All File Changes

v313_preview2 to v313_base (2015-03-02 to 2015-03-09) v313

• src/hg/hgAi/hgAi.c
  • lines changed 1, context: html, text, full: html, text
    Updating lodash library to latest version.
    
  • lines changed 15, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
  • lines changed 39, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
• src/hg/hgBeacon/README.txt
  • lines changed 19, context: html, text, full: html, text
    during its last code review, hgBeacon was criticized,
    partially, because it's calling bigBedInfo and bigBedToBed and so requires
    copies of these in the cgi-bin dir. This change makes hgBeacon easier to
    install as it does not need the external tools anymore.
    It also adds a tester that can be pointed at the hgBeacon to see if it
    works, at least the basic functions.
    It also makes it easier to import VCF files, as it can import these
    directly.
    
  • lines changed 13, context: html, text, full: html, text
    fixing the help message and the tester in hgBeacon.
    
• src/hg/hgBeacon/help.txt
  • lines changed 45, context: html, text, full: html, text
    during its last code review, hgBeacon was criticized,
    partially, because it's calling bigBedInfo and bigBedToBed and so requires
    copies of these in the cgi-bin dir. This change makes hgBeacon easier to
    install as it does not need the external tools anymore.
    It also adds a tester that can be pointed at the hgBeacon to see if it
    works, at least the basic functions.
    It also makes it easier to import VCF files, as it can import these
    directly.
    
  • lines changed 14, context: html, text, full: html, text
    fixing the help message and the tester in hgBeacon.
    
  • lines changed 1, context: html, text, full: html, text
    typo in help message
    
• src/hg/hgBeacon/hgBeacon
  • lines changed 511, context: html, text, full: html, text
    during its last code review, hgBeacon was criticized,
    partially, because it's calling bigBedInfo and bigBedToBed and so requires
    copies of these in the cgi-bin dir. This change makes hgBeacon easier to
    install as it does not need the external tools anymore.
    It also adds a tester that can be pointed at the hgBeacon to see if it
    works, at least the basic functions.
    It also makes it easier to import VCF files, as it can import these
    directly.
    
  • lines changed 28, context: html, text, full: html, text
    fixing the help message and the tester in hgBeacon.
    
• src/hg/hgBeacon/makefile
  • lines changed 7, context: html, text, full: html, text
    fixing the help message and the tester in hgBeacon.
    
• src/hg/hgBeacon/testBeacon
  • lines changed 68, context: html, text, full: html, text
    during its last code review, hgBeacon was criticized,
    partially, because it's calling bigBedInfo and bigBedToBed and so requires
    copies of these in the cgi-bin dir. This change makes hgBeacon easier to
    install as it does not need the external tools anymore.
    It also adds a tester that can be pointed at the hgBeacon to see if it
    works, at least the basic functions.
    It also makes it easier to import VCF files, as it can import these
    directly.
    
  • lines changed 7, context: html, text, full: html, text
    fixing the help message and the tester in hgBeacon.
    
• src/hg/hgChooseDb/hgChooseDb.c
  • lines changed 1, context: html, text, full: html, text
    Updating lodash library to latest version.
    
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed short label for Jackson Lab per request, refs #14871
    
• src/hg/hgGene/hgGeneData/Mouse/links.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed short label for Jackson Lab per request, refs #14871
    
• src/hg/hgGene/hgGeneData/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed short label for Jackson Lab per request, refs #14871
    
• src/hg/hgMirror/makefile
  • lines changed 3, context: html, text, full: html, text
    removing pylint from hgMirror makefile as it adds an additional
    dependency for mirrors.
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 45, context: html, text, full: html, text
    add a menu in hgTracksUi to let folks choose a coalescent ancestor when
    resolving duplications (per Joel)
    
• src/hg/hgTrackUi/makefile
  • lines changed 1, context: html, text, full: html, text
    add a menu in hgTracksUi to let folks choose a coalescent ancestor when
    resolving duplications (per Joel)
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 18, context: html, text, full: html, text
    Added a link to chrom.sizes file (on hgdownload) at the end of the sequence size table on the chromInfo page.
    refs #14870
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 4, context: html, text, full: html, text
    add a menu in hgTracksUi to let folks choose a coalescent ancestor when
    resolving duplications (per Joel)
    
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 1, context: html, text, full: html, text
    Adding news announcement about UDR and to FAQ about downloads, refs #14918
    
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 12, context: html, text, full: html, text
    Adding news announcement about UDR and to FAQ about downloads, refs #14918
    
  • lines changed 1, context: html, text, full: html, text
    Adding feedback from Erich about UDR, updating date to today for news release refs #14918
    
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 1, context: html, text, full: html, text
    Adding small changes to Quick Start html per code review, refs #14931
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    Releasing new video and posting announcements. refs #14239
    
  • lines changed 3, context: html, text, full: html, text
    Adding a link to the blog. refs #14239
    
  • lines changed 1, context: html, text, full: html, text
    Fixing a typo. refs #14239
    
  • lines changed 78, context: html, text, full: html, text
    Adding news announcement about UDR and to FAQ about downloads, refs #14918
    
  • lines changed 9, context: html, text, full: html, text
    Adding feedback from Erich about UDR, updating date to today for news release refs #14918
    
  • lines changed 1, context: html, text, full: html, text
    Correcting a sizeable -> sizable error in my news release item.
    
• src/hg/htdocs/images/Aquila_chrysaetos.jpg
  • lines changed 0, context: html, text, full: html, text
    adding Golden Eagle refs #14560
    
  • lines changed 0, context: html, text, full: html, text
    correct sciName for Golden Eagle refs #14560
    
• src/hg/htdocs/images/Aquila_chrysaetos_canadensis.jpg
  • lines changed 0, context: html, text, full: html, text
    correct sciName for Golden Eagle refs #14560
    
• src/hg/htdocs/images/Bison_bison_bison.jpg
  • lines changed 0, context: html, text, full: html, text
    photo courtesy Lauren Dobson Texas A and M University refs #14560
    
• src/hg/htdocs/indexNews.html
  • lines changed 52, context: html, text, full: html, text
    Releasing new video and posting announcements. refs #14239
    
  • lines changed 3, context: html, text, full: html, text
    Adding a link to the blog. refs #14239
    
  • lines changed 47, context: html, text, full: html, text
    Adding news announcement about UDR and to FAQ about downloads, refs #14918
    
  • lines changed 4, context: html, text, full: html, text
    Adding feedback from Erich about UDR, updating date to today for news release refs #14918
    
  • lines changed 2, context: html, text, full: html, text
    Correcting a sizeable -> sizable error in my news release item.
    
• src/hg/htdocs/training/vids/index.html
  • lines changed 11, context: html, text, full: html, text
    Updating video link to revised vid. refs #14239
    
• src/hg/inc/cartJson.h
  • lines changed 3, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
  • lines changed 15, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v313
    
• src/hg/js/external/lodash.2.4.1.compat.min.js
  • lines changed 61, context: html, text, full: html, text
    Updating lodash library to latest version.
    
• src/hg/js/external/lodash.3.3.1.compat.min.js
  • lines changed 91, context: html, text, full: html, text
    Updating lodash library to latest version.
    
• src/hg/js/external/makefile
  • lines changed 1, context: html, text, full: html, text
    Updating lodash library to latest version.
    
  • lines changed 1, context: html, text, full: html, text
    Added recursive jshint target to all subdirs.
    
• src/hg/js/install.mk
  • lines changed 1, context: html, text, full: html, text
    Make output less verbose
    
• src/hg/js/model/hgAi/hgAiModel.js
  • lines changed 431, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
  • lines changed 21, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
  • lines changed 15, context: html, text, full: html, text
    Don't fetch the top 2 levels of groupedTrackDb after all because the
    partial groupedTrackDb was causing subtrack dataSources to be pruned
    because they weren't found there. It made things a little jumpy anyway.
    refs #14579
    
  • lines changed 10, context: html, text, full: html, text
    Since groupedTrackDb is so large for hg19, it can actually arrive after
    the user has already switched to a different database and received the
    groupTrackDb for the new database. Prevent clobbering by including the
    database to which this particular groupedTrackDb belongs.
    
• src/hg/js/model/lib/CladeOrgDbMixin.js
  • lines changed 9, context: html, text, full: html, text
    Use _.capitalize instead of writing own; use _.last instead of pop so we don't mutate path.
    
  • lines changed 4, context: html, text, full: html, text
    oops! CladeOrgDbMixin.js had a little out-of-place, no-op code.
    
  • lines changed 141, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
• src/hg/js/model/lib/ImModel.js
  • lines changed 6, context: html, text, full: html, text
    Make sure that the handler function passed into register* is really a function.
    
  • lines changed 1, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
• src/hg/js/model/lib/PositionSearchMixin.js
  • lines changed 1, context: html, text, full: html, text
    oops! CladeOrgDbMixin.js had a little out-of-place, no-op code.
    
  • lines changed 7, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
• src/hg/js/react/hgAi/hgAi.jsx
  • lines changed 232, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
• src/hg/js/react/lib/LabeledSelect.jsx
  • lines changed 4, context: html, text, full: html, text
    Added support for disabling an option.
    
• src/hg/js/react/react.mk
  • lines changed 3, context: html, text, full: html, text
    Added recursive jshint target to all subdirs.
    
• src/hg/js/subdirs.mk
  • lines changed 5, context: html, text, full: html, text
    Added recursive jshint target to all subdirs.
    
• src/hg/lib/cartJson.c
  • lines changed 163, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
  • lines changed 159, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
  • lines changed 6, context: html, text, full: html, text
    Since groupedTrackDb is so large for hg19, it can actually arrive after
    the user has already switched to a different database and received the
    groupTrackDb for the new database. Prevent clobbering by including the
    database to which this particular groupedTrackDb belongs.
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 23, context: html, text, full: html, text
    Added aquChr2; refs #14560
    
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    Added aquChr Aquila chrysaetos canadensis refs #14560
    
• src/hg/makeDb/hgLoadOutJoined/hgLoadOutJoined.c
  • lines changed 1, context: html, text, full: html, text
    can not compare unsigned to less than zero found by Mac compiler Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn) refs #9741
    
• src/hg/makeDb/trackDb/birds/aquChr2/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Golden Eagle refs #14560
    
• src/hg/makeDb/trackDb/birds/aquChr2/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding Golden Eagle refs #14560
    
• src/hg/makeDb/trackDb/birds/aquChr2/gold.html
  • lines changed 33, context: html, text, full: html, text
    adding Golden Eagle refs #14560
    
• src/hg/makeDb/trackDb/birds/aquChr2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Golden Eagle refs #14560
    
  • lines changed 5, context: html, text, full: html, text
    add gold table search rule refs #14560
    
• src/hg/makeDb/trackDb/bison/bisBis1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Bison bisBis1 refs #14560
    
• src/hg/makeDb/trackDb/bison/bisBis1/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding Bison bisBis1 refs #14560
    
• src/hg/makeDb/trackDb/bison/bisBis1/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding Bison bisBis1 refs #14560
    
• src/hg/makeDb/trackDb/bison/bisBis1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Bison bisBis1 refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch2.ra
  • lines changed 7, context: html, text, full: html, text
    added search rule for hg38 patch2 haplotype names refs #14167
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    collect all new chain/nets into one composite before proper sorting refs #14560
    
• src/hg/makeDb/trackDb/human/newChainNet.ra
  • lines changed 1018, context: html, text, full: html, text
    collect all new chain/nets into one composite before proper sorting refs #14560
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding Golden Eagle refs #14560
    
  • lines changed 1, context: html, text, full: html, text
    adding Bison bisBis1 refs #14560
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html
  • lines changed 2, context: html, text, full: html, text
    Adding human and removing tarsier from type of alignment table, refs #14410
    
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Seipel pages, refs #14410
    
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
  • lines changed 2, context: html, text, full: html, text
    remove bogus information in genePredToBigGenePred usage message
    
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 5, context: html, text, full: html, text
    making clinvar ottoupdates easier to use
    
• src/hg/utils/otto/clinvar/doUpdate.sh
  • lines changed 4, context: html, text, full: html, text
    making clinvar ottoupdates easier to use
    
• src/hg/utils/phyloTrees/120way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/120way.scientificNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/122way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/122way.scientificNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/123way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/123way.scientificNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/126way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/129way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/130way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/131way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/166way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/171way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/172way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/174way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/181way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/181way.scientificNames.nh
  • lines changed 2, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/183way.commonNames.nh
  • lines changed 6, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/183way.nh
  • lines changed 7, context: html, text, full: html, text
    fixup some distances based on 17-way hg38 track and upgrade to rn6 and felCat8 refs #14560
    
• src/hg/utils/phyloTrees/183way.scientificNames.nh
  • lines changed 5, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/191way.commonNames.nh
  • lines changed 191, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/191way.dissect.txt
  • lines changed 2667, context: html, text, full: html, text
    update to 191-way refs #14560
    
• src/hg/utils/phyloTrees/191way.nh
  • lines changed 191, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/191way.scientificNames.nh
  • lines changed 191, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/191wayChainNet.pl
  • lines changed 219, context: html, text, full: html, text
    update to 191-way refs #14560
    
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 19, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
  • lines changed 2, context: html, text, full: html, text
    adding nasLar1 and xenTro1 refs #14560
    
• src/hg/utils/phyloTrees/findScores.pl
  • lines changed 7, context: html, text, full: html, text
    output in format ready for trackDb override statements refs #14560
    
• src/hg/utils/phyloTrees/makefile
  • lines changed 7, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 19, context: html, text, full: html, text
    catching up with new assemblies nasLar rhiRox fukDam cavAep camBac camDro bosInd bisBis aquChr gavGan vipBer nanPar refs #14560
    
• src/hg/utils/phyloTrees/primates.txt
  • lines changed 6, context: html, text, full: html, text
    catching up with new assemblies nasLar rhiRox fukDam cavAep camBac camDro bosInd bisBis aquChr gavGan vipBer nanPar refs #14560
    
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 3, context: html, text, full: html, text
    differenate info message about where sciName comes from refs #14560
    
  • lines changed 22, context: html, text, full: html, text
    updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
    
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 12, context: html, text, full: html, text
    catching up with new assemblies nasLar rhiRox fukDam cavAep camBac camDro bosInd bisBis aquChr gavGan vipBer nanPar refs #14560
    
• src/inc/jsonWrite.h
  • lines changed 3, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
• src/lib/jsonWrite.c
  • lines changed 8, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
• src/makefile
  • lines changed 3, context: html, text, full: html, text
    removing utils/ for hgBeacon from the main and the utils makefile
    
  • lines changed 1, context: html, text, full: html, text
    removing unnecessary line from the alpha target
    
• src/utils/bigBedInfo/makefile
  • lines changed 28, context: html, text, full: html, text
    during its last code review, hgBeacon was criticized,
    partially, because it's calling bigBedInfo and bigBedToBed and so requires
    copies of these in the cgi-bin dir. This change makes hgBeacon easier to
    install as it does not need the external tools anymore.
    It also adds a tester that can be pointed at the hgBeacon to see if it
    works, at least the basic functions.
    It also makes it easier to import VCF files, as it can import these
    directly.
    
• src/utils/bigBedToBed/makefile
  • lines changed 29, context: html, text, full: html, text
    during its last code review, hgBeacon was criticized,
    partially, because it's calling bigBedInfo and bigBedToBed and so requires
    copies of these in the cgi-bin dir. This change makes hgBeacon easier to
    install as it does not need the external tools anymore.
    It also adds a tester that can be pointed at the hgBeacon to see if it
    works, at least the basic functions.
    It also makes it easier to import VCF files, as it can import these
    directly.
    
• src/utils/makefile
  • lines changed 14, context: html, text, full: html, text
    removing utils/ for hgBeacon from the main and the utils makefile
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v313 final build refs #14887
    

• lines changed: 7490
• files changed: 131