All File Changes

v331_base to v332_preview (2016-04-11 to 2016-04-18) v332

• confs/hgwbeta.hg.conf
  • lines changed 1, context: html, text, full: html, text
    Installing updated hg.conf files from UCSC servers
    
• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    Installing updated hg.conf files from UCSC servers
    
  • lines changed 1, context: html, text, full: html, text
    Installing updated hg.conf files from UCSC servers
    
• src/hg/cirm/cdw/cdwCheckValidation/cdwCheckValidation.c
  • lines changed 316, context: html, text, full: html, text
    Fixing up this program as per Jims suggestions in our last F2F, refs #17100
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 7, context: html, text, full: html, text
    Improving usage message for cdwSubmit.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 50, context: html, text, full: html, text
    Wrapping format column with a hyperlink that will display file in web browser for formats that web browsers support.
    
  • lines changed 1, context: html, text, full: html, text
    Adding a third search mode to trixSearch(), for less stringent searches such as autocomplete.
    The first two modes were previously designated by a boolean expand -- now there is an enum
    trixSearchMode whose first two values correspond to that (expand==FALSE = tsmExact,
    expand==TRUE = tsmExpand). The third mode, tsmFirstFive, returns matches of five or more
    characters even if there are many characters left in a long word. For example, "arabi" will
    match "arabidopsis" in tsmFirstFive mode, but not in tsmExpand mode because that leaves six
    unmatched letters after "arabi".
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 3, context: html, text, full: html, text
    Adding three new tags - dna_concentration, rin, and version
    
• src/hg/cirm/cdw/makefile
  • lines changed 2, context: html, text, full: html, text
    Adding cdwVcfStats to the utilities made.
    
• src/hg/encode/hgEncodeApi/hgEncodeApi.c
  • lines changed 3, context: html, text, full: html, text
    Unifying some triplicate code to print an HTTP error 400 response (Bad Request) and exit.
    
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/edwScriptSubmitStatus.c
  • lines changed 16, context: html, text, full: html, text
    Unifying some triplicate code to print an HTTP error 400 response (Bad Request) and exit.
    
• src/hg/hgApi/hgApi.c
  • lines changed 3, context: html, text, full: html, text
    Unifying some triplicate code to print an HTTP error 400 response (Bad Request) and exit.
    
• src/hg/hgChooseDb/hgChooseDb.c
  • lines changed 1, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 1, context: html, text, full: html, text
    Adding a third search mode to trixSearch(), for less stringent searches such as autocomplete.
    The first two modes were previously designated by a boolean expand -- now there is an enum
    trixSearchMode whose first two values correspond to that (expand==FALSE = tsmExact,
    expand==TRUE = tsmExpand). The third mode, tsmFirstFive, returns matches of five or more
    characters even if there are many characters left in a long word. For example, "arabi" will
    match "arabidopsis" in tsmFirstFive mode, but not in tsmExpand mode because that leaves six
    unmatched letters after "arabi".
    
• src/hg/hgGateway/hgGateway.c
  • lines changed 769, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
  • lines changed 10, context: html, text, full: html, text
    Species autocomplete fixes: make sure 'grch37' properly selects hg19 and make it appear before genome matches. Make genome matches appear before sciName matches. If user types hg19 and hits enter, don't mismatch on some bogus labelly value. refs #15277
    
  • lines changed 3, context: html, text, full: html, text
    Keep forcing hgwdev-demo6 to use dbDbTaxonomy.rr.js (phylo tree of RR species) for testing, but use dbDbTaxonomy.hgwdev.js on other hgwdev* hosts. refs #15277
    
  • lines changed 1, context: html, text, full: html, text
    Yikes, the new hgGateway was showing inactive dbs. refs #15277
    
  • lines changed 1, context: html, text, full: html, text
    Use hubConnectStatusListFromCart instead of hubConnectStatusListFromCartAll, which connects to hubs even if they're set to 0 (not connected) in cart.
    
• src/hg/hgGateway/hgGateway.html
  • lines changed 249, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
  • lines changed 1, context: html, text, full: html, text
    Change the label above the popular species icons from "MODEL SPECIES" to "POPULAR SPECIES". refs #15277
    
  • lines changed 6, context: html, text, full: html, text
    Removed some code that separated assembly descriptions into 3 divs, with the middle div containing a list of links to sections in the bottom div. refs #15277
    
  • lines changed 2, context: html, text, full: html, text
    Hide the Find Position section contents until they're filled in, so we don't see empty containers jumping around. refs #15277 sorta
    
• src/hg/hgGateway/makefile
  • lines changed 11, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/hgGtexApi/hgGtexApi.c
  • lines changed 3, context: html, text, full: html, text
    Unifying some triplicate code to print an HTTP error 400 response (Bad Request) and exit.
    
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    Adding a third search mode to trixSearch(), for less stringent searches such as autocomplete.
    The first two modes were previously designated by a boolean expand -- now there is an enum
    trixSearchMode whose first two values correspond to that (expand==FALSE = tsmExact,
    expand==TRUE = tsmExpand). The third mode, tsmFirstFive, returns matches of five or more
    characters even if there are many characters left in a long word. For example, "arabi" will
    match "arabidopsis" in tsmFirstFive mode, but not in tsmExpand mode because that leaves six
    unmatched letters after "arabi".
    
• src/hg/hgSuggest/hgSuggest.c
  • lines changed 11, context: html, text, full: html, text
    Unifying some triplicate code to print an HTTP error 400 response (Bad Request) and exit.
    
• src/hg/hgTables/hgTables.c
  • lines changed 3, context: html, text, full: html, text
    Fixes #17163. It is now using regular hgBotDelay() in htmlOpen() and calling new function hgBotDelayNoWarn() in textOpen().
    
• src/hg/hgTracks/chromGraphTrack.c
  • lines changed 3, context: html, text, full: html, text
    Fixes missing &r=winStart&l=winEnd which TimD had removed as a step towards his dynamic portal view, but which we are not using, and it messes up hgc clicks for multi-region. refs #16898
    
• src/hg/hgTracks/expRatioTracks.c
  • lines changed 5, context: html, text, full: html, text
    Fixes missing &r=winStart&l=winEnd which TimD had removed as a step towards his dynamic portal view, but which we are not using, and it messes up hgc clicks for multi-region. refs #16898
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 10, context: html, text, full: html, text
    Fixing problem where tracks with data only on certain chroms could get filtered out if they do not match the chromName of the first window. Now it looks across all windows chromNames and only hides the track if it is not found on all chroms of all window regions. No RM issue. Discovered with custom regions with multiple different chroms and a bam custom track that only had data from chr21.
    
• src/hg/hgTracks/searchTracks.c
  • lines changed 1, context: html, text, full: html, text
    Adding a third search mode to trixSearch(), for less stringent searches such as autocomplete.
    The first two modes were previously designated by a boolean expand -- now there is an enum
    trixSearchMode whose first two values correspond to that (expand==FALSE = tsmExact,
    expand==TRUE = tsmExpand). The third mode, tsmFirstFive, returns matches of five or more
    characters even if there are many characters left in a long word. For example, "arabi" will
    match "arabidopsis" in tsmFirstFive mode, but not in tsmExpand mode because that leaves six
    unmatched letters after "arabi".
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 26, context: html, text, full: html, text
    Fixing clipping problem with pgSnp for multi-region. refs #16898
    
  • lines changed 4, context: html, text, full: html, text
    Fixes missing &r=winStart&l=winEnd which TimD had removed as a step towards his dynamic portal view, but which we are not using, and it messes up hgc clicks for multi-region. refs #16898
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    adding Entrez nuccore link to gold fragment details page refs #17168
    
  • lines changed 6, context: html, text, full: html, text
    fix silly bug in code that never gets executed unless something is seriuosly wrong.
    
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 3, context: html, text, full: html, text
    static docs prep, rheMac8 release & macFas5 announce, fixing rheMac8 .ra for beta display, refs #16744, refs#11174
    
  • lines changed 1, context: html, text, full: html, text
    Adding gorGor4 to credits and FAQreleases html pages in preparation for release, refs #16220
    
  • lines changed 1, context: html, text, full: html, text
    Fixing up releases page, refs #16220
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 7, context: html, text, full: html, text
    static docs prep, rheMac8 release & macFas5 announce, fixing rheMac8 .ra for beta display, refs #16744, refs#11174
    
  • lines changed 2, context: html, text, full: html, text
    Updating credits for rheMac8, refs #16744
    
  • lines changed 18, context: html, text, full: html, text
    Adding gorGor4 to credits and FAQreleases html pages in preparation for release, refs #16220
    
• src/hg/htdocs/goldenPath/help/bigChain.html
  • lines changed 246, context: html, text, full: html, text
    place holders for files to describe bigPsl, bigMaf, and bigChain.
    
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 246, context: html, text, full: html, text
    place holders for files to describe bigPsl, bigMaf, and bigChain.
    
• src/hg/htdocs/goldenPath/help/bigPsl.html
  • lines changed 246, context: html, text, full: html, text
    place holders for files to describe bigPsl, bigMaf, and bigChain.
    
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 4, context: html, text, full: html, text
    Adding a note about Custom Tracks Google Drive from user input MLQ refs #17182
    
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 237, context: html, text, full: html, text
    Adding changes to Session Gallery page refs #1263
    
  • lines changed 39, context: html, text, full: html, text
    Adding changes to Session Gallery page refs #1263
    
  • lines changed 123, context: html, text, full: html, text
    Adding sessions, rearranging layout to new added topics refs #1263
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 49, context: html, text, full: html, text
    static docs prep, rheMac8 release & macFas5 announce, fixing rheMac8 .ra for beta display, refs #16744, refs#11174
    
  • lines changed 20, context: html, text, full: html, text
    Adding gorilla release to staging area for announcement. Wait on release until macFas5 and rheMac8 are ready for release for a tri-announcement, refs #16220
    
  • lines changed 108, context: html, text, full: html, text
    Adding announcement for snp146 for hg19 and hg38, slight edits to 3-primate announcement, edited dates on staged lens patents announcement, refs #16777
    
  • lines changed 3, context: html, text, full: html, text
    HTML encoding quotes in announcement, refs #16777
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    Updated link for Max's GBiB pub.
    
• src/hg/htdocs/images/Rousettus_aegyptiacus.jpg
  • lines changed 0, context: html, text, full: html, text
    photographer Oren Peles wikimedia commons via https://commons.wikimedia.org/wiki/User:MathKnight refs #17167
    
• src/hg/htdocs/images/aboVariantDetails.png
  • lines changed 0, context: html, text, full: html, text
    Adding images for sessions gallery refs #1263
    
• src/hg/htdocs/images/gtexAnnounceExample.png
  • lines changed 0, context: html, text, full: html, text
    Adding screenshot of gtex track in prep for announcement, refs #15645
    
  • lines changed 0, context: html, text, full: html, text
    Hopefully better picture for gtex announcement, refs #15646
    
• src/hg/htdocs/images/hg18.stop2.png
  • lines changed 0, context: html, text, full: html, text
    Adding images for sessions gallery refs #1263
    
• src/hg/htdocs/images/homeIconSprite.png
  • lines changed 0, context: html, text, full: html, text
    Changed background color to transparent (alpha) so that this will take on the background color of its container.
    
• src/hg/htdocs/images/jWestIcons55px.png
  • lines changed 0, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/htdocs/images/jWestIconsAlpha65px.png
  • lines changed 0, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/htdocs/images/session.hg19.AluY.png
  • lines changed 0, context: html, text, full: html, text
    Adding sessions, rearranging layout to new added topics refs #1263
    
• src/hg/htdocs/images/session.hg19.CAGrepeat.png
  • lines changed 0, context: html, text, full: html, text
    Adding images for sessions gallery refs #1263
    
• src/hg/htdocs/images/session.hg19.OMIM.png
  • lines changed 0, context: html, text, full: html, text
    Adding images for sessions gallery refs #1263
    
• src/hg/htdocs/images/session.hg19.SNPcolor.png
  • lines changed 0, context: html, text, full: html, text
    Adding images for sessions gallery refs #1263
    
• src/hg/htdocs/images/session.hg19.chimp.png
  • lines changed 0, context: html, text, full: html, text
    Adding images for sessions gallery refs #1263
    
• src/hg/htdocs/images/session.hg19.chimp2.png
  • lines changed 0, context: html, text, full: html, text
    Adding images for sessions gallery refs #1263
    
• src/hg/htdocs/images/session.hg19.chimp3.png
  • lines changed 0, context: html, text, full: html, text
    Adding images for sessions gallery refs #1263
    
• src/hg/htdocs/images/session.hg19.codonNums.png
  • lines changed 0, context: html, text, full: html, text
    Adding images for sessions gallery refs #1263
    
• src/hg/htdocs/images/session.hg19.microArray.png
  • lines changed 0, context: html, text, full: html, text
    Adding images for sessions gallery refs #1263
    
• src/hg/htdocs/images/session.hg19.segDup.png
  • lines changed 0, context: html, text, full: html, text
    Adding images for sessions gallery refs #1263
    
• src/hg/htdocs/images/session.hg19.split.png
  • lines changed 0, context: html, text, full: html, text
    Adding images for sessions gallery refs #1263
    
• src/hg/htdocs/images/session.hg19.split2.png
  • lines changed 0, context: html, text, full: html, text
    Adding image for sessions gallery refs #1263
    
• src/hg/htdocs/images/session.hg19.wobble.png
  • lines changed 0, context: html, text, full: html, text
    Adding an image for sessions gallery refs #1263
    
• src/hg/htdocs/images/ucscHelixLogo.png
  • lines changed 0, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/htdocs/images/ucscLogo.svg
  • lines changed 3, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/htdocs/inc/jWestFooter.html
  • lines changed 52, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/htdocs/indexNews.html
  • lines changed 50, context: html, text, full: html, text
    static docs prep, rheMac8 release & macFas5 announce, fixing rheMac8 .ra for beta display, refs #16744, refs#11174
    
  • lines changed 28, context: html, text, full: html, text
    Adding gorilla release to staging area for announcement. Wait on release until macFas5 and rheMac8 are ready for release for a tri-announcement, refs #16220
    
  • lines changed 129, context: html, text, full: html, text
    Adding announcement for snp146 for hg19 and hg38, slight edits to 3-primate announcement, edited dates on staged lens patents announcement, refs #16777
    
  • lines changed 1, context: html, text, full: html, text
    Correcting link to news archives, no redmine
    
  • lines changed 2, context: html, text, full: html, text
    HTML encoding quotes in announcement, refs #16777
    
  • lines changed 27, context: html, text, full: html, text
    Staging gtex announcement, refs #15645
    
  • lines changed 42, context: html, text, full: html, text
    Resolving merge conflict on indexNews page, refs #15645
    
  • lines changed 6, context: html, text, full: html, text
    Fixing broken urls on indexNews page
    
  • lines changed 69, context: html, text, full: html, text
    Staging GTEx announcement, refs #15645
    
• src/hg/htdocs/style/jWest.afterNiceMenu.css
  • lines changed 19, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/htdocs/style/jWest.css
  • lines changed 418, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
  • lines changed 1, context: html, text, full: html, text
    jwSectionTitle wasn't extending quite all the way to the edge as intended. refs #15277 note 148
    
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/htdocs/training/index.html
  • lines changed 7, context: html, text, full: html, text
    adjusts timepoint landing of link into middle of a vid. adds appearance at Bar Harbor summer course to training list
    
  • lines changed 1, context: html, text, full: html, text
    adding better link to ESHG workshop
    
  • lines changed 2, context: html, text, full: html, text
    added second link to ESHG workshop, showing day/time
    
• src/hg/htdocs/training/vids/index.html
  • lines changed 2, context: html, text, full: html, text
    adjusts timepoint landing of link into middle of a vid. adds appearance at Bar Harbor summer course to training list
    
• src/hg/inc/api.h
  • lines changed 3, context: html, text, full: html, text
    Unifying some triplicate code to print an HTTP error 400 response (Bad Request) and exit.
    
• src/hg/inc/botDelay.h
  • lines changed 5, context: html, text, full: html, text
    Fixes #17163. It is now using regular hgBotDelay() in htmlOpen() and calling new function hgBotDelayNoWarn() in textOpen().
    
• src/hg/inc/dbDb.h
  • lines changed 5, context: html, text, full: html, text
    Adding taxId column to dbDb.{as,c,h,sql} -- the column seems to have been
    in our dbDb tables for years, just not in these files.
    
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    Now that dbDb has a taxId field, update hDbForTaxon to use it instead of going throught UniProt.
    Also added hTaxId() for looking up a db's taxId.
    
• src/hg/inc/hubConnect.h
  • lines changed 13, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/inc/trackHub.h
  • lines changed 5, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/inc/web.h
  • lines changed 6, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/js/dbDbTaxonomy.hgwdev.js
  • lines changed 1087, context: html, text, full: html, text
    Adding dbDbTaxonomy.pl along with makeDb/doc instructions for generating/updating two new JS files that contain phylogenetic trees for hgwdev's and rr's species.
    
    dbDbTaxonomy.pl uses taxIds extracted from hgcentral(test) to build a phylogenetic tree using NCBI Taxonomy database dump files.
    It finds ancestors of the hgcentral species' taxIds to build a tree, and adds node names to ancestor nodes.
    It assigns priorities to nodes based on a list of 'favored species' in the order we'd like to see them listed when the tree is traversed.
    Then it dumps out Javascript encoding the tree as recursive Arrays. The JS output can be included as a script in HTML.
    
    refs #15277
    
• src/hg/js/dbDbTaxonomy.rr.js
  • lines changed 530, context: html, text, full: html, text
    Adding dbDbTaxonomy.pl along with makeDb/doc instructions for generating/updating two new JS files that contain phylogenetic trees for hgwdev's and rr's species.
    
    dbDbTaxonomy.pl uses taxIds extracted from hgcentral(test) to build a phylogenetic tree using NCBI Taxonomy database dump files.
    It finds ancestors of the hgcentral species' taxIds to build a tree, and adds node names to ancestor nodes.
    It assigns priorities to nodes based on a list of 'favored species' in the order we'd like to see them listed when the tree is traversed.
    Then it dumps out Javascript encoding the tree as recursive Arrays. The JS output can be included as a script in HTML.
    
    refs #15277
    
• src/hg/js/hgGateway.js
  • lines changed 1537, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
  • lines changed 49, context: html, text, full: html, text
    Added support for removal of duplicate items from species autocomplete results.
    refs #15277 (see note 142)
    
  • lines changed 104, context: html, text, full: html, text
    Refactored autocompleteCat options so that species autocomplete can do even more customized post-processing of results from server (insert phylo tree matches between dbDb matches and assembly hub matches). refs #15277
    
  • lines changed 81, context: html, text, full: html, text
    Removed some code that separated assembly descriptions into 3 divs, with the middle div containing a list of links to sections in the bottom div. refs #15277
    
  • lines changed 3, context: html, text, full: html, text
    Updating icon genome and placement for dbDbTaxonomy.hgwdev.js. refs #15277
    
  • lines changed 5, context: html, text, full: html, text
    Hide the Find Position section contents until they're filled in, so we don't see empty containers jumping around. refs #15277 sorta
    
• src/hg/js/install.mk
  • lines changed 4, context: html, text, full: html, text
    Added topAlpha target for installation of top-level *.js files only.
    
• src/hg/js/jquery-ui.js
  • lines changed 31, context: html, text, full: html, text
    Extended jquery-ui's autocomplete by adding new options enterSelectsIdentical and enterTerm,
    so that when the user hits Enter in the text input, instead of ignoring it we can select a
    menu item whose value is equal to the term and/or invoke a callback (enterTerm) so the app
    can react to the Enter key in its own way. There are only additions to jquery-ui's code,
    no changes to existing behavior unless the new options are passed in.
    
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/js/model/lib/cart.js
  • lines changed 2, context: html, text, full: html, text
    Typo fix in comments.
    
  • lines changed 18, context: html, text, full: html, text
    Added a flag, set by cart.debug(true/false), to turn on and off the
    console.log messages.
    
• src/hg/lib/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/lib/api.c
  • lines changed 11, context: html, text, full: html, text
    Unifying some triplicate code to print an HTTP error 400 response (Bad Request) and exit.
    
• src/hg/lib/bigBedFind.c
  • lines changed 1, context: html, text, full: html, text
    Adding a third search mode to trixSearch(), for less stringent searches such as autocomplete.
    The first two modes were previously designated by a boolean expand -- now there is an enum
    trixSearchMode whose first two values correspond to that (expand==FALSE = tsmExact,
    expand==TRUE = tsmExpand). The third mode, tsmFirstFive, returns matches of five or more
    characters even if there are many characters left in a long word. For example, "arabi" will
    match "arabidopsis" in tsmFirstFive mode, but not in tsmExpand mode because that leaves six
    unmatched letters after "arabi".
    
• src/hg/lib/botDelay.c
  • lines changed 19, context: html, text, full: html, text
    Fixes #17163. It is now using regular hgBotDelay() in htmlOpen() and calling new function hgBotDelayNoWarn() in textOpen().
    
• src/hg/lib/cart.c
  • lines changed 3, context: html, text, full: html, text
    Adding a NULL check before using oldVars.
    
• src/hg/lib/customTrack.c
  • lines changed 1, context: html, text, full: html, text
    Fixing buffer overflow caused by one of Hiram's hub genomes, hub_1642_GCF_000721765.1_Aureobasidium_pullulans_var._namibiae_CBS_147.97_v1.0 :)
    
• src/hg/lib/dbDb.as
  • lines changed 1, context: html, text, full: html, text
    Adding taxId column to dbDb.{as,c,h,sql} -- the column seems to have been
    in our dbDb tables for years, just not in these files.
    
• src/hg/lib/dbDb.c
  • lines changed 11, context: html, text, full: html, text
    Adding taxId column to dbDb.{as,c,h,sql} -- the column seems to have been
    in our dbDb tables for years, just not in these files.
    
• src/hg/lib/dbDb.sql
  • lines changed 1, context: html, text, full: html, text
    Adding taxId column to dbDb.{as,c,h,sql} -- the column seems to have been
    in our dbDb tables for years, just not in these files.
    
• src/hg/lib/hdb.c
  • lines changed 37, context: html, text, full: html, text
    Now that dbDb has a taxId field, update hDbForTaxon to use it instead of going throught UniProt.
    Also added hTaxId() for looking up a db's taxId.
    
  • lines changed 9, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
  • lines changed 2, context: html, text, full: html, text
    Yikes, the new hgGateway was showing inactive dbs. refs #15277
    
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    Adding a third search mode to trixSearch(), for less stringent searches such as autocomplete.
    The first two modes were previously designated by a boolean expand -- now there is an enum
    trixSearchMode whose first two values correspond to that (expand==FALSE = tsmExact,
    expand==TRUE = tsmExpand). The third mode, tsmFirstFive, returns matches of five or more
    characters even if there are many characters left in a long word. For example, "arabi" will
    match "arabidopsis" in tsmFirstFive mode, but not in tsmExpand mode because that leaves six
    unmatched letters after "arabi".
    
• src/hg/lib/hubConnect.c
  • lines changed 49, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/lib/jWestBanner.html
  • lines changed 32, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/lib/makefile
  • lines changed 6, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/lib/trackHub.c
  • lines changed 20, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/lib/web.c
  • lines changed 31, context: html, text, full: html, text
    Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
    It has icons for selecting popular species, an autocomplete input for typing in species or common names,
    as well as a phylogenetic tree display that shows the relationships of the species that we host.
    It has a menu for selecting the assembly of the selected species' genome and the usual assembly
    description.
    
    refs #15277
    
• src/hg/logCrawl/userDbCrawl/makefile
  • lines changed 3, context: html, text, full: html, text
    Writing something that will lightly filter a userDb or sessionDb dump and convert it to var/val/count table.
    
• src/hg/logCrawl/userDbCrawl/userDbVvc.c
  • lines changed 150, context: html, text, full: html, text
    Writing something that will lightly filter a userDb or sessionDb dump and convert it to var/val/count table.
    
• src/hg/makeDb/doc/dbDbTaxonomy.txt
  • lines changed 99, context: html, text, full: html, text
    Adding dbDbTaxonomy.pl along with makeDb/doc instructions for generating/updating two new JS files that contain phylogenetic trees for hgwdev's and rr's species.
    
    dbDbTaxonomy.pl uses taxIds extracted from hgcentral(test) to build a phylogenetic tree using NCBI Taxonomy database dump files.
    It finds ancestors of the hgcentral species' taxIds to build a tree, and adds node names to ancestor nodes.
    It assigns priorities to nodes based on a list of 'favored species' in the order we'd like to see them listed when the tree is traversed.
    Then it dumps out Javascript encoding the tree as recursive Arrays. The JS output can be included as a script in HTML.
    
    refs #15277
    
• src/hg/makeDb/doc/felCat3.txt
  • lines changed 16, context: html, text, full: html, text
    liftOver from felCat3 to felCat8 refs #16879
    
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 19, context: html, text, full: html, text
    liftOver to galGal5 refs #17168
    
• src/hg/makeDb/doc/galGal5/initialBuild.txt
  • lines changed 565, context: html, text, full: html, text
    beginning build for galGal5 refs #17168
    
  • lines changed 147, context: html, text, full: html, text
    fixup INSDC track construction procedure added gold search rule and running RM and TRF refs #17168
    
  • lines changed 162, context: html, text, full: html, text
    running genbank refs #17168
    
  • lines changed 10, context: html, text, full: html, text
    running genbank blatServer assigned and liftOver to galGal4 refs #17168
    
• src/hg/makeDb/doc/galVar1/initialBuild.txt
  • lines changed 128, context: html, text, full: html, text
    done and in the pushQ refs #17180
    
  • lines changed 13, context: html, text, full: html, text
    added blat server refs #17180
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 20, context: html, text, full: html, text
    fixup chrM INSDC name refs #17132
    
  • lines changed 212, context: html, text, full: html, text
    mm10 vs rn6 alignment and 4-way multiz to support UCSC Genes on mm10, refs #15315
    
• src/hg/makeDb/doc/proteins/160229.txt
  • lines changed 199, context: html, text, full: html, text
    Adding makedocs for latest version of uniProt and proteins databases, refs #15315
    
• src/hg/makeDb/doc/rn3.txt
  • lines changed 16, context: html, text, full: html, text
    liftOver from rn3 ro rn6 refs #16879
    
• src/hg/makeDb/doc/rouAeg1/initialBuild.txt
  • lines changed 625, context: html, text, full: html, text
    beginning rouAeg1 build refs #17167
    
  • lines changed 192, context: html, text, full: html, text
    added INSDC track and gold assembly search rule and running RM and TRF refs #17167
    
• src/hg/makeDb/doc/uniProt/sp160229.txt
  • lines changed 2, context: html, text, full: html, text
    Adding makedocs for latest version of uniProt and proteins databases, refs #15315
    
• src/hg/makeDb/genbank/etc/align-genbank
  • lines changed 1, context: html, text, full: html, text
    up the maximum parallel genbank alignment processes to 16 from 8
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added galVar1 - Galeopterus variegatus/Malayan flying lemur refs #17180
    
• src/hg/makeDb/genbank/etc/gbMetadataTables.txt
  • lines changed 24, context: html, text, full: html, text
    change genbank table list to more explicit names
    
• src/hg/makeDb/genbank/etc/gbPerAssemblyTables.txt
  • lines changed 27, context: html, text, full: html, text
    change genbank table list to more explicit names
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    Added galGal5; refs #17168
    
  • lines changed 1, context: html, text, full: html, text
    fixup galGal5; refs #17168
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    turning on genbank updates for gorGor4 on hgwbeta, refs #16220
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added galVar1 - Galeopterus variegatus/Malayan flying lemur refs #17180
    
• src/hg/makeDb/genbank/etc/metaTables.txt
  • lines changed 24, context: html, text, full: html, text
    change genbank table list to more explicit names
    
• src/hg/makeDb/genbank/etc/perAss.txt
  • lines changed 27, context: html, text, full: html, text
    change genbank table list to more explicit names
    
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 2, context: html, text, full: html, text
    Adding rheMac8 to rr genbank updates refs #16744
    
  • lines changed 2, context: html, text, full: html, text
    adding gorGor4 to genbank updates on the rr
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 10, context: html, text, full: html, text
    adding rules for galVar1 refs #17180
    
  • lines changed 7, context: html, text, full: html, text
    Updating all.joiner settings for gwas to point to new snp track, because apparently that's a thing. refs #14465
    
• src/hg/makeDb/trackDb/bats/rouAeg1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding rouAeg1 to the build refs #17167
    
• src/hg/makeDb/trackDb/bats/rouAeg1/gap.html
  • lines changed 29, context: html, text, full: html, text
    adding rouAeg1 to the build refs #17167
    
• src/hg/makeDb/trackDb/bats/rouAeg1/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding rouAeg1 to the build refs #17167
    
• src/hg/makeDb/trackDb/bats/rouAeg1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding rouAeg1 to the build refs #17167
    
• src/hg/makeDb/trackDb/chicken/galGal5/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files for galGal5 refs #17168
    
• src/hg/makeDb/trackDb/chicken/galGal5/gap.html
  • lines changed 32, context: html, text, full: html, text
    initial files for galGal5 refs #17168
    
• src/hg/makeDb/trackDb/chicken/galGal5/gold.html
  • lines changed 36, context: html, text, full: html, text
    initial files for galGal5 refs #17168
    
• src/hg/makeDb/trackDb/chicken/galGal5/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files for galGal5 refs #17168
    
• src/hg/makeDb/trackDb/gorilla/gorGor4/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    Fixing assemblyAcc search on gorGor4, refs #16220
    
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 2, context: html, text, full: html, text
    Removing release tags for human/gorGor4 chain/net track, refs #16220
    
  • lines changed 2, context: html, text, full: html, text
    Fixing rheMac8 chain/net tracks, refs #16744
    
• src/hg/makeDb/trackDb/human/gwasCatalog.html
  • lines changed 53, context: html, text, full: html, text
    Updating documentation for the GWAS track, now hosted at EBI
    
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 7, context: html, text, full: html, text
    Hiding old SNP track by default ahead of snp146 release, refs #16777
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Updating GWAS SNP table version in tdb for use by hgc, refs #14465
    
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
  • lines changed 2, context: html, text, full: html, text
    Hiding old SNP track by default ahead of snp146 release, refs #16777
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Updating GWAS SNP table version in tdb for use by hgc, refs #14465
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Hiding old SNP track by default ahead of snp146 release, refs #16777
    
  • lines changed 1, context: html, text, full: html, text
    Updating longLabel for gwasCatalog tracks, no redmine
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    initial files for galGal5 refs #17168
    
  • lines changed 1, context: html, text, full: html, text
    adding rouAeg1 to the build refs #17167
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
  • lines changed 1, context: html, text, full: html, text
    static docs prep, rheMac8 release & macFas5 announce, fixing rheMac8 .ra for beta display, refs #16744, refs#11174
    
• src/hg/makeDb/trackDb/trackDb.genbank.ra
  • lines changed 2, context: html, text, full: html, text
    make sure the mrna accession and keyword hgFind trackDb entries end up
    being included on a make strict
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    Split the search refSeqComposite into two searches: refSeqCompositeAccession for short-circuit matching of NM_ and similar accessions, and refSeqCompositeName for matching gene symbols that also appear in ncbiRefSeq.name. Better to use semiShortCircuit instead of shortCircuit in general.
    
• src/hg/oneShot/freen/freen.c
  • lines changed 68, context: html, text, full: html, text
    Helping test new error message in fileModTime.
    
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 9, context: html, text, full: html, text
    fixup coding gene selection refs #13673
    
• src/hg/utils/automation/prepConfig.pl
  • lines changed 131, context: html, text, full: html, text
    add script to prepare the config.ra file for a genome assembly refs #17167
    
  • lines changed 19, context: html, text, full: html, text
    reorganize to use single genomic.fna.gz file and correct preparation of db.config.ra data refs #17168
    
  • lines changed 13, context: html, text, full: html, text
    correctly set genomeCladePriority refs #17168
    
• src/hg/utils/automation/ucscCompositeAgp.pl
  • lines changed 22, context: html, text, full: html, text
    reorganize to use single genomic.fna.gz file and correct preparation of db.config.ra data refs #17168
    
• src/hg/utils/automation/unlocalizedWithChroms.pl
  • lines changed 41, context: html, text, full: html, text
    reorganize to use single genomic.fna.gz file and correct preparation of db.config.ra data refs #17168
    
• src/hg/utils/automation/unplacedWithChroms.pl
  • lines changed 25, context: html, text, full: html, text
    reorganize to use single genomic.fna.gz file and correct preparation of db.config.ra data refs #17168
    
• src/hg/utils/dbDbTaxonomy.pl
  • lines changed 360, context: html, text, full: html, text
    Adding dbDbTaxonomy.pl along with makeDb/doc instructions for generating/updating two new JS files that contain phylogenetic trees for hgwdev's and rr's species.
    
    dbDbTaxonomy.pl uses taxIds extracted from hgcentral(test) to build a phylogenetic tree using NCBI Taxonomy database dump files.
    It finds ancestors of the hgcentral species' taxIds to build a tree, and adds node names to ancestor nodes.
    It assigns priorities to nodes based on a list of 'favored species' in the order we'd like to see them listed when the tree is traversed.
    Then it dumps out Javascript encoding the tree as recursive Arrays. The JS output can be included as a script in HTML.
    
    refs #15277
    
• src/hg/utils/otto/omim/checkOmimUpload.sh
  • lines changed 1, context: html, text, full: html, text
    Suppressing unimportant error message
    
• src/hg/visiGene/hgVisiGene/fullTextExperiment.c
  • lines changed 1, context: html, text, full: html, text
    Adding a third search mode to trixSearch(), for less stringent searches such as autocomplete.
    The first two modes were previously designated by a boolean expand -- now there is an enum
    trixSearchMode whose first two values correspond to that (expand==FALSE = tsmExact,
    expand==TRUE = tsmExpand). The third mode, tsmFirstFive, returns matches of five or more
    characters even if there are many characters left in a long word. For example, "arabi" will
    match "arabidopsis" in tsmFirstFive mode, but not in tsmExpand mode because that leaves six
    unmatched letters after "arabi".
    
• src/hg/visiGene/hgVisiGene/printCaption.c
  • lines changed 1, context: html, text, full: html, text
    Now that dbDb has a taxId field, update hDbForTaxon to use it instead of going throught UniProt.
    Also added hTaxId() for looking up a db's taxId.
    
• src/hg/visiGene/hgVisiGene/probePage.c
  • lines changed 1, context: html, text, full: html, text
    Now that dbDb has a taxId field, update hDbForTaxon to use it instead of going throught UniProt.
    Also added hTaxId() for looking up a db's taxId.
    
• src/hg/visiGene/hgVisiGene/visiSearch.c
  • lines changed 1, context: html, text, full: html, text
    Adding a third search mode to trixSearch(), for less stringent searches such as autocomplete.
    The first two modes were previously designated by a boolean expand -- now there is an enum
    trixSearchMode whose first two values correspond to that (expand==FALSE = tsmExact,
    expand==TRUE = tsmExpand). The third mode, tsmFirstFive, returns matches of five or more
    characters even if there are many characters left in a long word. For example, "arabi" will
    match "arabidopsis" in tsmFirstFive mode, but not in tsmExpand mode because that leaves six
    unmatched letters after "arabi".
    
• src/inc/htmshell.h
  • lines changed 4, context: html, text, full: html, text
    Unifying some triplicate code to print an HTTP error 400 response (Bad Request) and exit.
    
• src/inc/trix.h
  • lines changed 20, context: html, text, full: html, text
    Adding a third search mode to trixSearch(), for less stringent searches such as autocomplete.
    The first two modes were previously designated by a boolean expand -- now there is an enum
    trixSearchMode whose first two values correspond to that (expand==FALSE = tsmExact,
    expand==TRUE = tsmExpand). The third mode, tsmFirstFive, returns matches of five or more
    characters even if there are many characters left in a long word. For example, "arabi" will
    match "arabidopsis" in tsmFirstFive mode, but not in tsmExpand mode because that leaves six
    unmatched letters after "arabi".
    
• src/index/trixSearch/trixSearch.c
  • lines changed 1, context: html, text, full: html, text
    Adding a third search mode to trixSearch(), for less stringent searches such as autocomplete.
    The first two modes were previously designated by a boolean expand -- now there is an enum
    trixSearchMode whose first two values correspond to that (expand==FALSE = tsmExact,
    expand==TRUE = tsmExpand). The third mode, tsmFirstFive, returns matches of five or more
    characters even if there are many characters left in a long word. For example, "arabi" will
    match "arabidopsis" in tsmFirstFive mode, but not in tsmExpand mode because that leaves six
    unmatched letters after "arabi".
    
• src/lib/htmshell.c
  • lines changed 15, context: html, text, full: html, text
    Unifying some triplicate code to print an HTTP error 400 response (Bad Request) and exit.
    
• src/lib/osunix.c
  • lines changed 1, context: html, text, full: html, text
    Improving error message in fileModTime.
    
• src/lib/trix.c
  • lines changed 15, context: html, text, full: html, text
    Adding a third search mode to trixSearch(), for less stringent searches such as autocomplete.
    The first two modes were previously designated by a boolean expand -- now there is an enum
    trixSearchMode whose first two values correspond to that (expand==FALSE = tsmExact,
    expand==TRUE = tsmExpand). The third mode, tsmFirstFive, returns matches of five or more
    characters even if there are many characters left in a long word. For example, "arabi" will
    match "arabidopsis" in tsmFirstFive mode, but not in tsmExpand mode because that leaves six
    unmatched letters after "arabi".
    
• src/lib/vcf.c
  • lines changed 1, context: html, text, full: html, text
    Relaxing checking of ID symbols in INFO and FORMAT metadata lines of VCF files.
    
• src/utils/paraMd5/paraMd5.c
  • lines changed 8, context: html, text, full: html, text
    Printout out some "I am alive" dots to stderr.
    
• src/utils/qa/bigPush.csh
  • lines changed 79, context: html, text, full: html, text
    Replacing bigPush.csh with bigPush.sh. Added new bigPush.sh to makefile. Script allows for pushing multiple tables for multiple assemblies. refs #16040
    
• src/utils/qa/bigPush.sh
  • lines changed 167, context: html, text, full: html, text
    Replacing bigPush.csh with bigPush.sh. Added new bigPush.sh to makefile. Script allows for pushing multiple tables for multiple assemblies. refs #16040
    
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    Replacing bigPush.csh with bigPush.sh. Added new bigPush.sh to makefile. Script allows for pushing multiple tables for multiple assemblies. refs #16040
    
• src/utils/qa/qaAutoTrack.sh
  • lines changed 14, context: html, text, full: html, text
    Changes based on CR. Added some dependecy notes to functions where it expects certain things to be set elsewhere in the script or by other functions. Simplified rounding method. Intialize output sting to include database. Change checkForIssues call to not use percentDiff for non-positional tables. refs #12561 #17041
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v332 preview1 refs #17072
    

• lines changed: 11599
• files changed: 215