All File Changes

v361_preview2 to v361_base (2018-02-05 to 2018-02-12) v361

• src/hg/hgCollection/hgCollection.c
  • lines changed 8, context: html, text, full: html, text
    bdd82165484a4faf7397933a9db170ede3b3ed0c Wed Feb 7 14:56:09 2018 -0800
    fixing bugs in hgCollection
  • lines changed 16, context: html, text, full: html, text
    66ec629db80c84d3524928baf4882560c8cf1b98 Thu Feb 8 11:36:19 2018 -0800
    Fixes to reorged hgCollection help. refs #11630
  • lines changed 4, context: html, text, full: html, text
    7f193dd4f12e64164e193a429605ed2d2249677b Fri Feb 9 12:13:14 2018 -0800
    if hgCollection has been called, always rebuild hub.
  • lines changed 3, context: html, text, full: html, text
    dd87997c2efcdedada6bdd4c1ccc0e157c3cd825 Fri Feb 9 15:32:48 2018 -0800
    fixed problem using hgTracks right click to add custom bedGraphs to a collection
  • lines changed 22, context: html, text, full: html, text
    3a91c4f9165ff5a106b7737f9066c95e798ce62a Fri Feb 9 19:24:12 2018 -0800
    read in staticStyle and label help container correctly
• src/hg/hgGenome/import.c
  • lines changed 1, context: html, text, full: html, text
    d8be7e6e88c0712589dac72c1f023c84028a0d1c Wed Feb 7 11:49:17 2018 -0800
    To prevent joinerRoute from searching over all databases for routes from some genome db to hgFixed metadata tables, add a new optional arg to joinerRelate to apply joinerExclusiveCheck to the genome db in addition to the current table's database. This reduces the time to find the route hg19.refSeqAli --> hgFixed.gbCdnaInfo --> hgFixed.cds from ~1.5s to ~0.1s. It also keeps the related-table selection in hgTables and hgIntegrator from showing >5000 related tables when starting with a genome db table and adding hgFixed.gbCdnaInfo. refs #20949
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 1, context: html, text, full: html, text
    d8be7e6e88c0712589dac72c1f023c84028a0d1c Wed Feb 7 11:49:17 2018 -0800
    To prevent joinerRoute from searching over all databases for routes from some genome db to hgFixed metadata tables, add a new optional arg to joinerRelate to apply joinerExclusiveCheck to the genome db in addition to the current table's database. This reduces the time to find the route hg19.refSeqAli --> hgFixed.gbCdnaInfo --> hgFixed.cds from ~1.5s to ~0.1s. It also keeps the related-table selection in hgTables and hgIntegrator from showing >5000 related tables when starting with a genome db table and adding hgFixed.gbCdnaInfo. refs #20949
• src/hg/hgTables/filterFields.c
  • lines changed 1, context: html, text, full: html, text
    d8be7e6e88c0712589dac72c1f023c84028a0d1c Wed Feb 7 11:49:17 2018 -0800
    To prevent joinerRoute from searching over all databases for routes from some genome db to hgFixed metadata tables, add a new optional arg to joinerRelate to apply joinerExclusiveCheck to the genome db in addition to the current table's database. This reduces the time to find the route hg19.refSeqAli --> hgFixed.gbCdnaInfo --> hgFixed.cds from ~1.5s to ~0.1s. It also keeps the related-table selection in hgTables and hgIntegrator from showing >5000 related tables when starting with a genome db table and adding hgFixed.gbCdnaInfo. refs #20949
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    d8be7e6e88c0712589dac72c1f023c84028a0d1c Wed Feb 7 11:49:17 2018 -0800
    To prevent joinerRoute from searching over all databases for routes from some genome db to hgFixed metadata tables, add a new optional arg to joinerRelate to apply joinerExclusiveCheck to the genome db in addition to the current table's database. This reduces the time to find the route hg19.refSeqAli --> hgFixed.gbCdnaInfo --> hgFixed.cds from ~1.5s to ~0.1s. It also keeps the related-table selection in hgTables and hgIntegrator from showing >5000 related tables when starting with a genome db table and adding hgFixed.gbCdnaInfo. refs #20949
• src/hg/hgTables/schema.c
  • lines changed 1, context: html, text, full: html, text
    d8be7e6e88c0712589dac72c1f023c84028a0d1c Wed Feb 7 11:49:17 2018 -0800
    To prevent joinerRoute from searching over all databases for routes from some genome db to hgFixed metadata tables, add a new optional arg to joinerRelate to apply joinerExclusiveCheck to the genome db in addition to the current table's database. This reduces the time to find the route hg19.refSeqAli --> hgFixed.gbCdnaInfo --> hgFixed.cds from ~1.5s to ~0.1s. It also keeps the related-table selection in hgTables and hgIntegrator from showing >5000 related tables when starting with a genome db table and adding hgFixed.gbCdnaInfo. refs #20949
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 6, context: html, text, full: html, text
    a593c39efc34df5cd82a0b4c1aed05ba5667d478 Thu Feb 8 08:37:22 2018 -0800
    add link to hgCollection in hgTrackUi for custom composites
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    4dfe3060fbc9ce3605ef2bb73ef775cff1813313 Mon Feb 5 13:35:49 2018 -0800
    Adding some needed url-encoding to chromInfoPage links
  • lines changed 1, context: html, text, full: html, text
    bdd82165484a4faf7397933a9db170ede3b3ed0c Wed Feb 7 14:56:09 2018 -0800
    fixing bugs in hgCollection
• src/hg/hgTracks/simpleTracks.c
  • lines changed 90, context: html, text, full: html, text
    80cc890ea7fc9beba757866c51c12d68163054bb Wed Dec 20 10:48:56 2017 -0800
    Remove abandoned experimental 'interactions' track type code from 2011 (with Braney's blessing). Cleanup before implementing new interaction track type (bigInteraction ?). refs #17512
• src/hg/hgTracks/sortWig.c
  • lines changed 1, context: html, text, full: html, text
    f4c5198315eb4f7d056b1243f7e0e035b3eddca6 Thu Feb 8 09:21:49 2018 -0800
    make sort order largest first when sorting by magnitude
  • lines changed 13, context: html, text, full: html, text
    8e951a2066395c920b27aa6c88b810bd2b0e0680 Fri Feb 9 09:50:43 2018 -0800
    fixed problem with sorting less than three tracks in a collection
• src/hg/hgTracks/wigTrack.c
  • lines changed 1, context: html, text, full: html, text
    a8a2a5e4ce457bc3a0be2ff4c0bbf69c75e83528 Thu Feb 8 08:17:53 2018 -0800
    fix bug is with line being drawn in wiggles even when value is NaN
• src/hg/hgc/hgc.c
  • lines changed 41, context: html, text, full: html, text
    2797186e7d69a8b79b92e30118bed55548f04caf Thu Feb 8 14:39:16 2018 -0800
    adding externalId column to ncbiRefSeqLink table refs #20215
  • lines changed 21, context: html, text, full: html, text
    ad3a176457ad1d21a0fedc47f349ec3484e751f1 Fri Feb 9 16:27:51 2018 -0800
    Cleaning up some old ugliness about the size parameter to isAllDna and isAllNt. hgc's printSnpAlignment code that parsed snpNNN.fa was using lineSize as length but lineSize is length+1. Then isAllDna was written with "i<size-1" as the loop test instead of "i < size". I didn't fix that properly when I separated out isAllNt from isAllDna. Later, I (re?)discovered that isAllNt needed length+1 as its size and just added some FIXME comments. Thanks Brian R for prodding me to actually fix it. refs #20895
• src/hg/htdocs/goldenPath/help/hgCollectionHelp.html
  • lines changed 11, context: html, text, full: html, text
    a27be95a97e1207fe1bbdae5ea56cc36bb4f32cc Wed Feb 7 11:09:02 2018 -0800
    Fix help doc for hgCollection. It was using static page framework but it's a CGI include. refs #11630
  • lines changed 91, context: html, text, full: html, text
    d8eaa59da8e3a09dff40d34a244e469e4af52d35 Thu Feb 8 10:42:26 2018 -0800
    Reorg help doc so it can be included by CGI and used as static page. refs #11630
  • lines changed 90, context: html, text, full: html, text
    d4dcf23b49372a8085e4a3a072710a69a40af5ac Thu Feb 8 10:46:27 2018 -0800
    Adding new include file for bare bones help, along with a ROUGH draft in progress for help doc, refs #11630
  • lines changed 2, context: html, text, full: html, text
    66ec629db80c84d3524928baf4882560c8cf1b98 Thu Feb 8 11:36:19 2018 -0800
    Fixes to reorged hgCollection help. refs #11630
  • lines changed 4, context: html, text, full: html, text
    eac9b169f8045be881c639db50043c5ae4077ecf Thu Feb 8 11:37:58 2018 -0800
    Resolve merge conflict. refs #11630
• src/hg/htdocs/goldenPath/help/hgCollectionHelpText.html
  • lines changed 136, context: html, text, full: html, text
    d4dcf23b49372a8085e4a3a072710a69a40af5ac Thu Feb 8 10:46:27 2018 -0800
    Adding new include file for bare bones help, along with a ROUGH draft in progress for help doc, refs #11630
  • lines changed 136, context: html, text, full: html, text
    30724b480205230461795413486e96f87f1e847f Thu Feb 8 12:14:15 2018 -0800
    Move help text to include dir. refs #11630
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 40, context: html, text, full: html, text
    2585ae1e4b0b8914b371f01d5c2348cd394dbae9 Tue Feb 6 14:13:27 2018 -0800
    Updating the Ensembl announcement, refs #20937
  • lines changed 20, context: html, text, full: html, text
    3a53c3bff2cf1df73aec1920ae01674a7854c02e Thu Feb 8 11:20:29 2018 -0800
    adding links to new isPCR video
  • lines changed 1, context: html, text, full: html, text
    80743029c3ffda007790d0e3189045cd18faf62a Thu Feb 8 13:51:42 2018 -0800
    correcting typo and nudging map to show Mexico workshops better
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 32, context: html, text, full: html, text
    23916ada8455250e65ae40715e4e7af954308ac7 Tue Feb 6 13:05:35 2018 -0800
    UI polish for hgCollection. Noting that use of col-* tags requires 12 columns per row (see template.html). Also, all rows should have at least one col-tag (i.e. col-12). Also note this uses hgGtexTransSettings CSS, so test that too. TODO is to move shared settings to gb.css. refs #11630
  • lines changed 5, context: html, text, full: html, text
    bdd82165484a4faf7397933a9db170ede3b3ed0c Wed Feb 7 14:56:09 2018 -0800
    fixing bugs in hgCollection
  • lines changed 1, context: html, text, full: html, text
    66ec629db80c84d3524928baf4882560c8cf1b98 Thu Feb 8 11:36:19 2018 -0800
    Fixes to reorged hgCollection help. refs #11630
  • lines changed 1, context: html, text, full: html, text
    3f682d77e84d372c3b0c156f56a2368d34f9a4de Thu Feb 8 12:16:23 2018 -0800
    Label change, approved by Cath. refs #11630
  • lines changed 14, context: html, text, full: html, text
    3da99d2f5f6b729819be38bf68fcced0ef23b5d7 Thu Feb 8 19:09:48 2018 -0800
    Another round of help doc edits, still in rough draft form, refs #11630
• src/hg/htdocs/inc/hgCollectionHelpInclude.html
  • lines changed 88, context: html, text, full: html, text
    d8eaa59da8e3a09dff40d34a244e469e4af52d35 Thu Feb 8 10:42:26 2018 -0800
    Reorg help doc so it can be included by CGI and used as static page. refs #11630
  • lines changed 86, context: html, text, full: html, text
    f2ad76999f3ae6b0d99bfbcf281853e49743df3d Thu Feb 8 12:13:13 2018 -0800
    Merge in Cath's newest draft of help docl, and markup a little for new styles. refs #11630
  • lines changed 180, context: html, text, full: html, text
    3da99d2f5f6b729819be38bf68fcced0ef23b5d7 Thu Feb 8 19:09:48 2018 -0800
    Another round of help doc edits, still in rough draft form, refs #11630
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    2585ae1e4b0b8914b371f01d5c2348cd394dbae9 Tue Feb 6 14:13:27 2018 -0800
    Updating the Ensembl announcement, refs #20937
  • lines changed 10, context: html, text, full: html, text
    3a53c3bff2cf1df73aec1920ae01674a7854c02e Thu Feb 8 11:20:29 2018 -0800
    adding links to new isPCR video
• src/hg/htdocs/style/gb.css
  • lines changed 1, context: html, text, full: html, text
    23916ada8455250e65ae40715e4e7af954308ac7 Tue Feb 6 13:05:35 2018 -0800
    UI polish for hgCollection. Noting that use of col-* tags requires 12 columns per row (see template.html). Also, all rows should have at least one col-tag (i.e. col-12). Also note this uses hgGtexTransSettings CSS, so test that too. TODO is to move shared settings to gb.css. refs #11630
  • lines changed 45, context: html, text, full: html, text
    99b6e480a0fb44c4fa413c145856673955abd850 Thu Feb 8 12:12:10 2018 -0800
    Adopt/adapt some styles from static pages, for use in CGI generated/included HTML such as track descriptions and help text. refs #11630
• src/hg/htdocs/style/hgGtexTrackSettings.css
  • lines changed 4, context: html, text, full: html, text
    23916ada8455250e65ae40715e4e7af954308ac7 Tue Feb 6 13:05:35 2018 -0800
    UI polish for hgCollection. Noting that use of col-* tags requires 12 columns per row (see template.html). Also, all rows should have at least one col-tag (i.e. col-12). Also note this uses hgGtexTransSettings CSS, so test that too. TODO is to move shared settings to gb.css. refs #11630
• src/hg/htdocs/training/index.html
  • lines changed 23, context: html, text, full: html, text
    3a53c3bff2cf1df73aec1920ae01674a7854c02e Thu Feb 8 11:20:29 2018 -0800
    adding links to new isPCR video
• src/hg/htdocs/training/trainingMap.html
  • lines changed 1, context: html, text, full: html, text
    80743029c3ffda007790d0e3189045cd18faf62a Thu Feb 8 13:51:42 2018 -0800
    correcting typo and nudging map to show Mexico workshops better
• src/hg/inc/annoStreamDbPslPlus.h
  • lines changed 6, context: html, text, full: html, text
    3f06ffc10df40e72dfa18a150eeca23fda6b41df Thu Feb 8 13:42:04 2018 -0800
    annoStreamDbPslPlus internally used a json config to join in CDS and sequence with the underlying PSL -- so annoStreamDbPslPlusNew did not accept an incoming config, so hgVai's RefSeq Status option was ignored. Add jsonObjectMerge so that the config from hgVai can be merged with the internal config, and make sure that the extra columns from the internal annoStreamDb are added to annoStreamDbPslPlusNew's asObj. We can't just use the internal annoStreamDb's asObj because the field names for CDS etc. fields would differ for refSeqAli vs ncbiRefSeq and column-matching to recognize annoStreamDbPslPlus would fail. refs #20948
• src/hg/inc/joiner.h
  • lines changed 3, context: html, text, full: html, text
    d8be7e6e88c0712589dac72c1f023c84028a0d1c Wed Feb 7 11:49:17 2018 -0800
    To prevent joinerRoute from searching over all databases for routes from some genome db to hgFixed metadata tables, add a new optional arg to joinerRelate to apply joinerExclusiveCheck to the genome db in addition to the current table's database. This reduces the time to find the route hg19.refSeqAli --> hgFixed.gbCdnaInfo --> hgFixed.cds from ~1.5s to ~0.1s. It also keeps the related-table selection in hgTables and hgIntegrator from showing >5000 related tables when starting with a genome db table and adding hgFixed.gbCdnaInfo. refs #20949
• src/hg/inc/ncbiRefSeqLink.h
  • lines changed 4, context: html, text, full: html, text
    2797186e7d69a8b79b92e30118bed55548f04caf Thu Feb 8 14:39:16 2018 -0800
    adding externalId column to ncbiRefSeqLink table refs #20215
• src/hg/inc/trackDb.h
  • lines changed 5, context: html, text, full: html, text
    9b0d9b4ac32562cf2ed51ffafaef6abe8bb2beb6 Tue Feb 6 08:10:16 2018 -0800
    add a function to get trackDb metadata as an slPair list. Change other functions to use this api
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    14f34a6c6cdc3691f0932bf2a5a77cd718f11ee4 Mon Feb 12 10:20:07 2018 -0800
    New version number v361
• src/hg/js/hgCollection.js
  • lines changed 9, context: html, text, full: html, text
    4d2d3fb439abe402e45cc69f790c2556423cf22d Tue Feb 6 16:00:53 2018 -0800
    add new tracks to the collection that contains the selected track.
  • lines changed 5, context: html, text, full: html, text
    bdd82165484a4faf7397933a9db170ede3b3ed0c Wed Feb 7 14:56:09 2018 -0800
    fixing bugs in hgCollection
  • lines changed 9, context: html, text, full: html, text
    eb63a9eebad06a2a327314f5ce36158b914e5648 Thu Feb 8 10:21:01 2018 -0800
    change legal characters in labels to include some punctuation
  • lines changed 2, context: html, text, full: html, text
    458aa0ae79276df6e1ebbf75764a1824bb4b0a64 Thu Feb 8 10:29:56 2018 -0800
    change default name and description for new collections
  • lines changed 1, context: html, text, full: html, text
    e6f0b39740cddadf24a8e524feadeef791ede8d0 Thu Feb 8 17:00:15 2018 -0800
    don't let people drop collections into other collections
• src/hg/js/utils.js
  • lines changed 2, context: html, text, full: html, text
    eb63a9eebad06a2a327314f5ce36158b914e5648 Thu Feb 8 10:21:01 2018 -0800
    change legal characters in labels to include some punctuation
• src/hg/lib/annoFormatVep.c
  • lines changed 1, context: html, text, full: html, text
    3f06ffc10df40e72dfa18a150eeca23fda6b41df Thu Feb 8 13:42:04 2018 -0800
    annoStreamDbPslPlus internally used a json config to join in CDS and sequence with the underlying PSL -- so annoStreamDbPslPlusNew did not accept an incoming config, so hgVai's RefSeq Status option was ignored. Add jsonObjectMerge so that the config from hgVai can be merged with the internal config, and make sure that the extra columns from the internal annoStreamDb are added to annoStreamDbPslPlusNew's asObj. We can't just use the internal annoStreamDb's asObj because the field names for CDS etc. fields would differ for refSeqAli vs ncbiRefSeq and column-matching to recognize annoStreamDbPslPlus would fail. refs #20948
  • lines changed 1, context: html, text, full: html, text
    7fa4a82cd43f5a4dae29815281e75d7874772176 Thu Feb 8 14:11:28 2018 -0800
    Thanks ChrisL for noticing that single-base deletion was written as a range when it should be just the pos. refs #20948
• src/hg/lib/annoStreamDbPslPlus.c
  • lines changed 70, context: html, text, full: html, text
    3f06ffc10df40e72dfa18a150eeca23fda6b41df Thu Feb 8 13:42:04 2018 -0800
    annoStreamDbPslPlus internally used a json config to join in CDS and sequence with the underlying PSL -- so annoStreamDbPslPlusNew did not accept an incoming config, so hgVai's RefSeq Status option was ignored. Add jsonObjectMerge so that the config from hgVai can be merged with the internal config, and make sure that the extra columns from the internal annoStreamDb are added to annoStreamDbPslPlusNew's asObj. We can't just use the internal annoStreamDb's asObj because the field names for CDS etc. fields would differ for refSeqAli vs ncbiRefSeq and column-matching to recognize annoStreamDbPslPlus would fail. refs #20948
  • lines changed 1, context: html, text, full: html, text
    a8e96a57b3485f554666c687262fcd295c0e7a6d Mon Feb 12 09:27:22 2018 -0800
    Forgot to check for NULL.
• src/hg/lib/cartTrackDb.c
  • lines changed 1, context: html, text, full: html, text
    d8be7e6e88c0712589dac72c1f023c84028a0d1c Wed Feb 7 11:49:17 2018 -0800
    To prevent joinerRoute from searching over all databases for routes from some genome db to hgFixed metadata tables, add a new optional arg to joinerRelate to apply joinerExclusiveCheck to the genome db in addition to the current table's database. This reduces the time to find the route hg19.refSeqAli --> hgFixed.gbCdnaInfo --> hgFixed.cds from ~1.5s to ~0.1s. It also keeps the related-table selection in hgTables and hgIntegrator from showing >5000 related tables when starting with a genome db table and adding hgFixed.gbCdnaInfo. refs #20949
• src/hg/lib/facetField.c
  • lines changed 11, context: html, text, full: html, text
    087a13bbad05abc419766da9ef4c4879bb90f294 Wed Feb 7 00:46:52 2018 -0800
    adjusting the selected facet count algorithm to handle the ignore-null-values option.
• src/hg/lib/hAnno.c
  • lines changed 1, context: html, text, full: html, text
    3f06ffc10df40e72dfa18a150eeca23fda6b41df Thu Feb 8 13:42:04 2018 -0800
    annoStreamDbPslPlus internally used a json config to join in CDS and sequence with the underlying PSL -- so annoStreamDbPslPlusNew did not accept an incoming config, so hgVai's RefSeq Status option was ignored. Add jsonObjectMerge so that the config from hgVai can be merged with the internal config, and make sure that the extra columns from the internal annoStreamDb are added to annoStreamDbPslPlusNew's asObj. We can't just use the internal annoStreamDb's asObj because the field names for CDS etc. fields would differ for refSeqAli vs ncbiRefSeq and column-matching to recognize annoStreamDbPslPlus would fail. refs #20948
• src/hg/lib/hui.c
  • lines changed 71, context: html, text, full: html, text
    9b0d9b4ac32562cf2ed51ffafaef6abe8bb2beb6 Tue Feb 6 08:10:16 2018 -0800
    add a function to get trackDb metadata as an slPair list. Change other functions to use this api
  • lines changed 1, context: html, text, full: html, text
    456acf5dcbad073045e995fa40c626c8e6abf9f8 Tue Feb 6 11:32:52 2018 -0800
    oops, fixed copy/paste error
  • lines changed 1, context: html, text, full: html, text
    cae73cb2d494295111944e1364459941899ad50c Thu Feb 8 07:17:48 2018 -0800
    fix bug that prevent options from being set on composites with only one track
• src/hg/lib/jksql.c
  • lines changed 27, context: html, text, full: html, text
    87d0536f281cfc327880cc356a00f7e6b443737f Thu Feb 8 17:05:51 2018 -0800
    Oops. I meant to turn this to default abort a long time ago.
• src/hg/lib/joiner.c
  • lines changed 10, context: html, text, full: html, text
    d8be7e6e88c0712589dac72c1f023c84028a0d1c Wed Feb 7 11:49:17 2018 -0800
    To prevent joinerRoute from searching over all databases for routes from some genome db to hgFixed metadata tables, add a new optional arg to joinerRelate to apply joinerExclusiveCheck to the genome db in addition to the current table's database. This reduces the time to find the route hg19.refSeqAli --> hgFixed.gbCdnaInfo --> hgFixed.cds from ~1.5s to ~0.1s. It also keeps the related-table selection in hgTables and hgIntegrator from showing >5000 related tables when starting with a genome db table and adding hgFixed.gbCdnaInfo. refs #20949
• src/hg/lib/ncbiRefSeqLink.as
  • lines changed 2, context: html, text, full: html, text
    2797186e7d69a8b79b92e30118bed55548f04caf Thu Feb 8 14:39:16 2018 -0800
    adding externalId column to ncbiRefSeqLink table refs #20215
• src/hg/lib/ncbiRefSeqLink.c
  • lines changed 11, context: html, text, full: html, text
    2797186e7d69a8b79b92e30118bed55548f04caf Thu Feb 8 14:39:16 2018 -0800
    adding externalId column to ncbiRefSeqLink table refs #20215
• src/hg/lib/ncbiRefSeqLink.sql
  • lines changed 1, context: html, text, full: html, text
    2797186e7d69a8b79b92e30118bed55548f04caf Thu Feb 8 14:39:16 2018 -0800
    adding externalId column to ncbiRefSeqLink table refs #20215
• src/hg/lib/tablesTables.c
  • lines changed 2, context: html, text, full: html, text
    c5253b59a6aa612d6d716621d5e1ca5fa395d0a9 Tue Feb 6 23:47:54 2018 -0800
    oops, from can be a list of tables.
• src/hg/lib/trackDbCustom.c
  • lines changed 109, context: html, text, full: html, text
    9b0d9b4ac32562cf2ed51ffafaef6abe8bb2beb6 Tue Feb 6 08:10:16 2018 -0800
    add a function to get trackDb metadata as an slPair list. Change other functions to use this api
  • lines changed 1, context: html, text, full: html, text
    456acf5dcbad073045e995fa40c626c8e6abf9f8 Tue Feb 6 11:32:52 2018 -0800
    oops, fixed copy/paste error
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    9a75927131a1e282aadced123687234bd9340c6d Thu Feb 8 12:00:38 2018 -0800
    sort metadata by name if it comes from "metadata" statements in a trackDb
• src/hg/lib/variantProjector.c
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    775c4ba0ea17856a61794426a32c2b7206e41df1 Mon Feb 5 10:48:52 2018 -0800
    Fix a few cases of assuming that some details were calculated when they weren't.
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    ad3a176457ad1d21a0fedc47f349ec3484e751f1 Fri Feb 9 16:27:51 2018 -0800
    Cleaning up some old ugliness about the size parameter to isAllDna and isAllNt. hgc's printSnpAlignment code that parsed snpNNN.fa was using lineSize as length but lineSize is length+1. Then isAllDna was written with "i<size-1" as the loop test instead of "i < size". I didn't fix that properly when I separated out isAllNt from isAllDna. Later, I (re?)discovered that isAllNt needed length+1 as its size and just added some FIXME comments. Thanks Brian R for prodding me to actually fix it. refs #20895
• src/hg/makeDb/doc/ucscToRefSeq.txt
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    e6d9c248e95c6de0099053752b60328f0fc0e92d Mon Feb 12 10:12:11 2018 -0800
    generic discussion of how to run up ucscToRefSeq track refs #20913
• src/hg/makeDb/schema/all.joiner
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    839d2f6fce40d1db8711359110dd8d83447ce70f Mon Feb 5 15:17:48 2018 -0800
    The identifier genbankAccession was not based on GenBank but rather on seq+extFile which is a catch-all and should not be related to genbank tables in general. Relating $gbd.seq to all GenBank-related tables was causing unnecessary slowness in joinerFindRoute. Rename the identifier to seqExtFile and use only where applicable.
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    3076f02c9ea73d93de1461992f6f7d6d51c35546 Tue Feb 6 09:00:51 2018 -0800
    Limit the use of splitPrefix to the old databases that actually have split tables. We stopped making those many years ago, and splitPrefix causes a sql wildcard search when a table isn't found. This change and the previous change reduce the number of SQL queries by over 5000 when joining hg19.refSeqAli and several hgFixed genbank tables. hg19 has only one set of split tables, chr*_gl, so it is omitted from oldSplit but has special rules for gl.
• src/hg/makeDb/schema/joinableFields/joinableFields.c
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    d8be7e6e88c0712589dac72c1f023c84028a0d1c Wed Feb 7 11:49:17 2018 -0800
    To prevent joinerRoute from searching over all databases for routes from some genome db to hgFixed metadata tables, add a new optional arg to joinerRelate to apply joinerExclusiveCheck to the genome db in addition to the current table's database. This reduces the time to find the route hg19.refSeqAli --> hgFixed.gbCdnaInfo --> hgFixed.cds from ~1.5s to ~0.1s. It also keeps the related-table selection in hgTables and hgIntegrator from showing >5000 related tables when starting with a genome db table and adding hgFixed.gbCdnaInfo. refs #20949
• src/hg/makeDb/schema/makefile
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    a0d8cb8a727257266fe5563d3e86fd502329a488 Tue Feb 6 09:54:01 2018 -0800
    Adding joinerRoute to makeDb/schema/makefile for top level build.
• src/hg/makeDb/trackDb/armadillo/dasNov3/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/baboon/papAnu2/defaultPriority.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.refGene.ra
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    f5c9f24f6b9af5e01ce858cba09f491ed4dfd2f2 Fri Feb 9 22:48:11 2018 -0800
    correct alpha beta public tags on refGene overrides refs #20215
• src/hg/makeDb/trackDb/balAcu/balAcu1/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.ra
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    ba6a71dbe5422c7ea341c3cca2c375b6cd9fd562 Fri Feb 9 22:57:13 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.refGene.ra
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    ba6a71dbe5422c7ea341c3cca2c375b6cd9fd562 Fri Feb 9 22:57:13 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/bonobo/panPan2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/calMil/calMil1/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/cat/felCat8/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/chicken/galGal5/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/chimp/panTro4/defaultPriority.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.refGene.ra
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    f5c9f24f6b9af5e01ce858cba09f491ed4dfd2f2 Fri Feb 9 22:48:11 2018 -0800
    correct alpha beta public tags on refGene overrides refs #20215
• src/hg/makeDb/trackDb/chimp/panTro5/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/chlorocebus/chlSab2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra
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    d5dc2901dd616116555fe196680097b6a0704eb1 Fri Feb 9 22:55:02 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.refGene.ra
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    d5dc2901dd616116555fe196680097b6a0704eb1 Fri Feb 9 22:55:02 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/dog/canFam3/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra
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    ac0402c703dc8d1fd914c14c4f59e49896e1baaa Wed Feb 7 11:09:33 2018 -0800
    adding ncbiRefSeq for rn6 ce11 sacCer3 danRer11 dm6 refs #20215
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    b5cdd1d92e39c13230a25b9896f1bce98dd2dfe8 Fri Feb 9 21:47:21 2018 -0800
    correct alpha tag on the refSeqComposite.ra refs #20215
• src/hg/makeDb/trackDb/drosophila/droPer1/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/drosophila/rmsk.html
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    ec080000a66da06e0fbf1649c7c29a42f29649bd Tue Feb 6 08:27:38 2018 -0800
    Fixing broken links for droPer1, no Redmine.
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
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    c2f98830fe6c0d0b45e4ee94a1b09bd4f57af0a8 Fri Feb 9 08:25:27 2018 -0800
    Fixing broken links for fr3, no Redmine.
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/galVar/galVar1/trackDb.ra
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    93a41c2f6ec108052f1b0ff0721211e097fa15bd Fri Feb 9 23:05:22 2018 -0800
    adding refSeqComposite alpha refs #20215
• src/hg/makeDb/trackDb/gator/allMis1/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra
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    dd58dd23296c3ae3025880ef3b6a01952bd14b18 Fri Feb 9 22:53:04 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.refGene.ra
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    dd58dd23296c3ae3025880ef3b6a01952bd14b18 Fri Feb 9 22:53:04 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/hedgehog/eriEur2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
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    81ecf226e4b100905ceb0935e388dce7dd498312 Fri Feb 9 21:32:39 2018 -0800
    refGene override moved to trackDb.refGene.ra refs #20215
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    55d77b0228ad39509c81008f511123a862caa25b Fri Feb 9 21:29:12 2018 -0800
    correct alpha,beta tags on the refSeqComposite vs. the refGene overrides refs #20215
• src/hg/makeDb/trackDb/human/hg19/trackDb.refGene.ra
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    55d77b0228ad39509c81008f511123a862caa25b Fri Feb 9 21:29:12 2018 -0800
    correct alpha,beta tags on the refSeqComposite vs. the refGene overrides refs #20215
• src/hg/makeDb/trackDb/human/hgmd.html
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    c9ba25cd6f0a72de5d667a41fb6c2cd65ada041b Mon Feb 5 11:54:28 2018 -0800
    Small edits to hgmd track description before release, refs #15536
• src/hg/makeDb/trackDb/human/trackDb.ra
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    6123bd9069923589ab36dde15b5f21b966b5e945 Mon Feb 5 12:16:55 2018 -0800
    Adding a conservative maxItems setting for hgmd so for popular genes the track doesn't go to dense overly quickly.
• src/hg/makeDb/trackDb/joinedRmsk.html
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    aabe8b19ddf3316cf549075ef1c5aa7e3658c11b Thu Feb 8 09:18:29 2018 -0800
    Fixing broken links for mm10, no Redmine.
• src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/lizard/anoCar2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/macaca/macFas5/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
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    7f2c3954f5f2d47527f5fc91b9f874b5469c647e Fri Feb 9 22:51:09 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.refGene.ra
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    7f2c3954f5f2d47527f5fc91b9f874b5469c647e Fri Feb 9 22:51:09 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/microbat/myoLuc2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/mouse/FaceBase24SampleTypesAvg.html
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    aabe8b19ddf3316cf549075ef1c5aa7e3658c11b Thu Feb 8 09:18:29 2018 -0800
    Fixing broken links for mm10, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm10/chainNet.html
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    aabe8b19ddf3316cf549075ef1c5aa7e3658c11b Thu Feb 8 09:18:29 2018 -0800
    Fixing broken links for mm10, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
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    aabe8b19ddf3316cf549075ef1c5aa7e3658c11b Thu Feb 8 09:18:29 2018 -0800
    Fixing broken links for mm10, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm10/mm10Strains1.html
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    aabe8b19ddf3316cf549075ef1c5aa7e3658c11b Thu Feb 8 09:18:29 2018 -0800
    Fixing broken links for mm10, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm10/ucscRetroAli6.html
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    aabe8b19ddf3316cf549075ef1c5aa7e3658c11b Thu Feb 8 09:18:29 2018 -0800
    Fixing broken links for mm10, no Redmine.
• src/hg/makeDb/trackDb/mouse/snp142.shared.html
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    aabe8b19ddf3316cf549075ef1c5aa7e3658c11b Thu Feb 8 09:18:29 2018 -0800
    Fixing broken links for mm10, no Redmine.
• src/hg/makeDb/trackDb/mouseLemur/micMur2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/panda/ailMel1/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/pig/susScr11/trackDb.ra
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    06f12519cf05aef69d9fdeee7f241060db99ef59 Fri Feb 9 22:58:05 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/pig/susScr11/trackDb.refGene.ra
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    06f12519cf05aef69d9fdeee7f241060db99ef59 Fri Feb 9 22:58:05 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
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    548c229eb797a61ea363c5f5437d87a7bce3d6ba Fri Feb 9 22:59:00 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/pig/susScr3/trackDb.refGene.ra
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    548c229eb797a61ea363c5f5437d87a7bce3d6ba Fri Feb 9 22:59:00 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/rat/rn6/cons20way.html
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    fca649d6b5b8b5f41076ce22047b8172d49eaeab Thu Feb 8 09:25:32 2018 -0800
    Fixing broken links for rn6, no Redmine.
• src/hg/makeDb/trackDb/rat/rn6/defaultPriority.ra
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    3d3c7589f5f4d3eb5849c6dfb32e1d5a8f5c6260 Thu Feb 8 06:45:06 2018 -0800
    adding ncbiRefSeq composite can not have overrides on refGene refs #20215
• src/hg/makeDb/trackDb/rat/rn6/ratChainNet.html
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    fca649d6b5b8b5f41076ce22047b8172d49eaeab Thu Feb 8 09:25:32 2018 -0800
    Fixing broken links for rn6, no Redmine.
• src/hg/makeDb/trackDb/rat/rn6/trackDb.ra
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    ac0402c703dc8d1fd914c14c4f59e49896e1baaa Wed Feb 7 11:09:33 2018 -0800
    adding ncbiRefSeq for rn6 ce11 sacCer3 danRer11 dm6 refs #20215
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    55d77b0228ad39509c81008f511123a862caa25b Fri Feb 9 21:29:12 2018 -0800
    correct alpha,beta tags on the refSeqComposite vs. the refGene overrides refs #20215
• src/hg/makeDb/trackDb/rat/rn6/trackDb.refGene.ra
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    55d77b0228ad39509c81008f511123a862caa25b Fri Feb 9 21:29:12 2018 -0800
    correct alpha,beta tags on the refSeqComposite vs. the refGene overrides refs #20215
• src/hg/makeDb/trackDb/rat/sgpGene.html
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    fca649d6b5b8b5f41076ce22047b8172d49eaeab Thu Feb 8 09:25:32 2018 -0800
    Fixing broken links for rn6, no Redmine.
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    ac0402c703dc8d1fd914c14c4f59e49896e1baaa Wed Feb 7 11:09:33 2018 -0800
    adding ncbiRefSeq for rn6 ce11 sacCer3 danRer11 dm6 refs #20215
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    9aa34beed680836d576d1a15a73d2fd513ab380d Thu Feb 8 14:44:05 2018 -0800
    now using dbPrefixUrls and dbPrefixLabels refs #20215
• src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/rhino/cerSim1/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/rhinopithecus/rhiRox1/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/sacCer/multizYeast.html
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    1d3d996c5297222279ab819c7a7da683efa599d8 Mon Feb 5 11:42:56 2018 -0800
    Updating the ftp links for sacCer1. Forgot to remove an extra /ftp/ in the URL, no Redmine.
• src/hg/makeDb/trackDb/sacCer/sacCer3/trackDb.ra
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    ac0402c703dc8d1fd914c14c4f59e49896e1baaa Wed Feb 7 11:09:33 2018 -0800
    adding ncbiRefSeq for rn6 ce11 sacCer3 danRer11 dm6 refs #20215
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    55d77b0228ad39509c81008f511123a862caa25b Fri Feb 9 21:29:12 2018 -0800
    correct alpha,beta tags on the refSeqComposite vs. the refGene overrides refs #20215
• src/hg/makeDb/trackDb/sheep/oviAri3/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/shrew/sorAra2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/snp137.shared.html
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    aabe8b19ddf3316cf549075ef1c5aa7e3658c11b Thu Feb 8 09:18:29 2018 -0800
    Fixing broken links for mm10, no Redmine.
• src/hg/makeDb/trackDb/snp138.shared.html
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    aabe8b19ddf3316cf549075ef1c5aa7e3658c11b Thu Feb 8 09:18:29 2018 -0800
    Fixing broken links for mm10, no Redmine.
• src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/tagTypes.tab
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    ac0402c703dc8d1fd914c14c4f59e49896e1baaa Wed Feb 7 11:09:33 2018 -0800
    adding ncbiRefSeq for rn6 ce11 sacCer3 danRer11 dm6 refs #20215
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    9aa34beed680836d576d1a15a73d2fd513ab380d Thu Feb 8 14:44:05 2018 -0800
    now using dbPrefixUrls and dbPrefixLabels refs #20215
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/tenrec/echTel2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/turkey/melGal5/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
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    ac0402c703dc8d1fd914c14c4f59e49896e1baaa Wed Feb 7 11:09:33 2018 -0800
    adding ncbiRefSeq for rn6 ce11 sacCer3 danRer11 dm6 refs #20215
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    55d77b0228ad39509c81008f511123a862caa25b Fri Feb 9 21:29:12 2018 -0800
    correct alpha,beta tags on the refSeqComposite vs. the refGene overrides refs #20215
• src/hg/makeDb/trackDb/worm/ce11/trackDb.refGene.ra
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    55d77b0228ad39509c81008f511123a862caa25b Fri Feb 9 21:29:12 2018 -0800
    correct alpha,beta tags on the refSeqComposite vs. the refGene overrides refs #20215
• src/hg/makeDb/trackDb/xenTro/xenLae2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/xenTro/xenTro7/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra
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    f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800
    turning on refSeqComposite for make alpha refs #20215
• src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.ra
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    6093c30a06d4fc075fad97207e07f2d7fffea225 Fri Feb 9 22:56:09 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.refGene.ra
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    6093c30a06d4fc075fad97207e07f2d7fffea225 Fri Feb 9 22:56:09 2018 -0800
    adding refSeqComposite alpha and correct beta tags on refGene refs #20215
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
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    ac0402c703dc8d1fd914c14c4f59e49896e1baaa Wed Feb 7 11:09:33 2018 -0800
    adding ncbiRefSeq for rn6 ce11 sacCer3 danRer11 dm6 refs #20215
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    55d77b0228ad39509c81008f511123a862caa25b Fri Feb 9 21:29:12 2018 -0800
    correct alpha,beta tags on the refSeqComposite vs. the refGene overrides refs #20215
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.refGene.ra
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    55d77b0228ad39509c81008f511123a862caa25b Fri Feb 9 21:29:12 2018 -0800
    correct alpha,beta tags on the refSeqComposite vs. the refGene overrides refs #20215
• src/hg/makefile
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    3db7aaad0c425d624fcbf6d586039f1824699c76 Mon Feb 5 14:45:19 2018 -0800
    deliver pslSomeRecords with the user apps refs #20215
• src/hg/pslSomeRecords/makefile
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    753797baccc232c3ce0a1e91590839dbcc377bb1 Tue Feb 6 09:39:10 2018 -0800
    deliver pslSomeRecords with the user apps refs #20215
• src/hg/utils/automation/dbAssemblyEquivalents.tab
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    5e52d1ec20a14f47c24836123e91966811d76914 Tue Feb 6 12:47:29 2018 -0800
    adding sacCer3 refs #20215
• src/hg/utils/automation/gff3ToRefLink.pl
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    51e28851adb6118bf2046b53e6d128abaf2dbef8 Tue Feb 6 15:36:23 2018 -0800
    adding out links for SGD, RGD, ZFIN refs #20215
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    6e75a4434cb410042b75fa3cc84acb4634d9a2e3 Thu Feb 8 14:36:01 2018 -0800
    adding XenBase BGD FlyBase and using externalId column refs #20215
• src/hg/utils/automation/ncbiRefSeqOtherAttrs.pl
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    51e28851adb6118bf2046b53e6d128abaf2dbef8 Tue Feb 6 15:36:23 2018 -0800
    adding out links for SGD, RGD, ZFIN refs #20215
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    6e75a4434cb410042b75fa3cc84acb4634d9a2e3 Thu Feb 8 14:36:01 2018 -0800
    adding XenBase BGD FlyBase and using externalId column refs #20215
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
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    55be59142c39b860e0cfa1a14dd8136fafd9b0cc Wed Feb 7 15:43:48 2018 -0800
    permit -allowMinimalGenes to handle gene features with only CDS as children
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.attrs
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    55be59142c39b860e0cfa1a14dd8136fafd9b0cc Wed Feb 7 15:43:48 2018 -0800
    permit -allowMinimalGenes to handle gene features with only CDS as children
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.gp
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    55be59142c39b860e0cfa1a14dd8136fafd9b0cc Wed Feb 7 15:43:48 2018 -0800
    permit -allowMinimalGenes to handle gene features with only CDS as children
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.out
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    55be59142c39b860e0cfa1a14dd8136fafd9b0cc Wed Feb 7 15:43:48 2018 -0800
    permit -allowMinimalGenes to handle gene features with only CDS as children
• src/hg/utils/gff3ToGenePred/tests/input/ncbiProblems.gff3
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    55be59142c39b860e0cfa1a14dd8136fafd9b0cc Wed Feb 7 15:43:48 2018 -0800
    permit -allowMinimalGenes to handle gene features with only CDS as children
• src/hg/utils/hubCheck/hubCheck.c
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    9b0d9b4ac32562cf2ed51ffafaef6abe8bb2beb6 Tue Feb 6 08:10:16 2018 -0800
    add a function to get trackDb metadata as an slPair list. Change other functions to use this api
• src/hg/utils/vcfToHgvs/tests/PGTdb/ncbiRefSeqLink.tab.gz
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    0a2b436d5f082becf730cea30457eb86ac1e1e3c Fri Feb 9 11:55:10 2018 -0800
    Added new column to test set ncbiRefSeqLink.tab.gz, corresponding to ncbiRefSeqLink.{as,sql} new column externalId, to avoid warning when loading the test set. refs #20215
• src/hg/utils/vcfToHgvs/vcfToHgvs.c
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    ad3a176457ad1d21a0fedc47f349ec3484e751f1 Fri Feb 9 16:27:51 2018 -0800
    Cleaning up some old ugliness about the size parameter to isAllDna and isAllNt. hgc's printSnpAlignment code that parsed snpNNN.fa was using lineSize as length but lineSize is length+1. Then isAllDna was written with "i<size-1" as the loop test instead of "i < size". I didn't fix that properly when I separated out isAllNt from isAllDna. Later, I (re?)discovered that isAllNt needed length+1 as its size and just added some FIXME comments. Thanks Brian R for prodding me to actually fix it. refs #20895
• src/inc/iupac.h
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    ad3a176457ad1d21a0fedc47f349ec3484e751f1 Fri Feb 9 16:27:51 2018 -0800
    Cleaning up some old ugliness about the size parameter to isAllDna and isAllNt. hgc's printSnpAlignment code that parsed snpNNN.fa was using lineSize as length but lineSize is length+1. Then isAllDna was written with "i<size-1" as the loop test instead of "i < size". I didn't fix that properly when I separated out isAllNt from isAllDna. Later, I (re?)discovered that isAllNt needed length+1 as its size and just added some FIXME comments. Thanks Brian R for prodding me to actually fix it. refs #20895
• src/inc/jsonParse.h
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    3f06ffc10df40e72dfa18a150eeca23fda6b41df Thu Feb 8 13:42:04 2018 -0800
    annoStreamDbPslPlus internally used a json config to join in CDS and sequence with the underlying PSL -- so annoStreamDbPslPlusNew did not accept an incoming config, so hgVai's RefSeq Status option was ignored. Add jsonObjectMerge so that the config from hgVai can be merged with the internal config, and make sure that the extra columns from the internal annoStreamDb are added to annoStreamDbPslPlusNew's asObj. We can't just use the internal annoStreamDb's asObj because the field names for CDS etc. fields would differ for refSeqAli vs ncbiRefSeq and column-matching to recognize annoStreamDbPslPlus would fail. refs #20948
• src/inc/srcVersion.h
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    14f34a6c6cdc3691f0932bf2a5a77cd718f11ee4 Mon Feb 12 10:20:07 2018 -0800
    New version number v361
• src/lib/dnautil.c
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    ad3a176457ad1d21a0fedc47f349ec3484e751f1 Fri Feb 9 16:27:51 2018 -0800
    Cleaning up some old ugliness about the size parameter to isAllDna and isAllNt. hgc's printSnpAlignment code that parsed snpNNN.fa was using lineSize as length but lineSize is length+1. Then isAllDna was written with "i<size-1" as the loop test instead of "i < size". I didn't fix that properly when I separated out isAllNt from isAllDna. Later, I (re?)discovered that isAllNt needed length+1 as its size and just added some FIXME comments. Thanks Brian R for prodding me to actually fix it. refs #20895
• src/lib/iupac.c
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    ad3a176457ad1d21a0fedc47f349ec3484e751f1 Fri Feb 9 16:27:51 2018 -0800
    Cleaning up some old ugliness about the size parameter to isAllDna and isAllNt. hgc's printSnpAlignment code that parsed snpNNN.fa was using lineSize as length but lineSize is length+1. Then isAllDna was written with "i<size-1" as the loop test instead of "i < size". I didn't fix that properly when I separated out isAllNt from isAllDna. Later, I (re?)discovered that isAllNt needed length+1 as its size and just added some FIXME comments. Thanks Brian R for prodding me to actually fix it. refs #20895
• src/lib/jsonParse.c
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    3f06ffc10df40e72dfa18a150eeca23fda6b41df Thu Feb 8 13:42:04 2018 -0800
    annoStreamDbPslPlus internally used a json config to join in CDS and sequence with the underlying PSL -- so annoStreamDbPslPlusNew did not accept an incoming config, so hgVai's RefSeq Status option was ignored. Add jsonObjectMerge so that the config from hgVai can be merged with the internal config, and make sure that the extra columns from the internal annoStreamDb are added to annoStreamDbPslPlusNew's asObj. We can't just use the internal annoStreamDb's asObj because the field names for CDS etc. fields would differ for refSeqAli vs ncbiRefSeq and column-matching to recognize annoStreamDbPslPlus would fail. refs #20948
• src/lib/vcf.c
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    ad3a176457ad1d21a0fedc47f349ec3484e751f1 Fri Feb 9 16:27:51 2018 -0800
    Cleaning up some old ugliness about the size parameter to isAllDna and isAllNt. hgc's printSnpAlignment code that parsed snpNNN.fa was using lineSize as length but lineSize is length+1. Then isAllDna was written with "i<size-1" as the loop test instead of "i < size". I didn't fix that properly when I separated out isAllNt from isAllDna. Later, I (re?)discovered that isAllNt needed length+1 as its size and just added some FIXME comments. Thanks Brian R for prodding me to actually fix it. refs #20895
• src/userApps/fetchKentSource.sh
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    ed9f39297a17ed41bd7043e138b10db491a78ca5 Mon Feb 5 15:45:47 2018 -0800
    deliver pslSomeRecords with the user apps refs #20215
• src/utils/qa/weeklybld/buildEnv.csh
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    c354a2511a0bfe8697e8e83e8b3d7745be920539 Mon Feb 12 10:18:37 2018 -0800
    v361 final build refs #20889

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