:25 2018 -0800
    added proteinId to attributes for GENCODE V19, VM16, and V27 for use by VAI
• src/hg/makeDb/doc/petMar3/initialBuild.txt
  • lines changed 2, context: html, text, full: html, text
    5ddf5c271e7aa9a88cca4864a7d41f333addbef3 Tue Mar 6 16:08:40 2018 -0800
    removing ggarbage refs #20819
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 31, context: html, text, full: html, text
    023c539ae092ef8db748d2d86744b46eef319feb Fri Mar 9 16:05:10 2018 -0800
    new things to ignore
• src/hg/makeDb/makeGencodeKnownGene/makeGencodeKnownGene.c
  • lines changed 1, context: html, text, full: html, text
    27f4b613573c4688872ccebd6260e5aefce86ac4 Thu Mar 8 13:59:34 2018 -0800
    wgEncodeGencodeAttrsLoad needs its new argument in a couple more places.
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 2, context: html, text, full: html, text
    5899cbd4120fc82ba0939dce519582841db961f7 Thu Mar 8 11:38:07 2018 -0800
    Add support for GENCODE protein id to wgEncodeGencodeAttrs* table. For backwards compatibility with existing tables, this was added as the last column of the table and the code checks for it's presences. RM 21077
  • lines changed 13, context: html, text, full: html, text
    e09f1a98e3dca1819c5fd9c834d2c85469c3df2d Fri Mar 9 10:05:25 2018 -0800
    added proteinId to attributes for GENCODE V19, VM16, and V27 for use by VAI
• src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c
  • lines changed 1, context: html, text, full: html, text
    27f4b613573c4688872ccebd6260e5aefce86ac4 Thu Mar 8 13:59:34 2018 -0800
    wgEncodeGencodeAttrsLoad needs its new argument in a couple more places.
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    e09f1a98e3dca1819c5fd9c834d2c85469c3df2d Fri Mar 9 10:05:25 2018 -0800
    added proteinId to attributes for GENCODE V19, VM16, and V27 for use by VAI
• src/hg/makeDb/trackDb/chainCi2.html
  • lines changed 2, context: html, text, full: html, text
    3d44a288acdae5153a4abffc8e16803c2472fb8c Tue Mar 6 09:14:10 2018 -0800
    Fixing broken links for strPur2, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.ra
  • lines changed 5, context: html, text, full: html, text
    c2c780666cf30f764fe4eb81b7fad350b0a7391a Thu Mar 8 15:56:39 2018 -0800
    Add trackDb setting to indicate if there is a direction to the interaction (interactDirectional). refs #17512
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    32d4fa98cb811c6f70a3b2c776ea0cda6625eb7f Mon Mar 5 16:06:59 2018 -0800
    fixing missing release tag error with bigDataUrl on native track
• src/hg/makeDb/trackDb/lamprey/petMar3/gap.html
  • lines changed 1, context: html, text, full: html, text
    16dd21bccf7d3d6b3cc7148f781f99c2331011f1 Fri Mar 9 15:52:57 2018 -0800
    Fixing redirected links for petMar3, refs #20819
• src/hg/makeDb/trackDb/lamprey/petMar3/gold.html
  • lines changed 1, context: html, text, full: html, text
    16dd21bccf7d3d6b3cc7148f781f99c2331011f1 Fri Mar 9 15:52:57 2018 -0800
    Fixing redirected links for petMar3, refs #20819
• src/hg/makeDb/trackDb/lamprey/petMar3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    ba1c65fa0bbb4b924ad6ad2a2e093aed9e783bb2 Tue Mar 6 16:57:26 2018 -0800
    Turning on the human chain/net to dense by default. refs #20819
• src/hg/makeDb/trackDb/netCi2.html
  • lines changed 2, context: html, text, full: html, text
    3d44a288acdae5153a4abffc8e16803c2472fb8c Tue Mar 6 09:14:10 2018 -0800
    Fixing broken links for strPur2, no Redmine.
• src/hg/makeDb/trackDb/refSeqComposite.ra
  • lines changed 2, context: html, text, full: html, text
    edb5b40b0bd807f0e562abc48b2dbabeb6d81c5d Tue Mar 6 12:36:41 2018 -0800
    add dontCheck rules to avoid errors during checkHgFindSpec refs #20215
  • lines changed 1, context: html, text, full: html, text
    785dc8b03d9b8a5d21281b93324db47a345aa5e9 Thu Mar 8 14:26:42 2018 -0800
    Darken the shade of the refSeq predicted track, refs #21066
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    c2c780666cf30f764fe4eb81b7fad350b0a7391a Thu Mar 8 15:56:39 2018 -0800
    Add trackDb setting to indicate if there is a direction to the interaction (interactDirectional). refs #17512
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons20way.html
  • lines changed 5, context: html, text, full: html, text
    11777fe37058a69c362addd7d6d43b64be4ba7af Thu Mar 8 15:20:33 2018 -0800
    Fixing broken links for tarSyr2, no Redmine.
• src/hg/makeDb/trackDb/worm/blastCe6SG.html
  • lines changed 1, context: html, text, full: html, text
    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/worm/chainCaePb1.html
  • lines changed 1, context: html, text, full: html, text
    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/worm/chainCaeRem2.html
  • lines changed 1, context: html, text, full: html, text
    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/worm/chainCe6.html
  • lines changed 1, context: html, text, full: html, text
    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/worm/chainPriPac1.html
  • lines changed 1, context: html, text, full: html, text
    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/worm/est.html
  • lines changed 1, context: html, text, full: html, text
    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/worm/intronEst.html
  • lines changed 1, context: html, text, full: html, text
    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/worm/mrna.html
  • lines changed 1, context: html, text, full: html, text
    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/worm/netCaePb1.html
  • lines changed 1, context: html, text, full: html, text
    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/worm/netCaeRem2.html
  • lines changed 1, context: html, text, full: html, text
    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/worm/netCe6.html
  • lines changed 1, context: html, text, full: html, text
    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/worm/netPriPac1.html
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    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/worm/xenoMrna.html
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    ab2f5012a616b662b8f99ef43760f9e22a9fd198 Wed Mar 7 08:31:50 2018 -0800
    Fixing broken links for cb3, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/UMassChIP-Seq.html
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    6e6d41a2e13d6ed080d3aa642decd7eef3e189e8 Fri Mar 9 11:01:54 2018 -0800
    Fixing broken links for danRer5, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer5/rmsk.html
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    6e6d41a2e13d6ed080d3aa642decd7eef3e189e8 Fri Mar 9 11:01:54 2018 -0800
    Fixing broken links for danRer5, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer5/vegaPseudoGene.html
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    6e6d41a2e13d6ed080d3aa642decd7eef3e189e8 Fri Mar 9 11:01:54 2018 -0800
    Fixing broken links for danRer5, no Redmine.
• src/hg/makefile
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    ae303e750ec6f1276cbf6815912262abd4e830c2 Tue Mar 6 10:12:16 2018 -0800
    adding geneBounds/clusterGenes to the userApps build per request no redmine
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
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    c37711d09c8d3951e4e36144c7abfd0b6e3bff71 Thu Mar 8 19:15:01 2018 -0800
    added -refseqHacks option to handle special refseq cases. Initially this handles gene with direct CDS where transcript accession in on the CDS record RM21079
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.attrs
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    c37711d09c8d3951e4e36144c7abfd0b6e3bff71 Thu Mar 8 19:15:01 2018 -0800
    added -refseqHacks option to handle special refseq cases. Initially this handles gene with direct CDS where transcript accession in on the CDS record RM21079
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.gp
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    c37711d09c8d3951e4e36144c7abfd0b6e3bff71 Thu Mar 8 19:15:01 2018 -0800
    added -refseqHacks option to handle special refseq cases. Initially this handles gene with direct CDS where transcript accession in on the CDS record RM21079
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.out
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    c37711d09c8d3951e4e36144c7abfd0b6e3bff71 Thu Mar 8 19:15:01 2018 -0800
    added -refseqHacks option to handle special refseq cases. Initially this handles gene with direct CDS where transcript accession in on the CDS record RM21079
• src/hg/utils/gff3ToGenePred/tests/expected/useNameTest.gp
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    c37711d09c8d3951e4e36144c7abfd0b6e3bff71 Thu Mar 8 19:15:01 2018 -0800
    added -refseqHacks option to handle special refseq cases. Initially this handles gene with direct CDS where transcript accession in on the CDS record RM21079
• src/hg/utils/gff3ToGenePred/tests/input/ncbiProblems.gff3
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    c37711d09c8d3951e4e36144c7abfd0b6e3bff71 Thu Mar 8 19:15:01 2018 -0800
    added -refseqHacks option to handle special refseq cases. Initially this handles gene with direct CDS where transcript accession in on the CDS record RM21079
• src/hg/utils/gff3ToGenePred/tests/makefile
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    c37711d09c8d3951e4e36144c7abfd0b6e3bff71 Thu Mar 8 19:15:01 2018 -0800
    added -refseqHacks option to handle special refseq cases. Initially this handles gene with direct CDS where transcript accession in on the CDS record RM21079
• src/utils/qa/weeklybld/buildEnv.csh
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    3a6f504f4698f92e2fdd87d2986e81a5d9750971 Mon Mar 12 10:24:46 2018 -0700
    v363 preview1 refs #20999

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