All File Changes

v283_preview to v283_preview2 (2013-04-23 to 2013-04-30) v283

• src/hg/autoSql/autoSql.c
  • lines changed 12, context: html, text, full: html, text
    Adding xxxCommaSepFieldNames output.
• src/hg/autoSql/tests/expected/doc.c
  • lines changed 6, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/doc.h
  • lines changed 4, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/doc2.c
  • lines changed 12, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/doc2.h
  • lines changed 8, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/hardTest.c
  • lines changed 6, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/hardTest.h
  • lines changed 4, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/mainTest.c
  • lines changed 18, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/mainTest.h
  • lines changed 12, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/newTest.c
  • lines changed 6, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/newTest.h
  • lines changed 4, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/polyTest.c
  • lines changed 9, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/polyTest.h
  • lines changed 6, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/simpleTest.c
  • lines changed 27, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/simpleTest.h
  • lines changed 18, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/symTest.c
  • lines changed 3, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/symTest.h
  • lines changed 2, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/encode3/encodeDataWarehouse/edwCreateUser/edwCreateUser.c
  • lines changed 46, context: html, text, full: html, text
    Moving most of the work to a library routine shared with edwWebCreateUser. Removing password from command line.
• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
  • lines changed 2, context: html, text, full: html, text
    Making replica hunting use fileId rather than valid file ID to avoid a validation race condition that sometimes caused a replicate not to be found.
  • lines changed 14, context: html, text, full: html, text
    Moving findElderReplicates to library.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless parameter to shuffleArrayOfChars.
  • lines changed 6, context: html, text, full: html, text
    Turns out we need to keep the sample bed files indefinitely, we never really know when we'll get another replicate. Therefore moving them out of main temp dir, which would otherwise get too big.
• src/hg/encode3/encodeDataWarehouse/edwResetPassword/edwResetPassword.c
  • lines changed 56, context: html, text, full: html, text
    Removing no longer needed edwResetPassword.
• src/hg/encode3/encodeDataWarehouse/edwResetPassword/makefile
  • lines changed 4, context: html, text, full: html, text
    Removing no longer needed edwResetPassword.
• src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c
  • lines changed 284, context: html, text, full: html, text
    Trying a daemon that will poll database table, but wake up early if it gets a signal.
• src/hg/encode3/encodeDataWarehouse/edwRunDaemon/makefile
  • lines changed 4, context: html, text, full: html, text
    Trying a daemon that will poll database table, but wake up early if it gets a signal.
• src/hg/encode3/encodeDataWarehouse/edwRunner/edwRunner.c
  • lines changed 1, context: html, text, full: html, text
    Marking edwRunner and edwSubmitSpooler as obsoleted by edwRunDaemon.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 4, context: html, text, full: html, text
    Removing old unused code.
  • lines changed 36, context: html, text, full: html, text
    Adding an error catcher so that file in manifest that have gone missing leave an error message in the edwSubmit record.
  • lines changed 12, context: html, text, full: html, text
    Moving sevral functions from applications to library.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/makefile
  • lines changed 17, context: html, text, full: html, text
    Adapting makefile to Hiram's new minimal style.
• src/hg/encode3/encodeDataWarehouse/edwSubmitSpooler/edwSubmitSpooler.c
  • lines changed 1, context: html, text, full: html, text
    Marking edwRunner and edwSubmitSpooler as obsoleted by edwRunDaemon.
• src/hg/encode3/encodeDataWarehouse/edwWebAuthLogin/edwWebAuthLogin.c
  • lines changed 90, context: html, text, full: html, text
    A Persona authentication checker web service. Seems to work. WiStill need to figure out how not to recompile it for hgwdev, hgwdev-kent, and so forth.
  • lines changed 6, context: html, text, full: html, text
    Removing hard-coding of hgwdev-kent in favor of HTTP_HOST.
  • lines changed 14, context: html, text, full: html, text
    Switching from HTTP_HOST to SERVER_NAME as it's more secure.
  • lines changed 5, context: html, text, full: html, text
    Tightening up security a bit per Laurence's suggestions.
• src/hg/encode3/encodeDataWarehouse/edwWebAuthLogin/makefile
  • lines changed 16, context: html, text, full: html, text
    A Persona authentication checker web service. Seems to work. WiStill need to figure out how not to recompile it for hgwdev, hgwdev-kent, and so forth.
• src/hg/encode3/encodeDataWarehouse/edwWebAuthLogout/edwWebAuthLogout.c
  • lines changed 14, context: html, text, full: html, text
    Persona logout helper.
  • lines changed 1, context: html, text, full: html, text
    Simplifying output nobody will read.
  • lines changed 1, context: html, text, full: html, text
    Adding another cookie besides email to make it harder for a user to spoof somebody else's email by altering their own browser cookies. This was Laurence's suggestion.
• src/hg/encode3/encodeDataWarehouse/edwWebAuthLogout/makefile
  • lines changed 16, context: html, text, full: html, text
    Persona logout helper.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 285, context: html, text, full: html, text
    Adding submission browser.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/makefile
  • lines changed 16, context: html, text, full: html, text
    Adding submission browser.
• src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/edwWebCreateUser.c
  • lines changed 55, context: html, text, full: html, text
    Making a CGI that lets old users add new users.
  • lines changed 11, context: html, text, full: html, text
    A little polish - making sure it really is one of our users, not just someone with a persona account.
  • lines changed 3, context: html, text, full: html, text
    Adding log out button. Improving security.
  • lines changed 1, context: html, text, full: html, text
    Just improving html readability with a newline user won't see.
• src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/makefile
  • lines changed 16, context: html, text, full: html, text
    Making a CGI that lets old users add new users.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
  • lines changed 32, context: html, text, full: html, text
    Changing to Persona authentication.
  • lines changed 11, context: html, text, full: html, text
    Adding log out button. Improving security.
  • lines changed 48, context: html, text, full: html, text
    Improving edwWebSubmit status output particularly for errors. Adding button to browse submissions. Moving fifo to a place where all engineers sandboxes and the alpha will share same fifo, which is good, since the point of the fifo is to avoid overloading the system.
  • lines changed 125, context: html, text, full: html, text
    Changing submission fifo, and making it so user can see how many people in submit fifo ahead of them.
  • lines changed 3, context: html, text, full: html, text
    Adding a half second delay to give daemons a little change to process before we present status page for first time.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 9, context: html, text, full: html, text
    Adding a few functions related to Persona and creating users.
  • lines changed 32, context: html, text, full: html, text
    Removing some unused security stuff and replacing it with a little more Persona based security stuff.
  • lines changed 37, context: html, text, full: html, text
    Moving sevral functions from applications to library.
  • lines changed 3, context: html, text, full: html, text
    Turns out we need to keep the sample bed files indefinitely, we never really know when we'll get another replicate. Therefore moving them out of main temp dir, which would otherwise get too big.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 4, context: html, text, full: html, text
    Removing several fields from edwUser table since Persona handling authentication. Adding a few more indexes. Having to take away length qualifiers on indexes of md5 and format fields since this makes MySQL want to call it's built in functions of same name.
  • lines changed 108, context: html, text, full: html, text
    Adding edwSubmitJob table in preparation for shifting edwSubmitSpooler to use a queue in database rather than just fifo.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 47, context: html, text, full: html, text
    Adding a few functions related to Persona and creating users.
  • lines changed 80, context: html, text, full: html, text
    Removing some unused security stuff and replacing it with a little more Persona based security stuff.
  • lines changed 3, context: html, text, full: html, text
    Moving edwPerson.js to be included earlier. Seems to work and the firefox developers tools were fussing about having the script tag outside of the html.
  • lines changed 87, context: html, text, full: html, text
    Moving sevral functions from applications to library.
  • lines changed 22, context: html, text, full: html, text
    Turns out we need to keep the sample bed files indefinitely, we never really know when we'll get another replicate. Therefore moving them out of main temp dir, which would otherwise get too big.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 10, context: html, text, full: html, text
    Removing several fields from edwUser table since Persona handling authentication. Adding a few more indexes. Having to take away length qualifiers on indexes of md5 and format fields since this makes MySQL want to call it's built in functions of same name.
  • lines changed 11, context: html, text, full: html, text
    Adding edwSubmitJob table in preparation for shifting edwSubmitSpooler to use a queue in database rather than just fifo.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 37, context: html, text, full: html, text
    Removing several fields from edwUser table since Persona handling authentication. Adding a few more indexes. Having to take away length qualifiers on indexes of md5 and format fields since this makes MySQL want to call it's built in functions of same name.
  • lines changed 232, context: html, text, full: html, text
    Adding edwSubmitJob table in preparation for shifting edwSubmitSpooler to use a queue in database rather than just fifo.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.h
  • lines changed 1195, context: html, text, full: html, text
    Adding edwSubmitJob table in preparation for shifting edwSubmitSpooler to use a queue in database rather than just fifo.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 14, context: html, text, full: html, text
    Removing several fields from edwUser table since Persona handling authentication. Adding a few more indexes. Having to take away length qualifiers on indexes of md5 and format fields since this makes MySQL want to call it's built in functions of same name.
  • lines changed 12, context: html, text, full: html, text
    Adding edwSubmitJob table in preparation for shifting edwSubmitSpooler to use a queue in database rather than just fifo.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 5, context: html, text, full: html, text
    Adjusting to new persona based authentication, and adding Mike, Cricket, and Venkat to automatically added users.
  • lines changed 1, context: html, text, full: html, text
    Adding mm10.
  • lines changed 1, context: html, text, full: html, text
    Adding Esther on database startup.
  • lines changed 35, context: html, text, full: html, text
    Changing to edwRunDaemon
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 4, context: html, text, full: html, text
    Adding new programs to edw web works.
  • lines changed 2, context: html, text, full: html, text
    Removing no longer needed edwResetPassword.
  • lines changed 1, context: html, text, full: html, text
    Adding edwRunDaemon.
  • lines changed 2, context: html, text, full: html, text
    Removing some obsolete now programs from build.
  • lines changed 1, context: html, text, full: html, text
    Removing directory that was never checked in.
• src/hg/encode3/importEncode2/README
  • lines changed 1, context: html, text, full: html, text
    Marking some stuff as unused in docs.
• src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c
  • lines changed 21, context: html, text, full: html, text
    Adding a copy of non-bigified bed to what gets in encode2->encode3 staging area per wrangler request.
• src/hg/encode3/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding encodeDataWarehouse to parent directory make file.
• src/hg/hgGateway/hgGateway.c
  • lines changed 4, context: html, text, full: html, text
    commenting out debug statements for now
• src/hg/hgGene/hgGene.c
  • lines changed 4, context: html, text, full: html, text
    indented details of Transcript and Coding Region and dropped colons because it was visually confusing. the colons after the titles made it look like data were missing from those lines
• src/hg/hgGene/hgGeneData/links.ra
  • lines changed 3, context: html, text, full: html, text
    pointing KG Wikipedia link to new table so genes without Wikipedia entries get no link on hgGene
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 2, context: html, text, full: html, text
    remove a parameter to a library routine that none of the callers was using. for Angie
• src/hg/hgLogin/hgLogin.c
  • lines changed 2, context: html, text, full: html, text
    Change per note 17 and 20 of redmine 8920.
  • lines changed 1, context: html, text, full: html, text
    Per redmine 8920 #23.
• src/hg/hgTables/bam.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/hg/hgTables/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/hg/hgTables/hgTables.c
  • lines changed 52, context: html, text, full: html, text
    libify the connection to all the hubs by request of Angie.
  • lines changed 2, context: html, text, full: html, text
    remove a parameter to a library routine that none of the callers was using. for Angie
• src/hg/hgTables/vcf.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/hg/hgTracks/hgTracks.c
  • lines changed 48, context: html, text, full: html, text
    libify the connection to all the hubs by request of Angie.
  • lines changed 6, context: html, text, full: html, text
    remove a parameter to a library routine that none of the callers was using. for Angie
• src/hg/hgTracks/retroGene.c
  • lines changed 98, context: html, text, full: html, text
    Removed retroGeneMethods and its use and associated functions. This was used when a BED format track was loaded, now PSL is loaded and retroAliMethods are used. Added code to format the label for track items and to add the prefix, retro-.
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 1, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/hg/hgc/retroClick.c
  • lines changed 20, context: html, text, full: html, text
    Made changes to RetroFinder details page to tidy up presentation and also to make the text more intuitive to the user.
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 1, context: html, text, full: html, text
    Add link to Ensembl ENCODE data, request from Paul Flicek
• src/hg/htdocs/ENCODE/index.html
  • lines changed 1, context: html, text, full: html, text
    Update user resources page to reflect OpenHelix pricing change for tutorials
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 13, context: html, text, full: html, text
    Update user resources page to reflect OpenHelix pricing change for tutorials
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    Whitespace change. refs #10669
• src/hg/htdocs/goldenPath/help/liftOver.html
  • lines changed 47, context: html, text, full: html, text
    Creating generic liftOver page to replace assembly-specific liftOver pages linked from the 'pool ball' images that accompany a track that has been lifted from a previous assembly
  • lines changed 11, context: html, text, full: html, text
    Made appropriate changes to the liftOver doc to make it generic
  • lines changed 3, context: html, text, full: html, text
    Made a change suggested by Bob
  • lines changed 1, context: html, text, full: html, text
    Changed text in title bar
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    Updated link to liftOver page
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 40, context: html, text, full: html, text
    Adding publications, adding PMID for 2012 -2013 references, see RM refs #10696
  • lines changed 12, context: html, text, full: html, text
    Doing small rearrange of top publications, giving better link, see RM refs #10696
• src/hg/htdocs/style/HGStyle.css
  • lines changed 22, context: html, text, full: html, text
    Added styles for gene haplotype alleles section of hgGene which will soon be checked in.
  • lines changed 3, context: html, text, full: html, text
    In moving haplotypes to be cart persistent, toggling visibility by class helps.
  • lines changed 2, context: html, text, full: html, text
    Collapsed 2 button styles into 1 for haplotypes.
• src/hg/inc/annoGratorGpVar.h
  • lines changed 2, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/hg/inc/cart.h
  • lines changed 5, context: html, text, full: html, text
    Added cartTimeoutBoolean, which allows setting a var to true and having it timeout after a given number of hours.
• src/hg/inc/genePred.h
  • lines changed 15, context: html, text, full: html, text
    Added routines for getting genePred coding DNA and determining coding position. To be used in haplotypes code about to be checked in.
• src/hg/inc/gpFx.h
  • lines changed 40, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
  • lines changed 3, context: html, text, full: html, text
    Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
    and gpFx. refs #6152
    
• src/hg/inc/haplotypes.h
  • lines changed 274, context: html, text, full: html, text
    First check-in of the bluk of code for geneAlleles tool and hgGene's 'Gene Haplotype Alleles' section. This haplotype code, still evolving, relies upon vcf files (1000 Genomes phase 1) to discover sets of individual variants within a protein coding gene model that are segregating as distinct haplotypes. Ongoing work is expected to strengthen scoring routines for better highlighting of unexpected results. Haplotypes are currently only built for protein coding genes, but can certainly be expanded to cover other gene models and indeed, an region of the genome.
  • lines changed 10, context: html, text, full: html, text
    Reworked the haplotypes section of hgGene for persistence of cart vars (they will timeout after 3 days) and added reset to default. Given that the section is scrolled out of visible range and that some display options can be burdensome, it seemed fitting that cart vars will expire when not actively used.
• src/hg/inc/hubConnect.h
  • lines changed 4, context: html, text, full: html, text
    libify the connection to all the hubs by request of Angie.
  • lines changed 3, context: html, text, full: html, text
    remove a parameter to a library routine that none of the callers was using. for Angie
• src/hg/inc/liftOver.h
  • lines changed 3, context: html, text, full: html, text
    teased out a few routines for a sans-MySQL version of liftOver stuff in the top-level lib.
• src/hg/inc/soTerm.h
  • lines changed 42, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
• src/hg/inc/variant.h
  • lines changed 6, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
  • lines changed 2, context: html, text, full: html, text
    typo fix in comment
  • lines changed 5, context: html, text, full: html, text
    Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
    and gpFx. refs #6152
    
• src/hg/js/alleles.js
  • lines changed 352, context: html, text, full: html, text
    Adding alleles.js which will handle the Gene Haploptype Alleles section of hgGene. Since this section could be added to hgc for any genePred model, the js code is not being put into a 'hgGene' specific file.
  • lines changed 67, context: html, text, full: html, text
    Reworked the haplotypes section of hgGene for persistence of cart vars (they will timeout after 3 days) and added reset to default. Given that the section is scrolled out of visible range and that some display options can be burdensome, it seemed fitting that cart vars will expire when not actively used.
  • lines changed 34, context: html, text, full: html, text
    More experimentation on buttons/controls with Brooke for haplotypes. At this point, we agree to leave things as they are until a wider audience has a chance to weigh in.
• src/hg/js/edwPersona.js
  • lines changed 45, context: html, text, full: html, text
    Code for ENCODE Data Warehouse login via Persona.
• src/hg/js/makefile
  • lines changed 2, context: html, text, full: html, text
    Code for ENCODE Data Warehouse login via Persona.
  • lines changed 1, context: html, text, full: html, text
    Adding alleles.js which will handle the Gene Haploptype Alleles section of hgGene. Since this section could be added to hgc for any genePred model, the js code is not being put into a 'hgGene' specific file.
  • lines changed 2, context: html, text, full: html, text
    Fixing merge conflict - Tim also added a new javascript module.
• src/hg/js/utils.js
  • lines changed 14, context: html, text, full: html, text
    Adding alleles.js which will handle the Gene Haploptype Alleles section of hgGene. Since this section could be added to hgc for any genePred model, the js code is not being put into a 'hgGene' specific file.
• src/hg/lib/annoFormatVep.c
  • lines changed 32, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
  • lines changed 53, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
  • lines changed 2, context: html, text, full: html, text
    Code review feedback, thanks Tim. refs #10680
• src/hg/lib/annoGratorGpVar.c
  • lines changed 44, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
  • lines changed 116, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
  • lines changed 48, context: html, text, full: html, text
    Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
    and gpFx. refs #6152
    
• src/hg/lib/cart.c
  • lines changed 31, context: html, text, full: html, text
    Added cartTimeoutBoolean, which allows setting a var to true and having it timeout after a given number of hours.
• src/hg/lib/customFactory.c
  • lines changed 1, context: html, text, full: html, text
    fix buffer overflow problem refs #10686
• src/hg/lib/encode3/encode2Manifest.c
  • lines changed 3, context: html, text, full: html, text
    Making meta and manifest readers work with URLs.
• src/hg/lib/ensemblLift.as
  • lines changed 6, context: html, text, full: html, text
    Bug #10496 adding ensemblLift.as
• src/hg/lib/genePred.c
  • lines changed 92, context: html, text, full: html, text
    Added routines for getting genePred coding DNA and determining coding position. To be used in haplotypes code about to be checked in.
• src/hg/lib/gpFx.c
  • lines changed 284, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
  • lines changed 197, context: html, text, full: html, text
    Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
    and gpFx. refs #6152
    
• src/hg/lib/haplotypes.c
  • lines changed 3340, context: html, text, full: html, text
    First check-in of the bluk of code for geneAlleles tool and hgGene's 'Gene Haplotype Alleles' section. This haplotype code, still evolving, relies upon vcf files (1000 Genomes phase 1) to discover sets of individual variants within a protein coding gene model that are segregating as distinct haplotypes. Ongoing work is expected to strengthen scoring routines for better highlighting of unexpected results. Haplotypes are currently only built for protein coding genes, but can certainly be expanded to cover other gene models and indeed, an region of the genome.
  • lines changed 206, context: html, text, full: html, text
    Reworked the haplotypes section of hgGene for persistence of cart vars (they will timeout after 3 days) and added reset to default. Given that the section is scrolled out of visible range and that some display options can be burdensome, it seemed fitting that cart vars will expire when not actively used.
  • lines changed 2, context: html, text, full: html, text
    Angie saw a compiler error that I didn't. Thus I correct an invalid assert.
  • lines changed 107, context: html, text, full: html, text
    More experimentation on buttons/controls with Brooke for haplotypes. At this point, we agree to leave things as they are until a wider audience has a chance to weigh in.
• src/hg/lib/hubConnect.c
  • lines changed 56, context: html, text, full: html, text
    libify the connection to all the hubs by request of Angie.
  • lines changed 6, context: html, text, full: html, text
    remove a parameter to a library routine that none of the callers was using. for Angie
• src/hg/lib/liftOver.c
  • lines changed 239, context: html, text, full: html, text
    teased out a few routines for a sans-MySQL version of liftOver stuff in the top-level lib.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    First check-in of the bluk of code for geneAlleles tool and hgGene's 'Gene Haplotype Alleles' section. This haplotype code, still evolving, relies upon vcf files (1000 Genomes phase 1) to discover sets of individual variants within a protein coding gene model that are segregating as distinct haplotypes. Ongoing work is expected to strengthen scoring routines for better highlighting of unexpected results. Haplotypes are currently only built for protein coding genes, but can certainly be expanded to cover other gene models and indeed, an region of the genome.
  • lines changed 1, context: html, text, full: html, text
    remove bogus duplicate listing of objects, refs #9858
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 2, context: html, text, full: html, text
    Adding NULL check.
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 49, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 12, context: html, text, full: html, text
    Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
    stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
    represent insertion positions the way they do.
    TODO: lots more testing! and convert gpFx to use localmem.
    refs #6152
    
• src/hg/lib/tests/expected/spDbTest
  • lines changed 20, context: html, text, full: html, text
    Updating test expected output.
• src/hg/lib/tests/spDbTest.c
  • lines changed 1, context: html, text, full: html, text
    Removing some slow parts of spDbTest.c
• src/hg/lib/variant.c
  • lines changed 20, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
  • lines changed 12, context: html, text, full: html, text
    Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
    and gpFx. refs #6152
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    added new knownToWikipedia table linked to knownGene.name. refs #10707
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 10, context: html, text, full: html, text
    Updating cv.ra links changing at geneontology website as notified by warning, caught by cv chronjob
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 10, context: html, text, full: html, text
    Updating cv.ra links changing at geneontology website as notified by warning, caught by cv chronjob
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Updated links from 'pool ball' icons which indicate a track that has been lifted from a previous assembly to new generic liftOver page
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 69, context: html, text, full: html, text
    Updated links from 'pool ball' icons which indicate a track that has been lifted from a previous assembly to new generic liftOver page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to liftOver page
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Updated links to liftOver page
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Updating visibility and shortLabel. refs #7409
• src/hg/mouseStuff/regionPicker/regionPicker.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/hg/oneShot/freen/freen.c
  • lines changed 25, context: html, text, full: html, text
    Testing around system call results and exit results as returned by wait.
• src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/regCompanionCorrelateEnhancerAndExpression.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/hg/utils/isca/checkISCA.sh
  • lines changed 1, context: html, text, full: html, text
    fix a pathname in a comment per Max
• src/hg/utils/trashLoad/makefile
  • lines changed 3, context: html, text, full: html, text
    initial contents for a trash file writing load test, refs #9858
• src/hg/utils/trashLoad/trashLoad.c
  • lines changed 115, context: html, text, full: html, text
    initial contents for a trash file writing load test, refs #9858
  • lines changed 41, context: html, text, full: html, text
    add testDir argument and calculate bytes per second refs #9858
  • lines changed 2, context: html, text, full: html, text
    add summary line for easier stat report collections refs #9858
• src/hg/visiGene/gensat/gensatRandomXml/gensatRandomXml.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/inc/annoFormatter.h
  • lines changed 12, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/inc/annoGrator.h
  • lines changed 2, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/inc/annoStreamer.h
  • lines changed 14, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
  • lines changed 1, context: html, text, full: html, text
    Code review feedback, thanks Tim. refs #10680
• src/inc/bits.h
  • lines changed 11, context: html, text, full: html, text
    Added a couple useful functions that will be needed by haplotypes code.
• src/inc/liftOverCore.h
  • lines changed 35, context: html, text, full: html, text
    teased out a few routines for a sans-MySQL version of liftOver stuff in the top-level lib.
  • lines changed 8, context: html, text, full: html, text
    Another frantic commit from Andy after inadvertantly breaking the compilation of hgTracks.
  • lines changed 5, context: html, text, full: html, text
    Added binRange.h too. I also removed the #ifndefs since Angie mentioned they're at the top of each of those headers anyway.
• src/inc/localmem.h
  • lines changed 3, context: html, text, full: html, text
    Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
    and gpFx. refs #6152
    
• src/inc/meta.h
  • lines changed 1, context: html, text, full: html, text
    Making meta and manifest readers work with URLs.
• src/inc/net.h
  • lines changed 4, context: html, text, full: html, text
    Making new library function netWaitForData that is a minor refactoring of a private existing net.c function.
• src/inc/obscure.h
  • lines changed 4, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/inc/vcf.h
  • lines changed 4, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/inc/vcfBits.h
  • lines changed 38, context: html, text, full: html, text
    Changes in preparation for checking in haplotypes code.
• src/lib/annoFormatter.c
  • lines changed 13, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/lib/annoGrateWig.c
  • lines changed 3, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/lib/annoGrator.c
  • lines changed 2, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/lib/annoGratorQuery.c
  • lines changed 1, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/lib/annoStreamer.c
  • lines changed 15, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/lib/bits.c
  • lines changed 71, context: html, text, full: html, text
    Added a couple useful functions that will be needed by haplotypes code.
• src/lib/liftOverCore.c
  • lines changed 246, context: html, text, full: html, text
    teased out a few routines for a sans-MySQL version of liftOver stuff in the top-level lib.
• src/lib/log.c
  • lines changed 8, context: html, text, full: html, text
    Making logDaemonize code be a little more robust.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    teased out a few routines for a sans-MySQL version of liftOver stuff in the top-level lib.
• src/lib/meta.c
  • lines changed 2, context: html, text, full: html, text
    Making meta and manifest readers work with URLs.
• src/lib/net.c
  • lines changed 14, context: html, text, full: html, text
    Making new library function netWaitForData that is a minor refactoring of a private existing net.c function.
• src/lib/obscure.c
  • lines changed 5, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/lib/vcf.c
  • lines changed 23, context: html, text, full: html, text
    Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
    be passed in along with the primary row, as it is for formatters now.
    refs #6152
    
• src/lib/vcfBits.c
  • lines changed 233, context: html, text, full: html, text
    Changes in preparation for checking in haplotypes code.
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    add parasol to the build utils list (but certainly *not* installed !) so errors can be caught, refs #9104
• src/parasol/makefile
  • lines changed 3, context: html, text, full: html, text
    add parasol to the build utils list (but certainly *not* installed !) so errors can be caught, refs #9104
• src/parasol/para/para.c
  • lines changed 2, context: html, text, full: html, text
    Fixing compile error that is making me wonder if para.c gets compiles usually.
• src/parasol/paraHub/paraHub.c
  • lines changed 1, context: html, text, full: html, text
    Fixing compile error that is making me wonder if para.c gets compiles usually.
• src/utils/cpgIslandExt/makefile
  • lines changed 21, context: html, text, full: html, text
    update to minimal makefile, refs #9104
• src/utils/qa/qaEnsGenes.csh
  • lines changed 6, context: html, text, full: html, text
    Changing comments in script to match Ensemble QA wiki notes, adding lnk to wiki reminder
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v283 preview2
• src/utils/shuffleLines/shuffleLines.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.

• lines changed: 10853
• files changed: 217